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comparison salmon.xml @ 8:8c23f01f10ae draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86
author bgruening
date Thu, 10 May 2018 06:48:12 -0400
parents 20007d82ae2d
children 32613ec39784
comparison
equal deleted inserted replaced
7:20007d82ae2d 8:8c23f01f10ae
8 <option value="U" selected="True">Not stranded (U)</option> 8 <option value="U" selected="True">Not stranded (U)</option>
9 <option value="SF">read 1 (or single-end read) comes from the forward strand (SF)</option> 9 <option value="SF">read 1 (or single-end read) comes from the forward strand (SF)</option>
10 <option value="SR">read 1 (or single-end read) comes from the reverse strand (SR)</option> 10 <option value="SR">read 1 (or single-end read) comes from the reverse strand (SR)</option>
11 </param> 11 </param>
12 </xml> 12 </xml>
13 <token name="@VERSION@">0.8.2</token> 13 <xml name="orientation">
14 <param name="orientation" type="select" label="Relative orientation of reads within a pair">
15 <option value="M">Mates are oriented in the same direction (M = matching)</option>
16 <option value="O">Mates are oriented away from each other (O = outward)</option>
17 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
18 </param>
19 </xml>
20 <token name="@VERSION@">0.9.1</token>
14 </macros> 21 </macros>
15 22
16 <requirements> 23 <requirements>
17 <requirement type="package" version="1.0.6">bzip2</requirement> 24 <requirement type="package" version="1.0.6">bzip2</requirement>
18 <requirement type="package" version="@VERSION@">salmon</requirement> 25 <requirement type="package" version="@VERSION@">salmon</requirement>
26 <requirement type="package" version="1.2">seqtk</requirement>
19 </requirements> 27 </requirements>
20 28
21 <stdio> 29 <stdio>
22 <exit_code range="1:" /> 30 <exit_code range="1:" />
23 <exit_code range=":-1" /> 31 <exit_code range=":-1" />
50 #set compressed = 'no' 58 #set compressed = 'no'
51 #if $single_or_paired.single_or_paired_opts == 'single': 59 #if $single_or_paired.single_or_paired_opts == 'single':
52 #if $single_or_paired.input_singles.ext == 'fasta': 60 #if $single_or_paired.input_singles.ext == 'fasta':
53 #set $ext = 'fasta' 61 #set $ext = 'fasta'
54 #else: 62 #else:
55 #if $single_or_paired.input_singles.is_of_type('fastq.gz'): 63 #if $single_or_paired.input_singles.is_of_type("fastq.gz", "fastqsanger.gz"):
56 #set compressed = 'GZ' 64 #set compressed = 'GZ'
57 #else if $single_or_paired.input_singles.is_of_type('fastq.bz2'): 65 #else if $single_or_paired.input_singles.is_of_type("fastq.bz2", "fastqsanger.bz2"):
58 #set compressed = 'BZ2' 66 #set compressed = 'BZ2'
59 #end if 67 #end if
60 #set $ext = 'fastq' 68 #set $ext = 'fastq'
61 #end if 69 #end if
62 ln -s $single_or_paired.input_singles ./single.$ext && 70 ln -s $single_or_paired.input_singles ./single.$ext &&
63 #else: 71 #else if $single_or_paired.single_or_paired_opts == 'paired':
64 #if $single_or_paired.input_mate1.ext == 'fasta': 72 #if $single_or_paired.input_mate1.ext == 'fasta':
65 #set $ext = 'fasta' 73 #set $ext = 'fasta'
66 #else: 74 #else:
67 #if $single_or_paired.input_mate1.is_of_type('fastq.gz'): 75 #if $single_or_paired.input_mate1.is_of_type("fastq.gz", "fastqsanger.gz"):
68 #set compressed = 'GZ' 76 #set compressed = 'GZ'
69 #else if $single_or_paired.input_mate1.is_of_type('fastq.bz2'): 77 #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
70 #set compressed = 'BZ2' 78 #set compressed = 'BZ2'
71 #end if 79 #end if
72 #set $ext = 'fastq' 80 #set $ext = 'fastq'
73 #end if 81 #end if
74 ln -s $single_or_paired.input_mate1 ./mate1.$ext && 82 ln -s $single_or_paired.input_mate1 ./mate1.$ext &&
75 ln -s $single_or_paired.input_mate2 ./mate2.$ext && 83 ln -s $single_or_paired.input_mate2 ./mate2.$ext &&
84 #else if $single_or_paired.single_or_paired_opts == 'paired_collection':
85 #if $single_or_paired.input_1.forward.ext == 'fasta':
86 #set $ext = 'fasta'
87 #else:
88 #if $single_or_paired.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
89 #set compressed = 'GZ'
90 #else if $single_or_paired.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
91 #set compressed = 'BZ2'
92 #end if
93 #set $ext = 'fastq'
94 #end if
95 ln -s ${single_or_paired.input_1.forward} ./mate1.$ext &&
96 ln -s ${single_or_paired.input_1.reverse} ./mate2.$ext &&
97 #else if $single_or_paired.single_or_paired_opts == 'paired_interleaved':
98 #if $single_or_paired.input_1.ext == 'fasta':
99 #set $ext = 'fasta'
100 #else:
101 #if $single_or_paired.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
102 #set compressed = 'GZ'
103 #else if $single_or_paired.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
104 #set compressed = 'BZ2'
105 #end if
106 #set $ext = 'fastq'
107 #end if
108 ln -s $single_or_paired.input_1 ./mate1.$ext &&
76 #end if 109 #end if
77 #if $geneMap: 110 #if $geneMap:
78 ln -s "$geneMap" ./geneMap.${geneMap.ext} && 111 ln -s "$geneMap" ./geneMap.${geneMap.ext} &&
79 #end if 112 #end if
80 salmon quant 113 salmon quant
81 --index $index_path 114 --index $index_path
82 #if $single_or_paired.single_or_paired_opts == 'single': 115 #if $single_or_paired.single_or_paired_opts == 'single':
83 --libType ${single_or_paired.strandedness} 116 --libType ${single_or_paired.strandedness}
84 #if $compressed == 'GZ': 117 #if $compressed == 'GZ':
85 --unmatedReads <(zcat ./single.$ext) 118 --unmatedReads <(zcat < ./single.$ext)
86 #else if $compressed == 'BZ2': 119 #else if $compressed == 'BZ2':
87 --unmatedReads <(bzcat ./single.$ext) 120 --unmatedReads <(bzcat < ./single.$ext)
88 #else: 121 #else:
89 --unmatedReads ./single.$ext 122 --unmatedReads ./single.$ext
90 #end if 123 #end if
91 #else: 124 #else:
92 #if $compressed == 'GZ': 125 #if $single_or_paired.single_or_paired_opts == 'paired_interleaved':
93 --mates1 <(zcat ./mate1.$ext) 126 #if $compressed == 'BZ2':
94 --mates2 <(zcat ./mate2.$ext) 127 --mates1 <(bzcat < ./mate1.$ext | seqtk seq -1)
95 #else if $compressed == 'BZ2': 128 --mates2 <(bzcat < ./mate1.$ext | seqtk seq -2)
96 --mates1 <(bzcat ./mate1.$ext) 129 #else:
97 --mates2 <(bzcat ./mate2.$ext) 130 --mates1 <(seqtk seq -1 ./mate1.$ext)
131 --mates2 <(seqtk seq -2 ./mate1.$ext)
132 #end if
98 #else: 133 #else:
99 --mates1 ./mate1.$ext 134 #if $compressed == 'GZ':
100 --mates2 ./mate2.$ext 135 --mates1 <(zcat < ./mate1.$ext)
136 --mates2 <(zcat < ./mate2.$ext)
137 #else if $compressed == 'BZ2':
138 --mates1 <(bzcat < ./mate1.$ext)
139 --mates2 <(bzcat < ./mate2.$ext)
140 #else:
141 --mates1 ./mate1.$ext
142 --mates2 ./mate2.$ext
143 #end if
101 #end if 144 #end if
102 --libType "${single_or_paired.orientation}${single_or_paired.strandedness}" 145 --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
103 #end if 146 #end if
104 --output ./output 147 --output ./output
105 #if str($quasi_orphans.type) == 'quasi': 148 #if str($quasi_orphans.type) == 'quasi':
111 $gcBias 154 $gcBias
112 --threads "\${GALAXY_SLOTS:-4}" 155 --threads "\${GALAXY_SLOTS:-4}"
113 --incompatPrior $adv.incompatPrior 156 --incompatPrior $adv.incompatPrior
114 $adv.consistentHits 157 $adv.consistentHits
115 $adv.dumpEq 158 $adv.dumpEq
116 #if str($adv.gcSizeSamp): 159 $adv.reduceGCMemory
117 --gcSizeSamp $adv.gcSizeSamp
118 #end if
119 #if str($adv.biasSpeedSamp): 160 #if str($adv.biasSpeedSamp):
120 --biasSpeedSamp $adv.biasSpeedSamp 161 --biasSpeedSamp $adv.biasSpeedSamp
121 #end if 162 #end if
122 $adv.strictIntersect 163 $adv.strictIntersect
123 #if str($adv.fldMax): 164 #if str($adv.fldMax):
193 </conditional> 234 </conditional>
194 <conditional name="single_or_paired"> 235 <conditional name="single_or_paired">
195 <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?"> 236 <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
196 <option value="single">Single-end</option> 237 <option value="single">Single-end</option>
197 <option value="paired">Paired-end</option> 238 <option value="paired">Paired-end</option>
239 <option value="paired_collection">Paired-end Dataset Collection</option>
240 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
198 </param> 241 </param>
199 <when value="single"> 242 <when value="single">
200 <param name="input_singles" type="data" format="fastq,fasta,fastq.gz" label="FASTQ/FASTA file" help="FASTQ file." /> 243 <param name="input_singles" type="data" format="fastq,fasta,fastq.gz,fastq.bz2" label="FASTQ/FASTA file" help="FASTQ file." />
201 <expand macro="strandedness" /> 244 <expand macro="strandedness" />
202 </when> 245 </when>
203 <when value="paired"> 246 <when value="paired">
204 <param name="input_mate1" type="data" format="fastq,fasta,fastq.gz" label="Mate pair 1" help="FASTQ file." /> 247 <param name="input_mate1" type="data" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Mate pair 1" help="FASTQ file." />
205 <param name="input_mate2" type="data" format="fastq,fasta,fastq.gz" label="Mate pair 2" help="FASTQ file." /> 248 <param name="input_mate2" type="data" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Mate pair 2" help="FASTQ file." />
206 <param name="orientation" type="select" label="Relative orientation of reads within a pair"> 249 <expand macro="orientation" />
207 <option value="M">Mates are oriented in the same direction (M = matching)</option>
208 <option value="O">Mates are oriented away from each other (O = outward)</option>
209 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
210 </param>
211 <expand macro="strandedness" /> 250 <expand macro="strandedness" />
251 </when>
252 <when value="paired_collection">
253 <param name="input_1" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
254 <expand macro="orientation" />
255 <expand macro="strandedness" />
256 </when>
257 <when value="paired_interleaved">
258 <param name="input_1" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="Interleaved FASTQ file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;. --interleaved"/>
259 <expand macro="orientation" />
260 <expand macro="strandedness" />
212 </when> 261 </when>
213 </conditional> 262 </conditional>
214 <conditional name="quasi_orphans"> 263 <conditional name="quasi_orphans">
215 <param argument="--type" type="select" label="Type of index" help="When using quasi, orphaned reads will be considered when performing lightweight-alignment."> 264 <param argument="--type" type="select" label="Type of index" help="When using quasi, orphaned reads will be considered when performing lightweight-alignment.">
216 <option value="quasi" selected="True">quasi</option> 265 <option value="quasi" selected="True">quasi</option>
245 <param argument="--incompatPrior" type="float" optional="True" value="9.9999999999999995e-21" 294 <param argument="--incompatPrior" type="float" optional="True" value="9.9999999999999995e-21"
246 label="Incompatible Prior" 295 label="Incompatible Prior"
247 help="This option sets the prior probability that an alignment that disagrees with the specified library type (--libType) results from the true fragment origin. Setting this to 0 specifies that alignments that disagree with the library type should be 'impossible', while setting it to 1 says that alignments that disagree with the library type are no less likely than those that do" /> 296 help="This option sets the prior probability that an alignment that disagrees with the specified library type (--libType) results from the true fragment origin. Setting this to 0 specifies that alignments that disagree with the library type should be 'impossible', while setting it to 1 says that alignments that disagree with the library type are no less likely than those that do" />
248 <param argument="--dumpEq" type="boolean" truevalue="--dumpEq" falsevalue="" checked="False" 297 <param argument="--dumpEq" type="boolean" truevalue="--dumpEq" falsevalue="" checked="False"
249 label="Dump the equivalence class counts that were computed during quasi-mapping." help=""/> 298 label="Dump the equivalence class counts that were computed during quasi-mapping." help=""/>
250 <param argument="--gcSizeSamp" type="integer" value="1" optional="True" 299 <param argument="--reduceGCMemory" type="boolean" truevalue="--reduceGCMemory" falsevalue="" optional="True" checked="False"
251 label="The value by which to down-sample transcripts when representing the GC content" help="Larger values will reduce memory usage, but may decrease the fidelity of bias modeling results."/> 300 label="If this option is selected, a more memory efficient (but slightly slower representation is used to compute fragment GC content."
301 help="Enabling this will reduce memory usage, but can also reduce speed. However, the results themselves will remain the same."/>
252 <param argument="--biasSpeedSamp" type="integer" value="1" optional="True" 302 <param argument="--biasSpeedSamp" type="integer" value="1" optional="True"
253 label="The value at which the fragment length PMF is down-sampled when evaluating GC fragment bias." help="Larger values speed up effective length correction, but may decrease the fidelity of bias modeling results."/> 303 label="The value at which the fragment length PMF is down-sampled when evaluating GC fragment bias." help="Larger values speed up effective length correction, but may decrease the fidelity of bias modeling results."/>
254 <param argument="--strictIntersect" type="boolean" truevalue="--strictIntersect" falsevalue="" checked="False" 304 <param argument="--strictIntersect" type="boolean" truevalue="--strictIntersect" falsevalue="" checked="False"
255 label="Modifies how orphans are assigned." help="When this flag is set, if the intersection of the quasi-mappings for the left and right is empty, then all mappings for the left and all mappings for the right read are reported as orphaned quasi-mappings."/> 305 label="Modifies how orphans are assigned." help="When this flag is set, if the intersection of the quasi-mappings for the left and right is empty, then all mappings for the left and all mappings for the right read are reported as orphaned quasi-mappings."/>
256 <param argument="--minLen" type="integer" value="19" optional="True" 306 <param argument="--minLen" type="integer" value="19" optional="True"
386 <has_text text="NR_031764" /> 436 <has_text text="NR_031764" />
387 <has_n_columns n="5" /> 437 <has_n_columns n="5" />
388 </assert_contents> 438 </assert_contents>
389 </output> 439 </output>
390 </test> 440 </test>
441 <test> <!-- bzipped input -->
442 <param name="single_or_paired_opts" value="paired" />
443 <param name="input_mate1" value="reads_1.fastq.bz2" ftype="fastqsanger.bz2" />
444 <param name="input_mate2" value="reads_2.fastq.bz2" ftype="fastqsanger.bz2" />
445 <param name="biasCorrect" value="False" />
446 <param name="TranscriptSource" value="history" />
447 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
448 <output name="output_quant">
449 <assert_contents>
450 <has_text text="EffectiveLength" />
451 <has_text text="TPM" />
452 <has_text text="NM_001168316" />
453 <has_text text="NM_174914" />
454 <has_text text="NM_018953" />
455 <has_text text="NR_003084" />
456 <has_text text="NM_017410" />
457 <has_text text="NM_153693" />
458 <has_text text="NR_031764" />
459 <has_n_columns n="5" />
460 </assert_contents>
461 </output>
462 </test>
463 <test> <!-- interleaved bz2 input -->
464 <param name="single_or_paired_opts" value="paired_interleaved" />
465 <param name="input_1" value="reads_both.fastq.bz2" ftype="fastqsanger.bz2" />
466 <param name="biasCorrect" value="False" />
467 <param name="TranscriptSource" value="history" />
468 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
469 <output name="output_quant">
470 <assert_contents>
471 <has_text text="EffectiveLength" />
472 <has_text text="TPM" />
473 <has_text text="NM_001168316" />
474 <has_text text="NM_174914" />
475 <has_text text="NM_018953" />
476 <has_text text="NR_003084" />
477 <has_text text="NM_017410" />
478 <has_text text="NM_153693" />
479 <has_text text="NR_031764" />
480 <has_n_columns n="5" />
481 </assert_contents>
482 </output>
483 </test>
484 <test> <!-- interleaved gz input -->
485 <param name="single_or_paired_opts" value="paired_interleaved" />
486 <param name="input_1" value="reads_both.fastq.gz" ftype="fastqsanger.gz" />
487 <param name="biasCorrect" value="False" />
488 <param name="TranscriptSource" value="history" />
489 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
490 <output name="output_quant">
491 <assert_contents>
492 <has_text text="EffectiveLength" />
493 <has_text text="TPM" />
494 <has_text text="NM_001168316" />
495 <has_text text="NM_174914" />
496 <has_text text="NM_018953" />
497 <has_text text="NR_003084" />
498 <has_text text="NM_017410" />
499 <has_text text="NM_153693" />
500 <has_text text="NR_031764" />
501 <has_n_columns n="5" />
502 </assert_contents>
503 </output>
504 </test>
391 <test> 505 <test>
392 <param name="single_or_paired_opts" value="paired" /> 506 <param name="single_or_paired_opts" value="paired" />
393 <param name="input_mate1" value="reads_1.fastq" /> 507 <param name="input_mate1" value="reads_1.fastq" />
394 <param name="input_mate2" value="reads_2.fastq" /> 508 <param name="input_mate2" value="reads_2.fastq" />
509 <param name="TranscriptSource" value="history" />
510 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
511 <param name="geneMap" value="gene_map.tab" ftype="tabular" />
512 <output name="output_quant">
513 <assert_contents>
514 <has_text text="EffectiveLength" />
515 <has_text text="TPM" />
516 <has_text text="NM_001168316" />
517 <has_text text="NM_174914" />
518 <has_text text="NM_018953" />
519 <has_text text="NR_003084" />
520 <has_text text="NM_017410" />
521 <has_text text="NM_153693" />
522 <has_text text="NR_031764" />
523 <has_n_columns n="5" />
524 </assert_contents>
525 </output>
526 <output name="output_gene_quant">
527 <assert_contents>
528 <has_text text="EffectiveLength" />
529 <has_text text="TPM" />
530 <has_text text="baz" />
531 <has_text text="bar" />
532 <has_text text="2283" />
533 <has_text text="1640" />
534 <has_n_columns n="5" />
535 </assert_contents>
536 </output>
537 </test>
538 <test>
539 <param name="single_or_paired_opts" value="paired_collection" />
540 <param name="input_1">
541 <collection type="paired">
542 <element name="forward" value="reads_1.fastq" ftype="fastqsanger" />
543 <element name="reverse" value="reads_2.fastq" ftype="fastqsanger" />
544 </collection>
545 </param>
395 <param name="TranscriptSource" value="history" /> 546 <param name="TranscriptSource" value="history" />
396 <param name="ownFile" value="transcripts.fasta" ftype="fasta" /> 547 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
397 <param name="geneMap" value="gene_map.tab" ftype="tabular" /> 548 <param name="geneMap" value="gene_map.tab" ftype="tabular" />
398 <output name="output_quant"> 549 <output name="output_quant">
399 <assert_contents> 550 <assert_contents>