Mercurial > repos > bgruening > salmonquantmerge

comparison macros.xml @ 6:88c07fc4024c 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 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
author bgruening
date Thu, 22 Jul 2021 14:06:29 +0000
parents 85b3dc9b6830
children 7e50e8d920db
comparison
equal deleted inserted replaced
5:cfb0849582e1 6:88c07fc4024c
1 <macros> 1 <macros>
2 <token name="@VERSION@">1.3.0</token> 2 <token name="@VERSION@">1.5.1</token>
3 <token name="@GALAXY_VERSION@">galaxy0</token> 3 <token name="@GALAXY_VERSION@">galaxy0</token>
4 <token name="@IDX_VERSION@">q7</token> 4 <token name="@IDX_VERSION@">q7</token>
5 <token name="@PROFILE_VERSION@">20.01</token>
5 <xml name="requirements"> 6 <xml name="requirements">
6 <requirements> 7 <requirements>
7 <requirement type="package" version="@VERSION@">salmon</requirement> 8 <requirement type="package" version="@VERSION@">salmon</requirement>
8 <requirement type="package" version="1.3">seqtk</requirement> 9 <requirement type="package" version="1.3">seqtk</requirement>
9 <requirement type="package" version="1.10">samtools</requirement> 10 <requirement type="package" version="1.12">samtools</requirement>
10 <requirement type="package" version="0.2.0">vpolo</requirement> 11 <requirement type="package" version="0.2.0">vpolo</requirement>
11 <requirement type="package" version="1.0.3">pandas</requirement> 12 <requirement type="package" version="1.3.0">pandas</requirement>
12 <requirement type="package" version="1.4.1">scipy</requirement> 13 <requirement type="package" version="1.7.0">scipy</requirement>
13 </requirements> 14 </requirements>
14 </xml>
15 <xml name="stranded">
16 <param name="strandedness" type="select" label="Specify the strandedness of the reads">
17 <option value="U" selected="True">Not stranded (U)</option>
18 <option value="SF">read comes from the forward strand (SF)</option>
19 <option value="SR">read comes from the reverse strand (SR)</option>
20 </param>
21 </xml> 15 </xml>
22 <xml name="orient"> 16 <xml name="orient">
23 <param name="orientation" type="select" label="Relative orientation of reads within a pair"> 17 <param name="orientation" type="select" label="Relative orientation of reads within a pair">
24 <option value="M">Mates are oriented in the same direction (M = matching)</option> 18 <option value="M">Mates are oriented in the same direction (M = matching)</option>
25 <option value="O">Mates are oriented away from each other (O = outward)</option> 19 <option value="O">Mates are oriented away from each other (O = outward)</option>
26 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option> 20 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
27 </param> 21 </param>
22 </xml>
23 <xml name="stranded">
24 <conditional name="libtype" >
25 <param name="strandedness" type="select" label="Specify the strandedness of the reads" help="--libtype">
26 <option value="A" selected="true">Infer automatically (A)</option>
27 <option value="U">Not stranded (U)</option>
28 <option value="SF">read comes from the forward strand (SF)</option>
29 <option value="SR">read comes from the reverse strand (SR)</option>
30 </param>
31 <yield/>
32 </conditional>
33 </xml>
34 <xml name="stranded_se">
35 <expand macro="stranded">
36 <when value="A"/>
37 <when value="U"/>
38 <when value="SF"/>
39 <when value="SR"/>
40 </expand>
41 </xml>
42 <xml name="stranded_pe">
43 <expand macro="stranded">
44 <when value="A">
45 </when>
46 <when value="U">
47 <expand macro="orient"/>
48 </when>
49 <when value="SF">
50 <expand macro="orient"/>
51 </when>
52 <when value="SR">
53 <expand macro="orient"/>
54 </when>
55 </expand>
28 </xml> 56 </xml>
29 <xml name="index"> 57 <xml name="index">
30 <conditional name="refTranscriptSource"> 58 <conditional name="refTranscriptSource">
31 <param name="TranscriptSource" type="select" label="Select a reference transcriptome from your history or use a built-in index?" 59 <param name="TranscriptSource" type="select" label="Select a reference transcriptome from your history or use a built-in index?"
32 help="Built-ins were indexed using default options"> 60 help="Built-ins were indexed using default options">
61 <option value="paired_collection">Paired-end Dataset Collection</option> 89 <option value="paired_collection">Paired-end Dataset Collection</option>
62 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option> 90 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
63 </param> 91 </param>
64 <when value="single"> 92 <when value="single">
65 <param name="input_singles" type="data" format="fastq,fasta,fastq.gz,fastq.bz2" label="FASTQ/FASTA file" help="FASTQ file." /> 93 <param name="input_singles" type="data" format="fastq,fasta,fastq.gz,fastq.bz2" label="FASTQ/FASTA file" help="FASTQ file." />
66 <expand macro="stranded"/> 94 <expand macro="stranded_se"/>
67 </when> 95 </when>
68 <when value="paired"> 96 <when value="paired">
69 <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." /> 97 <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." />
70 <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." /> 98 <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." />
71 <expand macro="orient"/> 99 <expand macro="stranded_pe"/>
72 <expand macro="stranded"/>
73 </when> 100 </when>
74 <when value="paired_collection"> 101 <when value="paired_collection">
75 <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;" /> 102 <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;" />
76 <expand macro="orient"/> 103 <expand macro="stranded_pe"/>
77 <expand macro="stranded"/>
78 </when> 104 </when>
79 <when value="paired_interleaved"> 105 <when value="paired_interleaved">
80 <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"/> 106 <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"/>
81 <expand macro="orient"/> 107 <expand macro="stranded_pe"/>
82 <expand macro="stranded"/>
83 </when> 108 </when>
84 </conditional> 109 </conditional>
85 </section> 110 </section>
86 <param argument="--type" type="select" label="Type of index" help="When using quasi, orphaned reads will be considered when performing lightweight-alignment."> 111 <param argument="--type" type="select" label="Type of index" help="When using quasi, orphaned reads will be considered when performing lightweight-alignment.">
87 <option value="quasi" selected="True">quasi</option> 112 <option value="quasi" selected="True">quasi</option>
138 help="Force hits gathered during quasi-mapping to be 'consistent' (i.e. co-linear and approximately the right distance apart)."/> 163 help="Force hits gathered during quasi-mapping to be 'consistent' (i.e. co-linear and approximately the right distance apart)."/>
139 <param name="quasiCoverage" type="integer" optional="True" label="Quasi Coverage" 164 <param name="quasiCoverage" type="integer" optional="True" label="Quasi Coverage"
140 help="[Experimental]: The fraction of the read that must be covered by MMPs (of length >= 31) if this read is to be considered as 'mapped'. This may help to avoid 'spurious' mappings. A value of 0 (the default) denotes no coverage threshold (a single 31-mer can yield a mapping). Since coverage by exact matching, large, MMPs is a rather strict condition, this value should likely be set to something low, if used."/> 165 help="[Experimental]: The fraction of the read that must be covered by MMPs (of length >= 31) if this read is to be considered as 'mapped'. This may help to avoid 'spurious' mappings. A value of 0 (the default) denotes no coverage threshold (a single 31-mer can yield a mapping). Since coverage by exact matching, large, MMPs is a rather strict condition, this value should likely be set to something low, if used."/>
141 </xml> 166 </xml>
142 <xml name="align"> 167 <xml name="align">
143 <param name="afile" type="data" format="bam" label="Alignment file"/> 168 <param name="afile" type="data" format="qname_input_sorted.bam,qname_sorted.bam" label="Alignment file"/>
169 <param argument="--ont" type="boolean" truevalue="--ont" falsevalue="" label="Is this Alignment file a Oxford Nanopore Technologies (ONT) dataset ?" help="Select this for both cDNA and direct RNA ONT datasets. Enables an alignment error model designed to work with long-read alignments and disables the length effect in the generative model when computing the conditional probability of observing a fragment given that it arises from a specific transcript. This is because in long-read sequencing, we do not expect to observe (i.e. sequence) multiple fragments from the same molecule, and thus we do not expect the transcript length to directly affect the observed fragment count directly"/>
144 <param name="transcript" type="data" format="fasta,fa" label="Transcript file"/> 170 <param name="transcript" type="data" format="fasta,fa" label="Transcript file"/>
145 <expand macro="stranded"/> 171 <expand macro="stranded_se"/>
146 <param name="discardOrphans" type="boolean" truevalue="--discardOrphans" falsevalue="" checked="False" 172 <param name="discardOrphans" type="boolean" truevalue="--discardOrphans" falsevalue="" checked="False"
147 label="Discard orphans" 173 label="Discard orphans"
148 help="Discard orphan alignments in the input. If this flag is passed, then only paired alignments will be considered toward quantification estimates. The default behavior is to consider orphan alignments if no valid paired mappings exist."/> 174 help="Discard orphan alignments in the input. If this flag is passed, then only paired alignments will be considered toward quantification estimates. The default behavior is to consider orphan alignments if no valid paired mappings exist."/>
149 <param name="noErrorModel" type="boolean" truevalue="--noErrorModel" falsevalue="" checked="False" 175 <param name="noErrorModel" type="boolean" truevalue="--noErrorModel" falsevalue="" checked="False"
150 label="No Error Model" 176 label="No Error Model"
228 help=" The purpose of ignoring the auxiliary models for the first numPreAuxModelSamples observations is to avoid applying these models before thier parameters have been learned sufficiently well." /> 254 help=" The purpose of ignoring the auxiliary models for the first numPreAuxModelSamples observations is to avoid applying these models before thier parameters have been learned sufficiently well." />
229 <param name="useEM" type="boolean" truevalue="--useEM" falsevalue="" checked="False" 255 <param name="useEM" type="boolean" truevalue="--useEM" falsevalue="" checked="False"
230 label="Use the traditional EM algorithm for optimization in the batch passes." 256 label="Use the traditional EM algorithm for optimization in the batch passes."
231 help=""/> 257 help=""/>
232 <param name="rangeFactorizationBins" type="integer" value="0" label="Range of factorization bins" 258 <param name="rangeFactorizationBins" type="integer" value="0" label="Range of factorization bins"
233 help="Factorizes the likelihood used in quantification by adopting a new notionof equivalence classes based on the conditional probabilities with which fragments are generated from different transcripts. This is a more fine-grained factorization than the normal rich equivalence classes. The default value (0) corresponds to the standard rich equivalence classes, and larger values imply a more fine-grained factorization. If range factorization is enabled, a common value to select for this parameter is 4."/> 259 help="Factorizes the likelihood used in quantification by adopting a new notion of equivalence classes based on the conditional probabilities with which fragments are generated from different transcripts. This is a more fine-grained factorization than the normal rich equivalence classes. The default value (0) corresponds to the standard rich equivalence classes, and larger values imply a more fine-grained factorization. If range factorization is enabled, a common value to select for this parameter is 4."/>
234 <param name="numGibbsSamples" type="integer" value="0" optional="True" 260 <param name="numGibbsSamples" type="integer" value="0" optional="True"
235 label="Number of Gibbs sampling rounds to perform." 261 label="Number of Gibbs sampling rounds to perform."
236 help="" /> 262 help="" />
237 <param name="noGammaDraw" type="boolean" truevalue="--noGammaDraw" falsevalue="" checked="False" 263 <param name="noGammaDraw" type="boolean" truevalue="--noGammaDraw" falsevalue="" checked="False"
238 label="No gamma draw" 264 label="No gamma draw"
358 #end if 384 #end if
359 385
360 salmon quant 386 salmon quant
361 --index '$index_path' 387 --index '$index_path'
362 #if $quant_type.input.single_or_paired.single_or_paired_opts == 'single': 388 #if $quant_type.input.single_or_paired.single_or_paired_opts == 'single':
363 --libType ${quant_type.input.single_or_paired.strandedness} 389 --libType ${quant_type.input.single_or_paired.libtype.strandedness}
364 #if $compressed == 'GZ': 390 #if $compressed == 'GZ':
365 --unmatedReads <(zcat < ./single.$ext) 391 --unmatedReads <(zcat < ./single.$ext)
366 #else if $compressed == 'BZ2': 392 #else if $compressed == 'BZ2':
367 --unmatedReads <(bzcat < ./single.$ext) 393 --unmatedReads <(bzcat < ./single.$ext)
368 #else: 394 #else:
369 --unmatedReads ./single.$ext 395 --unmatedReads ./single.$ext
370 #end if 396 #end if
371 #else: 397 #else:
372 --libType '${quant_type.input.single_or_paired.orientation}${quant_type.input.single_or_paired.strandedness}' 398 --libType
399 #if $quant_type.input.single_or_paired.libtype.strandedness == 'A'
400 A
401 #else
402 ${quant_type.input.single_or_paired.libtype.orientation}${quant_type.input.single_or_paired.libtype.strandedness}
403 #end if
373 #if $quant_type.input.single_or_paired.single_or_paired_opts == 'paired_interleaved': 404 #if $quant_type.input.single_or_paired.single_or_paired_opts == 'paired_interleaved':
374 #if $compressed == 'BZ2': 405 #if $compressed == 'BZ2':
375 --mates1 <(bzcat < ./mate1.$ext | seqtk seq -1) 406 --mates1 <(bzcat < ./mate1.$ext | seqtk seq -1)
376 --mates2 <(bzcat < ./mate1.$ext | seqtk seq -2) 407 --mates2 <(bzcat < ./mate1.$ext | seqtk seq -2)
377 #else: 408 #else:
433 #if $geneMap: 464 #if $geneMap:
434 ln -s "$geneMap" ./geneMap.${geneMap.ext} && 465 ln -s "$geneMap" ./geneMap.${geneMap.ext} &&
435 #end if 466 #end if
436 salmon quant 467 salmon quant
437 -t '${quant_type.transcript}' 468 -t '${quant_type.transcript}'
438 -l '${quant_type.strandedness}' 469 -l '${quant_type.libtype.strandedness}'
439 -a '${quant_type.afile}' 470 -a '${quant_type.afile}'
471 $quant_type.ont
440 --threads "\${GALAXY_SLOTS:-4}" 472 --threads "\${GALAXY_SLOTS:-4}"
441 ${quant_type.discardOrphans} 473 ${quant_type.discardOrphans}
442 ${quant_type.noErrorModel} 474 ${quant_type.noErrorModel}
443 #if $quant_type.numErrorBins: 475 #if $quant_type.numErrorBins:
444 --numErrorBins '${quant_type.numErrorBins}' 476 --numErrorBins '${quant_type.numErrorBins}'