Codebase list seer / e4b83f0
Autogenerate manpages - needs manual editing Andreas Tille 7 years ago
6 changed file(s) with 191 addition(s) and 0 deletion(s). Raw diff Collapse all Expand all
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debian/createmanpages less more
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 $DEBFULLNAME for the Debian distribution and
7 can be used for any other usage of the program.
8 "
9
10 progname=blast_top_hits
11 help2man --no-info --no-discard-stderr --help-option=" -h" \
12 --name='reduces a blast or blat output file to the top hit for each query sequence only' \
13 --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
14 echo $AUTHOR >> $MANDIR/${progname}.1
15
16 progname=combineKmers
17 help2man --no-info --no-discard-stderr --help-option=" -h" \
18 --name='basic algorithm to combine kmer counts across samples' \
19 --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
20 echo $AUTHOR >> $MANDIR/${progname}.1
21
22 progname=filter_seer
23 help2man --no-info --no-discard-stderr --help-option=" -h" \
24 --name='post filtering of significant kmers' \
25 --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
26 echo $AUTHOR >> $MANDIR/${progname}.1
27
28 progname=kmds
29 help2man --no-info --no-discard-stderr --help-option=" -h" \
30 --name='control for population structure' \
31 --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
32 echo $AUTHOR >> $MANDIR/${progname}.1
33
34 progname=map_back
35 help2man --no-info --no-discard-stderr --help-option=" -h" \
36 --name='context of significant kmers' \
37 --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
38 echo $AUTHOR >> $MANDIR/${progname}.1
39
40 progname=seer
41 help2man --no-info --no-discard-stderr --help-option=" -h" \
42 --name='sequence element enrichment analysis' \
43 --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
44 echo $AUTHOR >> $MANDIR/${progname}.1
45
46 progname=R_mds
47 help2man --no-info --no-discard-stderr --help-option=" -h" \
48 --name='project distance matrix into lower number of dimensions' \
49 --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
50 echo $AUTHOR >> $MANDIR/${progname}.1
51
52 progname=hits_to_fastq
53 help2man --no-info --no-discard-stderr --help-option=" -h" \
54 --name='create a fastq for mapping from significant kmers' \
55 --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
56 echo $AUTHOR >> $MANDIR/${progname}.1
57
58 progname=mapping_to_phandango
59 help2man --no-info --no-discard-stderr --help-option=" -h" \
60 --name='create a plot file for visualisation in phandango' \
61 --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
62 echo $AUTHOR >> $MANDIR/${progname}.1
63
64 progname=mash2matrix
65 help2man --no-info --no-discard-stderr --help-option=" -h" \
66 --name='create all pairwise distances between samples' \
67 --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
68 echo $AUTHOR >> $MANDIR/${progname}.1
69
70 progname=reformat_output
71 help2man --no-info --no-discard-stderr --help-option=" -h" \
72 --name='reformats output for easier reading as tsv' \
73 --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
74 echo $AUTHOR >> $MANDIR/${progname}.1
75
76 cat <<EOT
77 Please enhance the help2man output.
78 The following web page might be helpful in doing so:
79 http://liw.fi/manpages/
80 EOT
81
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debian/mans/R_mds.1 less more
0 .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
1 .TH R_MDS "1" "March 2017" "R_mds 1.1.2" "User Commands"
2 .SH NAME
3 R_mds \- project distance matrix into lower number of dimensions
4 .SH SYNOPSIS
5 .B R_mds
6 \fI\,-k <filtered_kmers.txt> -p <pheno_file>\/\fR
7 .SH DESCRIPTION
8 Projects distance matrix into lower number of dimensions
9 Requires R and rhdf5 to be installed, see github wiki for more details
10 .IP
11 Options
12 .IP
13 Required
14 \fB\-d\fR, \fB\-\-dist\fR Distance matrix output by kmds
15 \fB\-p\fR, \fB\-\-pheno\fR Phenotype file used by seer
16 .IP
17 Optional
18 \fB\-o\fR, \fB\-\-output\fR Output prefix (default 'all_structure')
19 \fB\-\-pc\fR Number of dimensions to project into (default 3)
20 \fB\-R\fR R executable (default 'which R')
21 \fB\-h\fR, \fB\-\-help\fR Displays this message
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.
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debian/mans/hits_to_fastq.1 less more
0 .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
1 .TH HITS_TO_FASTQ "1" "March 2017" "hits_to_fastq 1.1.2" "User Commands"
2 .SH NAME
3 hits_to_fastq \- create a fastq for mapping from significant kmers
4 .SH SYNOPSIS
5 .B hits_to_fastq
6 \fI\,-k <significant_kmers.txt> -b <bonferroni_correction>\/\fR
7 .SH DESCRIPTION
8 Creates a fastq for mapping from significant kmers
9 .IP
10 Options
11 .IP
12 Required
13 \fB\-k\fR, \fB\-\-kmers\fR Significant kmers, as output by seer
14 \fB\-b\fR, \fB\-\-bonf\fR Bonferroni correction to use (try 10e\-8)
15 .IP
16 Optional
17 \fB\-h\fR, \fB\-\-help\fR Displays this message
18 .SH AUTHOR
19 This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
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debian/mans/mapping_to_phandango.1 less more
0 .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
1 .TH MAPPING_TO_PHANDANGO "1" "March 2017" "mapping_to_phandango 1.1.2" "User Commands"
2 .SH NAME
3 mapping_to_phandango \- create a plot file for visualisation in phandango
4 .SH SYNOPSIS
5 .B mapping_to_phandango
6 \fI\,-s <sam_file> -k <seer_kmers> > phandango.plot\/\fR
7 .SH DESCRIPTION
8 Creates a plot file for visualisation in phandango
9 .IP
10 Options
11 .IP
12 Required
13 \fB\-s\fR, \fB\-\-sam\fR Sam file of kmers mapped to reference (unsorted)
14 \fB\-k\fR, \fB\-\-kmers\fR Kmers that were mapped
15 .IP
16 Optional
17 \fB\-m\fR, \fB\-\-map\fR Minimum mapping quality
18 .TP
19 \fB\-h\fR, \fB\-\-help\fR
20 Displays this message
21 .SH AUTHOR
22 This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
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debian/mans/mash2matrix.1 less more
0 .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
1 .TH MASH2MATRIX "1" "March 2017" "mash2matrix 1.1.2" "User Commands"
2 .SH NAME
3 mash2matrix \- create all pairwise distances between samples
4 .SH SYNOPSIS
5 .B mash2matrix
6 \fI\,<matrix_in> > all_distances.csv\/\fR
7 .SH DESCRIPTION
8 Uses mash (http://mash.readthedocs.io/) to create all pairwise distances
9 between samples.
10 .PP
11 NB: the input to mash should be the same order as the .pheno file
12 generate <assemblies.fa> with:
13 cut \fB\-f\fR 1 metadata.pheno | tr '
14 \&' ' '
15 .PP
16 Then run
17 mash sketch \fB\-o\fR reference <assemblies.fa>
18 mash dist reference.msh reference.msh > mash_distances.txt
19 \&./mash2matrix.pl mash_distances.txt > all_distances.csv
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.
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debian/mans/reformat_output.1 less more
0 .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
1 .TH REFORMAT_OUTPUT "1" "March 2017" "reformat_output 1.1.2" "User Commands"
2 .SH NAME
3 reformat_output \- reformats output for easier reading as tsv
4 .SH SYNOPSIS
5 .B hits_to_matrix.pl
6 \fI\,-k <filtered_kmers.txt> -p <pheno_file>\/\fR
7 .SH DESCRIPTION
8 Reformats output for easier reading as tsv. Prints to stdout
9 .IP
10 Options
11 .IP
12 Required
13 \fB\-k\fR, \fB\-\-kmers\fR Filtered significant kmers, as output by seer + filter_seer
14 \fB\-p\fR, \fB\-\-pheno\fR Phenotype file used by seer
15 .IP
16 Optional
17 \fB\-h\fR, \fB\-\-help\fR Displays this message
18 .SH AUTHOR
19 This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.