Codebase list fastaq / e7a6029
Fix edam syntax input+output is singular Andreas Tille 5 years ago
1 changed file(s) with 147 addition(s) and 147 deletion(s). Raw diff Collapse all Expand all
+147
-147
debian/upstream/edam less more
55 - name: add_indels
66 function:
77 - Sequence mutation and randomisation
8 inputs:
9 - data: Sequence
10 formats: [FASTA, FASTQ]
11 outputs:
8 input:
9 - data: Sequence
10 formats: [FASTA, FASTQ]
11 output:
1212 - data: Sequence
1313 formats: [FASTA, FASTQ]
1414 - name: caf_to_fastq
1515 function:
1616 - Formatting
17 inputs:
17 input:
1818 - data: Sequence assembly report
1919 formats: [CAF]
20 outputs:
20 output:
2121 - data: Sequence
2222 formats: [FASTQ]
2323 - name: capillary_to_pairs
2424 function:
2525 - Sequence file editing
26 inputs:
27 - data: Sequence
28 formats: [FASTA]
29 outputs:
26 input:
27 - data: Sequence
28 formats: [FASTA]
29 output:
3030 - data: Sequence
3131 formats: [FASTA]
3232 - name: chunker
3333 function:
3434 - Splitting
35 inputs:
36 - data: Sequence
37 formats: [FASTA, FASTQ]
38 outputs:
35 input:
36 - data: Sequence
37 formats: [FASTA, FASTQ]
38 output:
3939 - data: Sequence
4040 formats: [FASTA, FASTQ]
4141 - name: count_sequences
4242 function:
4343 - Data handling
44 inputs:
45 - data: Sequence
46 formats: [FASTA, FASTQ]
47 outputs:
44 input:
45 - data: Sequence
46 formats: [FASTA, FASTQ]
47 output:
4848 - data: Sequence
4949 formats: [FASTA, FASTQ]
5050 - name: deinterleave
5151 function:
5252 - Splitting
53 inputs:
54 - data: Sequence
55 formats: [FASTA]
56 outputs:
53 input:
54 - data: Sequence
55 formats: [FASTA]
56 output:
5757 - data: Sequence
5858 formats: [FASTA]
5959 - name: enumerate_names
6060 function:
6161 - Sequence file editing
62 inputs:
63 - data: Sequence
64 formats: [FASTA, FASTQ]
65 outputs:
62 input:
63 - data: Sequence
64 formats: [FASTA, FASTQ]
65 output:
6666 - data: Sequence
6767 formats: [FASTA, FASTQ]
6868 - name: expand_nucleotides
6969 function:
7070 - Sequence generation (nucleic acid)
71 inputs:
72 - data: Sequence
73 formats:
74 - FASTA
75 - FASTQ
76 outputs:
71 input:
72 - data: Sequence
73 formats:
74 - FASTA
75 - FASTQ
76 output:
7777 - data: Sequence
7878 formats:
7979 - FASTA
8181 - name: fasta_to_fastq
8282 function:
8383 - Formatting
84 inputs:
84 input:
8585 - data: Sequence
8686 formats:
8787 - FASTA
8888 - qual
89 outputs:
89 output:
9090 - data: Sequence
9191 formats: [FASTQ]
9292 - name: filter
9393 function:
9494 - Sequence file editing
95 inputs:
96 - data: Sequence
97 formats: [FASTA, FASTQ]
98 outputs:
95 input:
96 - data: Sequence
97 formats: [FASTA, FASTQ]
98 output:
9999 - data: Sequence
100100 formats:
101101 - FASTA
103103 - name: get_ids
104104 function:
105105 - ID retrieval
106 inputs:
107 - data: Sequence
108 formats: [FASTA, FASTQ]
109 outputs:
106 input:
107 - data: Sequence
108 formats: [FASTA, FASTQ]
109 output:
110110 - data: Sequence
111111 formats: [FASTA, FASTQ]
112112 - name: get_seq_flanking_gaps
113113 function:
114114 - Sequence database search
115 inputs:
116 - data: Sequence
117 formats: [FASTA]
118 outputs:
115 input:
116 - data: Sequence
117 formats: [FASTA]
118 output:
119119 - data: Sequence
120120 formats: [FASTA]
121121 - name: interleave
122122 function:
123123 - Aggregation
124 inputs:
125 - data: Sequence
126 formats: [FASTA, FASTQ]
127 outputs:
124 input:
125 - data: Sequence
126 formats: [FASTA, FASTQ]
127 output:
128128 - data: Sequence
129129 formats: [FASTA, FASTQ]
130130 - name: make_random_contigs
131131 function:
132132 - Random sequence generation
133 outputs:
133 output:
134134 - data: Sequence
135135 formats: [FASTQ]
136136 - name: merge
137137 function:
138138 - Aggregation
139 inputs:
140 - data: Sequence
141 formats:
142 - FASTA
143 - FASTQ
144 outputs:
139 input:
140 - data: Sequence
141 formats:
142 - FASTA
143 - FASTQ
144 output:
145145 - data: Sequence
146146 formats:
147147 - FASTA
149149 - name: replace_bases
150150 function:
151151 - Sequence mutation and randomization
152 inputs:
153 - data: Sequence
154 formats:
155 - FASTA
156 - FASTQ
157 outputs:
152 input:
153 - data: Sequence
154 formats:
155 - FASTA
156 - FASTQ
157 output:
158158 - data: Sequence
159159 formats:
160160 - FASTA
162162 - name: reverse_complement
163163 function:
164164 - Nucleic acid sequence reverse and complement
165 inputs:
166 - data: Sequence
167 formats: [FASTA, FASTQ]
168 outputs:
165 input:
166 - data: Sequence
167 formats: [FASTA, FASTQ]
168 output:
169169 - data: Sequence
170170 formats: [FASTA, FASTQ]
171171 - name: scaffolds_to_contigs
172172 function:
173173 - Sequence generation (nucleic acid)
174 inputs:
175 - data: Sequence
176 formats: [FASTA, FASTQ]
177 outputs:
174 input:
175 - data: Sequence
176 formats: [FASTA, FASTQ]
177 output:
178178 - data: Sequence
179179 formats: [FASTA, FASTQ]
180180 - name: search_for_seq
181181 function:
182182 - Sequence database search
183 inputs:
184 - data: Sequence
185 formats: [FASTA, FASTQ]
186 outputs:
183 input:
184 - data: Sequence
185 formats: [FASTA, FASTQ]
186 output:
187187 - data: Sequence
188188 formats: [FASTA, FASTQ]
189189 - name: sequence_trim
190190 function:
191191 - Sequence trimming
192 inputs:
193 - data: Sequence
194 formats: [FASTA, FASTQ]
195 outputs:
192 input:
193 - data: Sequence
194 formats: [FASTA, FASTQ]
195 output:
196196 - data: Sequence
197197 formats:
198198 - FASTA
200200 - name: sort_by_size
201201 function:
202202 - Sequence file editing
203 inputs:
204 - data: Sequence
205 formats:
206 - FASTA
207 - FASTQ
208 outputs:
203 input:
204 - data: Sequence
205 formats:
206 - FASTA
207 - FASTQ
208 output:
209209 - data: Sequence
210210 formats:
211211 - FASTA
213213 - name: split_by_base_count
214214 function:
215215 - Splitting
216 inputs:
217 - data: Sequence
218 formats:
219 - FASTA
220 - FASTQ
221 outputs:
216 input:
217 - data: Sequence
218 formats:
219 - FASTA
220 - FASTQ
221 output:
222222 - data: Sequence
223223 formats:
224224 - FASTA
226226 - name: strip_illumina_suffix
227227 function:
228228 - Sequence file editing
229 inputs:
230 - data: Sequence
231 formats:
232 - FASTA
233 - FASTQ
234 outputs:
229 input:
230 - data: Sequence
231 formats:
232 - FASTA
233 - FASTQ
234 output:
235235 - data: Sequence
236236 formats:
237237 - FASTA
239239 - name: to_fake_qual
240240 function:
241241 - Generation
242 inputs:
243 - data: Sequence
244 formats: [FASTA, FASTQ]
245 outputs:
242 input:
243 - data: Sequence
244 formats: [FASTA, FASTQ]
245 output:
246246 - data: Sequence
247247 formats: [qual]
248248 - name: to_fasta
249249 function:
250250 - Formatting
251 inputs:
251 input:
252252 - data: Sequence
253253 formats:
254254 - FASTA
257257 - EMBL format
258258 - GenBank format
259259 - PHYLIP format
260 outputs:
260 output:
261261 - data: Sequence
262262 formats: [FASTA]
263263 - name: to_mira_xml
264264 function:
265265 - Generation
266 inputs:
267 - data: Sequence
268 formats:
269 - FASTA
270 - FASTQ
271 outputs:
266 input:
267 - data: Sequence
268 formats:
269 - FASTA
270 - FASTQ
271 output:
272272 - data: Sequence
273273 formats:
274274 - XML
275275 - name: to_orfs_gff
276276 function:
277277 - Coding region prediction
278 inputs:
279 - data: Sequence
280 formats:
281 - FASTA
282 - FASTQ
283 outputs:
278 input:
279 - data: Sequence
280 formats:
281 - FASTA
282 - FASTQ
283 output:
284284 - data: Sequence features
285285 formats:
286286 - GFF3
287287 - name: to_perfect_reads
288288 function:
289289 - Generation
290 inputs:
291 - data: Sequence
292 formats:
293 - FASTA
294 - FASTQ
295 outputs:
290 input:
291 - data: Sequence
292 formats:
293 - FASTA
294 - FASTQ
295 output:
296296 - data: Sequence
297297 formats:
298298 - FASTQ
299299 - name: to_random_subset
300300 function:
301301 - Random sequence generation
302 inputs:
303 - data: Sequence
304 formats: [FASTA, FASTQ]
305 outputs:
302 input:
303 - data: Sequence
304 formats: [FASTA, FASTQ]
305 output:
306306 - data: Sequence
307307 formats: [FASTQ]
308308 - name: to_tiling_bam
309309 function:
310310 - Generation
311 inputs:
312 - data: Sequence
313 formats: [FASTA]
314 outputs:
311 input:
312 - data: Sequence
313 formats: [FASTA]
314 output:
315315 - data: Alignment
316316 formats: [BAM]
317317 - name: translate
318318 function:
319319 - DNA translation
320 inputs:
321 - data: Sequence
322 formats: [FASTA, FASTQ]
323 outputs:
320 input:
321 - data: Sequence
322 formats: [FASTA, FASTQ]
323 output:
324324 - data: Sequence
325325 formats: [FASTA]
326326 - name: trim_Ns_at_end
327327 function:
328328 - Sequence trimming
329 inputs:
330 - data: Sequence
331 formats: [FASTA, FASTQ]
332 outputs:
329 input:
330 - data: Sequence
331 formats: [FASTA, FASTQ]
332 output:
333333 - data: Sequence
334334 formats: [FASTA, FASTQ]
335335 - name: trim_contigs
336336 function:
337337 - Sequence trimming
338 inputs:
339 - data: Sequence
340 formats: [FASTA, FASTQ]
341 outputs:
338 input:
339 - data: Sequence
340 formats: [FASTA, FASTQ]
341 output:
342342 - data: Sequence
343343 formats: [FASTA, FASTQ]
344344 - name: trim_ends
345345 function:
346346 - Sequence trimming
347 inputs:
348 - data: Sequence
349 formats: [FASTA, FASTQ]
350 outputs:
351 - data: Sequence
352 formats: [FASTA, FASTQ]
347 input:
348 - data: Sequence
349 formats: [FASTA, FASTQ]
350 output:
351 - data: Sequence
352 formats: [FASTA, FASTQ]