Mercurial > repos > bgruening > salmon

comparison salmon.xml @ 2:1b22d8a18acc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243
author bgruening
date Thu, 13 Apr 2017 08:18:26 -0400
parents c1d822f84e1a
children 5a60f347f566
comparison
equal deleted inserted replaced
1:c1d822f84e1a 2:1b22d8a18acc
11 </param> 11 </param>
12 </xml> 12 </xml>
13 </macros> 13 </macros>
14 14
15 <requirements> 15 <requirements>
16 <requirement type="package" version="1.0.6">bzip2</requirement>
16 <requirement type="package" version="0.7.2">salmon</requirement> 17 <requirement type="package" version="0.7.2">salmon</requirement>
17 </requirements> 18 </requirements>
18 19
19 <stdio> 20 <stdio>
20 <exit_code range="1:" /> 21 <exit_code range="1:" />
43 #set $index_path = './index' 44 #set $index_path = './index'
44 #else: 45 #else:
45 #set $index_path = $refTranscriptSource.index.fields.path 46 #set $index_path = $refTranscriptSource.index.fields.path
46 #end if 47 #end if
47 && 48 &&
49 #set compressed = 'no'
48 #if $single_or_paired.single_or_paired_opts == 'single': 50 #if $single_or_paired.single_or_paired_opts == 'single':
49 #if $single_or_paired.input_singles.ext == 'fasta': 51 #if $single_or_paired.input_singles.ext == 'fasta':
50 #set $ext = 'fasta' 52 #set $ext = 'fasta'
51 #else: 53 #else:
54 #if $single_or_paired.input_singles.is_of_type('fastq.gz'):
55 #set compressed = 'GZ'
56 #else if $single_or_paired.input_singles.is_of_type('fastq.bz2'):
57 #set compressed = 'BZ2'
58 #end if
52 #set $ext = 'fastq' 59 #set $ext = 'fastq'
53 #end if 60 #end if
54 ln -s $single_or_paired.input_singles ./single.$ext && 61 ln -s $single_or_paired.input_singles ./single.$ext &&
55 #else: 62 #else:
56 #if $single_or_paired.input_mate1.ext == 'fasta': 63 #if $single_or_paired.input_mate1.ext == 'fasta':
57 #set $ext = 'fasta' 64 #set $ext = 'fasta'
58 #else: 65 #else:
66 #if $single_or_paired.input_mate1.is_of_type('fastq.gz'):
67 #set compressed = 'GZ'
68 #else if $single_or_paired.input_mate1.is_of_type('fastq.bz2'):
69 #set compressed = 'BZ2'
70 #end if
59 #set $ext = 'fastq' 71 #set $ext = 'fastq'
60 #end if 72 #end if
61 ln -s $single_or_paired.input_mate1 ./mate1.$ext && 73 ln -s $single_or_paired.input_mate1 ./mate1.$ext &&
62 ln -s $single_or_paired.input_mate2 ./mate2.$ext && 74 ln -s $single_or_paired.input_mate2 ./mate2.$ext &&
63 #end if 75 #end if
66 #end if 78 #end if
67 salmon quant 79 salmon quant
68 --index $index_path 80 --index $index_path
69 #if $single_or_paired.single_or_paired_opts == 'single': 81 #if $single_or_paired.single_or_paired_opts == 'single':
70 --libType ${single_or_paired.strandedness} 82 --libType ${single_or_paired.strandedness}
71 --unmatedReads ./single.$ext 83 #if $compressed == 'GZ':
84 --unmatedReads <(zcat ./single.$ext)
85 #else if $compressed == 'BZ2':
86 --unmatedReads <(bzcat ./single.$ext)
87 #else:
88 --unmatedReads ./single.$ext
89 #end if
72 #else: 90 #else:
73 --mates1 ./mate1.$ext 91 #if $compressed == 'GZ':
74 --mates2 ./mate2.$ext 92 --mates1 <(zcat ./mate1.$ext)
93 --mates2 <(zcat ./mate2.$ext)
94 #else if $compressed == 'BZ2':
95 --mates1 <(bzcat ./mate1.$ext)
96 --mates2 <(bzcat ./mate2.$ext)
97 #else:
98 --mates1 ./mate1.$ext
99 --mates2 ./mate2.$ext
100 #end if
75 --libType "${single_or_paired.orientation}${single_or_paired.strandedness}" 101 --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
76 #end if 102 #end if
77 --output ./output 103 --output ./output
78 #if str($quasi_orphans.type) == 'quasi': 104 #if str($quasi_orphans.type) == 'quasi':
79 --allowOrphans 105 --allowOrphans
166 <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?"> 192 <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
167 <option value="single">Single-end</option> 193 <option value="single">Single-end</option>
168 <option value="paired">Paired-end</option> 194 <option value="paired">Paired-end</option>
169 </param> 195 </param>
170 <when value="single"> 196 <when value="single">
171 <param name="input_singles" type="data" format="fastq,fasta" label="FASTQ/FASTA file" help="FASTQ file." /> 197 <param name="input_singles" type="data" format="fastq,fasta,fastq.gz" label="FASTQ/FASTA file" help="FASTQ file." />
172 <expand macro="strandedness" /> 198 <expand macro="strandedness" />
173 </when> 199 </when>
174 <when value="paired"> 200 <when value="paired">
175 <param name="input_mate1" type="data" format="fastq,fasta" label="Mate pair 1" help="FASTQ file." /> 201 <param name="input_mate1" type="data" format="fastq,fasta,fastq.gz" label="Mate pair 1" help="FASTQ file." />
176 <param name="input_mate2" type="data" format="fastq,fasta" label="Mate pair 2" help="FASTQ file." /> 202 <param name="input_mate2" type="data" format="fastq,fasta,fastq.gz" label="Mate pair 2" help="FASTQ file." />
177 <param name="orientation" type="select" label="Relative orientation of reads within a pair"> 203 <param name="orientation" type="select" label="Relative orientation of reads within a pair">
178 <option value="M">Mates are oriented in the same direction (M = matching)</option> 204 <option value="M">Mates are oriented in the same direction (M = matching)</option>
179 <option value="O">Mates are oriented away from each other (O = outward)</option> 205 <option value="O">Mates are oriented away from each other (O = outward)</option>
180 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option> 206 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
181 </param> 207 </param>
331 <has_text text="NR_031764" /> 357 <has_text text="NR_031764" />
332 <has_n_columns n="5" /> 358 <has_n_columns n="5" />
333 </assert_contents> 359 </assert_contents>
334 </output> 360 </output>
335 </test> 361 </test>
362 <test> <!-- gzipped input -->
363 <param name="single_or_paired_opts" value="paired" />
364 <param name="input_mate1" value="reads_1.fastq.gz" ftype="fastqsanger.gz" />
365 <param name="input_mate2" value="reads_2.fastq.gz" ftype="fastqsanger.gz" />
366 <param name="biasCorrect" value="False" />
367 <param name="TranscriptSource" value="history" />
368 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
369 <output name="output_quant">
370 <assert_contents>
371 <has_text text="EffectiveLength" />
372 <has_text text="TPM" />
373 <has_text text="NM_001168316" />
374 <has_text text="NM_174914" />
375 <has_text text="NM_018953" />
376 <has_text text="NR_003084" />
377 <has_text text="NM_017410" />
378 <has_text text="NM_153693" />
379 <has_text text="NR_031764" />
380 <has_n_columns n="5" />
381 </assert_contents>
382 </output>
383 </test>
336 <test> 384 <test>
337 <param name="single_or_paired_opts" value="paired" /> 385 <param name="single_or_paired_opts" value="paired" />
338 <param name="input_mate1" value="reads_1.fastq" /> 386 <param name="input_mate1" value="reads_1.fastq" />
339 <param name="input_mate2" value="reads_2.fastq" /> 387 <param name="input_mate2" value="reads_2.fastq" />
340 <param name="TranscriptSource" value="history" /> 388 <param name="TranscriptSource" value="history" />