Switch to cpan for the source
Michael R. Crusoe
4 years ago
| 2 | 2 | * Team upload. |
| 3 | 3 | * debian/patches/samtools1.10: remove version parsing code that can't handle |
| 4 | 4 | samtools version 1.10 |
| 5 | * Switch to cpan for the source | |
| 5 | 6 | |
| 6 | 7 | -- Michael R. Crusoe <michael.crusoe@gmail.com> Wed, 25 Dec 2019 13:28:31 +0100 |
| 7 | 8 |
| 3 | 3 | Section: perl |
| 4 | 4 | # Testsuite: autopkgtest-pkg-perl |
| 5 | 5 | Priority: optional |
| 6 | Build-Depends: debhelper-compat (= 12), | |
| 7 | libtext-csv-perl, | |
| 8 | samtools, | |
| 9 | smalt, | |
| 10 | tabix, | |
| 11 | bwa, | |
| 12 | libtrycatch-perl, | |
| 13 | libtest-most-perl, | |
| 14 | libtest-files-perl, | |
| 15 | libbio-perl-perl, | |
| 16 | dh-dist-zilla, | |
| 17 | libdist-zilla-plugin-checkextratests-perl, | |
| 18 | libdist-zilla-plugin-requiresexternal-perl, | |
| 19 | libdist-zilla-plugin-git-perl, | |
| 20 | libdist-zilla-plugin-podweaver-perl, | |
| 21 | libdist-zilla-role-pluginbundle-pluginremover-perl, | |
| 22 | libdist-zilla-plugin-test-compile-perl, | |
| 23 | libdist-zilla-plugin-modulebuildtiny-fallback-perl, | |
| 24 | libdist-zilla-config-slicer-perl, | |
| 25 | libtest-file-sharedir-perl, | |
| 26 | libdist-zilla-plugin-modulebuildtiny-perl, | |
| 27 | libdist-zilla-plugin-readmefrompod-perl, | |
| 28 | libdist-zilla-plugin-makemaker-awesome-perl, | |
| 29 | libtest-pod-perl, | |
| 30 | libdist-zilla-plugin-test-reportprereqs-perl, | |
| 31 | libdist-zilla-plugin-metaprovides-package-perl | |
| 6 | Build-Depends: debhelper-compat (= 12) | |
| 7 | Build-Depends-Indep: libbio-perl-perl, | |
| 8 | libenv-path-perl, | |
| 9 | libexception-class-perl, | |
| 10 | libmoose-perl, | |
| 11 | libtest-exception-perl, | |
| 12 | libtest-files-perl, | |
| 13 | libtest-most-perl, | |
| 14 | libtest-simple-perl, | |
| 15 | libtext-csv-perl, | |
| 16 | libtry-tiny-perl, | |
| 17 | perl, | |
| 18 | samtools, | |
| 19 | smalt, | |
| 20 | tabix, | |
| 21 | bwa | |
| 32 | 22 | Standards-Version: 4.4.1 |
| 33 | 23 | Vcs-Browser: https://salsa.debian.org/med-team/bio-tradis |
| 34 | 24 | Vcs-Git: https://salsa.debian.org/med-team/bio-tradis.git |
| 36 | 26 | |
| 37 | 27 | Package: bio-tradis |
| 38 | 28 | Architecture: all |
| 39 | Depends: ${perl:Depends}, | |
| 40 | ${misc:Depends}, | |
| 29 | Depends: ${misc:Depends}, | |
| 30 | ${perl:Depends}, | |
| 31 | libbio-perl-perl, | |
| 32 | libexception-class-perl, | |
| 33 | libmoose-perl, | |
| 34 | libtext-csv-perl, | |
| 35 | libtry-tiny-perl | |
| 41 | 36 | smalt, |
| 42 | 37 | samtools, |
| 43 | 38 | tabix, |
| 0 | #!/bin/sh | |
| 1 | MANDIR=debian/mans | |
| 2 | mkdir -p $MANDIR | |
| 3 | ||
| 4 | VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'` | |
| 5 | ||
| 6 | AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and | |
| 7 | can be used for any other usage of the program. | |
| 8 | " | |
| 9 | ||
| 10 | progname=add_tradis_tags | |
| 11 | help2man --no-info --no-discard-stderr --help-option=" " \ | |
| 12 | --name='Adds transposon sequence and quality tags to the read strings and outputs a BAM' \ | |
| 13 | --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 | |
| 14 | echo $AUTHOR >> $MANDIR/${progname}.1 | |
| 15 | ||
| 16 | progname=bacteria_tradis | |
| 17 | help2man --no-info --no-discard-stderr --help-option=" " \ | |
| 18 | --name='bio-tradis: run a TraDIS analysis' \ | |
| 19 | --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 | |
| 20 | echo $AUTHOR >> $MANDIR/${progname}.1 | |
| 21 | ||
| 22 | progname=check_tradis_tags | |
| 23 | help2man --no-info --no-discard-stderr --help-option=" " \ | |
| 24 | --name='bio-tradis: check for the existence of tradis tags in a bam' \ | |
| 25 | --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 | |
| 26 | echo $AUTHOR >> $MANDIR/${progname}.1 | |
| 27 | ||
| 28 | progname=combine_tradis_plots | |
| 29 | help2man --no-info --no-discard-stderr --help-option=" " \ | |
| 30 | --name='bio-tradis: combine multiple plotfiles and generate updated statistics' \ | |
| 31 | --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 | |
| 32 | echo $AUTHOR >> $MANDIR/${progname}.1 | |
| 33 | ||
| 34 | progname=filter_tradis_tags | |
| 35 | help2man --no-info --no-discard-stderr --help-option=" " \ | |
| 36 | --name='bio-tradis: filters a BAM file and outputs reads' \ | |
| 37 | --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 | |
| 38 | echo $AUTHOR >> $MANDIR/${progname}.1 | |
| 39 | ||
| 40 | progname=remove_tradis_tags | |
| 41 | help2man --no-info --no-discard-stderr --help-option=" " \ | |
| 42 | --name='bio-tradis: remove transposon sequence and quality tags from the read strings' \ | |
| 43 | --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 | |
| 44 | echo $AUTHOR >> $MANDIR/${progname}.1 | |
| 45 | ||
| 46 | progname=tradis_comparison | |
| 47 | help2man --no-info --no-discard-stderr --help-option=" " \ | |
| 48 | --name='bio-tradis: compares two experimental conditions using the method of Dembek et al.' \ | |
| 49 | --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 | |
| 50 | echo $AUTHOR >> $MANDIR/${progname}.1 | |
| 51 | ||
| 52 | progname=tradis_essentiality | |
| 53 | help2man --no-info --no-discard-stderr --help-option=" " \ | |
| 54 | --name='bio-tradis: produces calls of gene essentiality using an adaptation of the method described in Langridge et al.' \ | |
| 55 | --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 | |
| 56 | echo $AUTHOR >> $MANDIR/${progname}.1 | |
| 57 | ||
| 58 | progname=tradis_gene_insert_sites | |
| 59 | help2man --no-info --no-discard-stderr --help-option=" " \ | |
| 60 | --name='bio-tradis: take in plot file(s) and an embl file and produce a tab delimited file' \ | |
| 61 | --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 | |
| 62 | echo $AUTHOR >> $MANDIR/${progname}.1 | |
| 63 | ||
| 64 | progname=tradis_merge_plots | |
| 65 | help2man --no-info --no-discard-stderr --help-option=" " \ | |
| 66 | --name='bio-tradis: Given a study name or ID, group by sample and tag, and generate tab files for input to R' \ | |
| 67 | --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 | |
| 68 | echo $AUTHOR >> $MANDIR/${progname}.1 | |
| 69 | ||
| 70 | progname=tradis_plot | |
| 71 | help2man --no-info --no-discard-stderr --help-option=" " \ | |
| 72 | --name='bio-tradis: create insertion site plot for Artemis' \ | |
| 73 | --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 | |
| 74 | echo $AUTHOR >> $MANDIR/${progname}.1 | |
| 75 | ||
| 76 | ||
| 77 | cat <<EOT | |
| 78 | Please enhance the help2man output. | |
| 79 | The following web page might be helpful in doing so: | |
| 80 | http://liw.fi/manpages/ | |
| 81 | EOT | |
| 82 |
| 0 | .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4. | |
| 1 | .TH ADD_TRADIS_TAGS "1" "March 2017" "add_tradis_tags 1.3.1" "User Commands" | |
| 2 | .SH NAME | |
| 3 | add_tradis_tags \- Adds transposon sequence and quality tags to the read strings and outputs a BAM | |
| 4 | .SH SYNOPSIS | |
| 5 | .B add_tags | |
| 6 | \fI\,-b file.bam \/\fR[\fI\,options\/\fR] | |
| 7 | .SH DESCRIPTION | |
| 8 | Adds transposon sequence and quality tags to the read strings and | |
| 9 | outputs a BAM. | |
| 10 | .SH OPTIONS | |
| 11 | .TP | |
| 12 | \fB\-b\fR | |
| 13 | bam file with tradis tags | |
| 14 | .TP | |
| 15 | \fB\-o\fR | |
| 16 | output BAM name (optional. default: <file>.tr.bam) | |
| 17 | .TP | |
| 18 | \fB\-v\fR | |
| 19 | verbose debugging output | |
| 20 | .SH AUTHOR | |
| 21 | This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. |
| 0 | .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4. | |
| 1 | .TH BACTERIA_TRADIS "1" "March 2017" "bacteria_tradis 1.3.1" "User Commands" | |
| 2 | .SH NAME | |
| 3 | bacteria_tradis \- bio-tradis: run a TraDIS analysis | |
| 4 | .SH SYNOPSIS | |
| 5 | .B bacteria_tradis | |
| 6 | [\fI\,options\/\fR] | |
| 7 | .SH DESCRIPTION | |
| 8 | Run a TraDIS analysis. This involves: | |
| 9 | 1: filtering the data with tags matching that passed via \fB\-t\fR option | |
| 10 | 2: removing the tags from the sequences | |
| 11 | 3: mapping | |
| 12 | 4: creating an insertion site plot | |
| 13 | 5: creating a stats summary | |
| 14 | .SH OPTIONS | |
| 15 | .TP | |
| 16 | \fB\-f\fR | |
| 17 | text file listing fastq files with tradis tags attached | |
| 18 | .TP | |
| 19 | \fB\-t\fR | |
| 20 | tag to search for | |
| 21 | .TP | |
| 22 | \fB\-r\fR | |
| 23 | reference genome in fasta format (.fa) | |
| 24 | .TP | |
| 25 | \fB\-td\fR | |
| 26 | tag direction \- 3 or 5 (optional. default = 3) | |
| 27 | .TP | |
| 28 | \fB\-mm\fR | |
| 29 | number of mismatches allowed when matching tag (optional. default = 0) | |
| 30 | .TP | |
| 31 | \fB\-m\fR | |
| 32 | mapping quality cutoff score (optional. default = 30) | |
| 33 | .TP | |
| 34 | \fB\-\-smalt_k\fR | |
| 35 | custom k\-mer value for SMALT mapping (optional) | |
| 36 | .TP | |
| 37 | \fB\-\-smalt_s\fR | |
| 38 | custom step size for SMALT mapping (optional) | |
| 39 | .TP | |
| 40 | \fB\-\-smalt_y\fR | |
| 41 | custom y parameter for SMALT (optional. default = 0.96) | |
| 42 | .TP | |
| 43 | \fB\-\-smalt_r\fR | |
| 44 | custom r parameter for SMALT (optional. default = \fB\-1\fR) | |
| 45 | .TP | |
| 46 | \fB\-n\fR | |
| 47 | number of threads to use for SMALT and samtools sort (optional. default = 1) | |
| 48 | .TP | |
| 49 | \fB\-e\fR | |
| 50 | set defaults for essentiality experiment (smalt_r = 0, \fB\-m\fR = 0) | |
| 51 | .TP | |
| 52 | \fB\-v\fR | |
| 53 | verbose debugging output | |
| 54 | .SH AUTHOR | |
| 55 | This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. |
| 0 | .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4. | |
| 1 | .TH CHECK_TRADIS_TAGS "1" "March 2017" "check_tradis_tags 1.3.1" "User Commands" | |
| 2 | .SH NAME | |
| 3 | check_tradis_tags \- bio-tradis: check for the existence of tradis tags in a bam | |
| 4 | .SH SYNOPSIS | |
| 5 | .B check_tags | |
| 6 | \fI\,-b file.bam\/\fR | |
| 7 | .SH DESCRIPTION | |
| 8 | Check for the existence of tradis tags in a bam | |
| 9 | .SH OPTIONS | |
| 10 | \fB\-b\fR : bam file with tradis tags | |
| 11 | .SH AUTHOR | |
| 12 | This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. |
| 0 | .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4. | |
| 1 | .TH COMBINE_TRADIS_PLOTS "1" "March 2017" "combine_tradis_plots 1.3.1" "User Commands" | |
| 2 | .SH NAME | |
| 3 | combine_tradis_plots \- bio-tradis: combine multiple plotfiles and generate updated statistics | |
| 4 | .SH SYNOPSIS | |
| 5 | .B combine_tradis_plots | |
| 6 | \fI\,-p plots.txt\/\fR | |
| 7 | .SH DESCRIPTION | |
| 8 | Combine multiple plotfiles and generate updated statistics for the combined | |
| 9 | files. Takes a tab\-delimited file with an ID as the first column followed by | |
| 10 | a list of plotfiles to combine per row. The ID will be used to name the new | |
| 11 | plotfile and as an identifier in the stats file, so ensure these are unique. | |
| 12 | .PP | |
| 13 | For example, an input file named plots_to_combine.txt: | |
| 14 | .IP | |
| 15 | tradis1 plot1.1.gz plot1.2.gz plot1.3.gz | |
| 16 | .IP | |
| 17 | tradis2 plot2.1.gz plot2.2.gz | |
| 18 | .IP | |
| 19 | tradis3 plot3.1.gz plot3.2.gz plot3.3.gz plot3.4.gz | |
| 20 | .PP | |
| 21 | will produce | |
| 22 | .nr step 1 1 | |
| 23 | .IP \n[step] 2 | |
| 24 | a directory named combined with 3 files \- tradis1.insertion_site_plot.gz, | |
| 25 | tradis2.insertion_site_plot.gz, tradis3.insertion_site_plot.gz | |
| 26 | .IP \n+[step] | |
| 27 | a stats file named plots_to_combine.stats | |
| 28 | .SH OPTIONS | |
| 29 | .TP | |
| 30 | \fB\-p\fR|plotfile | |
| 31 | file with plots to be combined | |
| 32 | .TP | |
| 33 | \fB\-o\fR|output_dir | |
| 34 | name of directory for output (default: combined) | |
| 35 | .SH AUTHOR | |
| 36 | This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. |
| 0 | .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4. | |
| 1 | .TH FILTER_TRADIS_TAGS "1" "March 2017" "filter_tradis_tags 1.3.1" "User Commands" | |
| 2 | .SH NAME | |
| 3 | filter_tradis_tags \- bio-tradis: filters a BAM file and outputs reads | |
| 4 | .SH SYNOPSIS | |
| 5 | .B filter_tags | |
| 6 | \fI\,-b file.bam -t tag \/\fR[\fI\,options\/\fR] | |
| 7 | .SH DESCRIPTION | |
| 8 | Filters a BAM file and outputs reads with tag matching \fB\-t\fR option | |
| 9 | .SH OPTIONS | |
| 10 | .TP | |
| 11 | \fB\-f\fR | |
| 12 | fastq file with tradis tags attached | |
| 13 | .TP | |
| 14 | \fB\-t\fR | |
| 15 | tag to search for | |
| 16 | .TP | |
| 17 | \fB\-m\fR | |
| 18 | number of mismatches to allow when matching tag (optional. default = 0) | |
| 19 | .TP | |
| 20 | \fB\-o\fR | |
| 21 | output file name (optional. default: <file>.tag.fastq) | |
| 22 | .SH AUTHOR | |
| 23 | This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. |
| 0 | .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4. | |
| 1 | .TH REMOVE_TRADIS_TAGS "1" "March 2017" "remove_tradis_tags 1.3.1" "User Commands" | |
| 2 | .SH NAME | |
| 3 | remove_tradis_tags \- bio-tradis: remove transposon sequence and quality tags from the read strings | |
| 4 | .SH SYNOPSIS | |
| 5 | .B remove_tags | |
| 6 | \fI\,-f file.fastq \/\fR[\fI\,options\/\fR] | |
| 7 | .SH DESCRIPTION | |
| 8 | Removes transposon sequence and quality tags from the read strings | |
| 9 | .SH OPTIONS | |
| 10 | .TP | |
| 11 | \fB\-f\fR | |
| 12 | fastq file with tradis tags | |
| 13 | .TP | |
| 14 | \fB\-t\fR | |
| 15 | tag to remove | |
| 16 | .TP | |
| 17 | \fB\-m\fR | |
| 18 | number of mismatches to allow when matching tag (optional. default = 0) | |
| 19 | .TP | |
| 20 | \fB\-o\fR | |
| 21 | output file name (optional. default: <file>.rmtag.fastq) | |
| 22 | .SH AUTHOR | |
| 23 | This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. |
| 0 | .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4. | |
| 1 | .TH TRADIS_COMPARISON "1" "March 2017" "tradis_comparison 1.3.1" "User Commands" | |
| 2 | .SH NAME | |
| 3 | tradis_comparison \- bio-tradis: compares two experimental conditions using the method of Dembek et al. | |
| 4 | .SH SYNOPSIS | |
| 5 | .B tradis_comparison | |
| 6 | [\fI\,-h\/\fR] [\fI\,-f\/\fR] [\fI\,-t read cutoff\/\fR] [\fI\,-o outputfile.csv\/\fR] [\fI\,-p outputplot.pdf\/\fR] \fI\,--controls controls.txt --conditions conditions.txt\/\fR | |
| 7 | .SH DESCRIPTION | |
| 8 | Compares two experimental conditions using the method of Dembek et al. | |
| 9 | mBio 2015. Read counts per gene are compared using edgeR. This analysis | |
| 10 | requires experimental replicates. | |
| 11 | .SH OPTIONS | |
| 12 | .SS Required Arguments: | |
| 13 | .TP | |
| 14 | \fB\-\-controls\fR | |
| 15 | control libraries, generally growth in a permissive condition | |
| 16 | .TP | |
| 17 | \fB\-\-conditions\fR | |
| 18 | libraries exposed to the experimental condition being | |
| 19 | compared | |
| 20 | .SS Optional Arguments: | |
| 21 | .TP | |
| 22 | \fB\-o\fR | |
| 23 | output filename | |
| 24 | .TP | |
| 25 | \fB\-p\fR | |
| 26 | output filename for diagnostic plots | |
| 27 | .TP | |
| 28 | \fB\-f\fR | |
| 29 | enable filtering on minimum read counts | |
| 30 | .TP | |
| 31 | \fB\-t\fR | |
| 32 | if \fB\-\-filter\fR is enabled, sets minimum read count necessary in one | |
| 33 | condition for a gene to be included in the comparison. | |
| 34 | .SH AUTHOR | |
| 35 | This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. |
| 0 | .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4. | |
| 1 | .TH TRADIS_ESSENTIALITY "1" "March 2017" "tradis_essentiality 1.3.1" "User Commands" | |
| 2 | .SH NAME | |
| 3 | tradis_essentiality \- bio-tradis: produces calls of gene essentiality using an adaptation of the method described in Langridge et al. | |
| 4 | .SH SYNOPSIS | |
| 5 | .B tradis_essentiality | |
| 6 | \fI\,data.tab\/\fR | |
| 7 | .SH DESCRIPTION | |
| 8 | Produces calls of gene essentiality using an adaptation of the method | |
| 9 | described in Langridge et al. Genome Research 2009 and Barquist et al. | |
| 10 | NAR 2013. A loess curve is fit to the distribution of insertion | |
| 11 | indices, and used to identify the minima between the 'essential' and | |
| 12 | \&'non\-essential' distributions. These distributions are then used to fit | |
| 13 | gamma distributions, which are then used to calculate log\-odds ratios, | |
| 14 | which are used to determine an insertion\-index threshold for gene | |
| 15 | essentiality. Note that this analysis requires a saturated mutant | |
| 16 | library, and is not suitable for the analysis of data sets with low | |
| 17 | insertion density. The script produces a number of diagnostic plots | |
| 18 | which can be used to verify that this condition has been met. | |
| 19 | .SH AUTHOR | |
| 20 | This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. |
| 0 | .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4. | |
| 1 | .TH TRADIS_GENE_INSERT_SITES "1" "March 2017" "tradis_gene_insert_sites 1.3.1" "User Commands" | |
| 2 | .SH NAME | |
| 3 | tradis_gene_insert_sites \- bio-tradis: take in plot file(s) and an embl file and produce a tab delimited file | |
| 4 | .SH SYNOPSIS | |
| 5 | .B tradis_gene_insert_sites | |
| 6 | ||
| 7 | .SH DESCRIPTION | |
| 8 | Take in a plot file(s) and an embl file and produce a tab delimited file with insert site details to use as input to an R script to t | |
| 9 | est for essentiality. | |
| 10 | .TP | |
| 11 | \fB\-o\fR|output_suffix | |
| 12 | <suffix to add to output files (optional, default = tradis_gene_insert_sites.csv)> | |
| 13 | .TP | |
| 14 | \fB\-trim5\fR | |
| 15 | <trim insertion sites from 5' end of gene (optional, default = 0)> | |
| 16 | .TP | |
| 17 | \fB\-trim3\fR | |
| 18 | <trim insertion sites from 3' end of gene (optional, default = 0)> | |
| 19 | .TP | |
| 20 | \fB\-j\fR|joined_output | |
| 21 | <output a single file with all info. default = one file per input file> | |
| 22 | .TP | |
| 23 | \fB\-h\fR|help | |
| 24 | display this message | |
| 25 | .SH EXAMPLES | |
| 26 | .IP | |
| 27 | tradis_gene_insert_sites my_annotation.embl my_insert_site_plot.gz | |
| 28 | .IP | |
| 29 | tradis_gene_insert_sites my_annotation.embl my_insert_site_plot | |
| 30 | .TP | |
| 31 | # multiple plot files | |
| 32 | tradis_gene_insert_sites my_annotation.embl plot1.gz plot2.gz plot3.gz plot4.gz | |
| 33 | .TP | |
| 34 | # specify an output suffix this will result in a file named my_insert_site_plot1.my_output.csv | |
| 35 | tradis_gene_insert_sites \fB\-o\fR my_output.csv my_annotation.embl my_insert_site_plot1 | |
| 36 | .TP | |
| 37 | # Trim insertion sites from start or end of gene | |
| 38 | tradis_gene_insert_sites my_annotation.embl \fB\-trim5\fR 0.1 \fB\-trim3\fR 0.1 my_annotation.embl my_insert_site_plot.gz | |
| 39 | .PP | |
| 40 | The trim parameter is the fraction of the gene length trimmed. | |
| 41 | .TP | |
| 42 | # place all info into a single file | |
| 43 | tradis_gene_insert_sites \fB\-o\fR output_suffix.csv \fB\-j\fR my_annotation.embl plot1.gz plot2.gz plot3.gz | |
| 44 | .PP | |
| 45 | Resulting file: joined_output.output_suffix.csv | |
| 46 | .SH AUTHOR | |
| 47 | This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. |
| 0 | .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4. | |
| 1 | .TH TRADIS_MERGE_PLOTS "1" "March 2017" "tradis_merge_plots 1.3.1" "User Commands" | |
| 2 | .SH NAME | |
| 3 | tradis_merge_plots \- bio-tradis: Given a study name or ID, group by sample and tag, and generate tab files for input to R | |
| 4 | .SH SYNOPSIS | |
| 5 | .B tradis_merge_plots | |
| 6 | [\fI\,options\/\fR] | |
| 7 | .SH DESCRIPTION | |
| 8 | Given a study name or ID, group by sample and tag, and generate tab files for input to R. | |
| 9 | .SH EXAMPLES | |
| 10 | .TP | |
| 11 | # run over sequencescape study 1234 | |
| 12 | tradis_merge_plots 1234 | |
| 13 | .TP | |
| 14 | # Provide a name instead of a study ID | |
| 15 | tradis_merge_plots "My Study" | |
| 16 | .TP | |
| 17 | # This help message | |
| 18 | tradis_merge_plots \fB\-h\fR | |
| 19 | .SH AUTHOR | |
| 20 | This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. |
| 0 | .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4. | |
| 1 | .TH TRADIS_PLOT "1" "March 2017" "tradis_plot 1.3.1" "User Commands" | |
| 2 | .SH NAME | |
| 3 | tradis_plot \- bio-tradis: create insertion site plot for Artemis | |
| 4 | .SH SYNOPSIS | |
| 5 | .B tradis_plot | |
| 6 | \fI\,-f file.bam \/\fR[\fI\,options\/\fR] | |
| 7 | .SH DESCRIPTION | |
| 8 | Create insertion site plot for Artemis | |
| 9 | .SH OPTIONS | |
| 10 | .TP | |
| 11 | \fB\-f\fR | |
| 12 | mapped, sorted bam file | |
| 13 | .TP | |
| 14 | \fB\-m\fR | |
| 15 | mapping quality must be greater than X (optional. default: 30) | |
| 16 | .TP | |
| 17 | \fB\-o\fR | |
| 18 | output base name for plot (optional. default: tradis.plot) | |
| 19 | .SH AUTHOR | |
| 20 | This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. |
| 2 | 2 | DH_VERBOSE := 1 |
| 3 | 3 | export LC_ALL=C.UTF-8 |
| 4 | 4 | |
| 5 | TEST_FILES = $(shell find t -name "*.t") | |
| 6 | ||
| 7 | 5 | %: |
| 8 | dh $@ --with dist-zilla | |
| 6 | dh $@ | |
| 9 | 7 | |
| 10 | 8 | override_dh_auto_test: |
| 11 | 9 | ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) |
| 12 | dh_auto_test -D .build/debian-build || true | |
| 10 | dh_auto_test | |
| 13 | 11 | endif |
| 0 | Archive: CPAN | |
| 1 | Contact: Carla Cummins <path-help@sanger.ac.uk> | |
| 0 | 2 | Reference: |
| 1 | 3 | Author: > |
| 2 | 4 | Lars Barquist and Matthew Mayho and Carla Cummins and Amy K. Cain and |
| 0 | 0 | version=4 |
| 1 | ||
| 2 | 1 | opts="uversionmangle=s/^1.1/1.1./,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \ |
| 3 | https://github.com/sanger-pathogens/Bio-Tradis/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) | |
| 2 | https://metacpan.org/release/Bio-Tradis .*/Bio-Tradis-v?@ANY_VERSION@@ARCHIVE_EXT@$ |