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comparison macros.xml @ 11:e661a3269313 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
author bgruening
date Mon, 05 Dec 2022 15:47:45 +0000
parents e4c01dcece8b
children f2000bc73102
comparison
equal deleted inserted replaced
10:e4c01dcece8b 11:e661a3269313
1 <macros> 1 <macros>
2 <token name="@VERSION@">1.5.1</token> 2 <token name="@TOOL_VERSION@">1.9.0</token>
3 <token name="@GALAXY_VERSION@">galaxy0</token> 3 <token name="@VERSION_SUFFIX@">1</token>
4 <token name="@IDX_VERSION@">q7</token> 4 <token name="@IDX_VERSION@">q7</token>
5 <token name="@PROFILE_VERSION@">20.01</token> 5 <token name="@PROFILE_VERSION@">20.01</token>
6 <xml name="requirements"> 6 <xml name="requirements">
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@VERSION@">salmon</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">salmon</requirement>
9 <requirement type="package" version="1.3">seqtk</requirement> 9 <requirement type="package" version="1.3">seqtk</requirement>
10 <requirement type="package" version="1.12">samtools</requirement> 10 <requirement type="package" version="1.16.1">samtools</requirement>
11 <requirement type="package" version="0.2.0">vpolo</requirement> 11 <requirement type="package" version="0.2.0">vpolo</requirement>
12 <requirement type="package" version="1.3.0">pandas</requirement> 12 <requirement type="package" version="1.5.2">pandas</requirement>
13 <requirement type="package" version="1.7.0">scipy</requirement> 13 <requirement type="package" version="3.0.0">graphviz</requirement>
14 <requirement type="package" version="1.9.3">scipy</requirement>
14 </requirements> 15 </requirements>
15 </xml> 16 </xml>
16 <xml name="orient"> 17 <xml name="orient">
17 <param name="orientation" type="select" label="Relative orientation of reads within a pair"> 18 <param name="orientation" type="select" label="Relative orientation of reads within a pair">
18 <option value="M">Mates are oriented in the same direction (M = matching)</option> 19 <option value="M">Mates are oriented in the same direction (M = matching)</option>
70 </options> 71 </options>
71 </param> 72 </param>
72 </when> <!-- build-in --> 73 </when> <!-- build-in -->
73 <when value="history"> 74 <when value="history">
74 <section name="s_index" title="Salmon index" expanded="true"> 75 <section name="s_index" title="Salmon index" expanded="true">
75 <param name="fasta" type="data" format="fasta" label="Transcripts fasta file"/> 76 <param name="fasta" type="data" format="fasta" label="Transcripts FASTA file"/>
77 <param name="genome" type="data" format="fasta" optional="true" label="Reference genome"
78 help="The reference genome is required for generating a decoy-away index. The decoy sequences are regions of the target genome
79 that are sequence similar to annotated transcripts. These are the regions of the genome most likely to cause mismapping." />
76 <param name="kmer" type="integer" value="31" label="Kmer length"/> 80 <param name="kmer" type="integer" value="31" label="Kmer length"/>
77 <param name="phash" type="boolean" label="Perfect Hash" truevalue="--perfectHash" falsevalue="" checked="false" 81 <param name="phash" type="boolean" label="Perfect Hash" truevalue="--perfectHash" falsevalue="" checked="false"
78 help="Build the index using a perfect hash rather than a dense hash. This will require less memory (especially during quantification), but will take longer to construct"/> 82 help="Build the index using a perfect hash rather than a dense hash. This will require less memory (especially during quantification),
83 but will take longer to construct"/>
79 </section> 84 </section>
80 </when> 85 </when>
81 </conditional> 86 </conditional>
82 </xml> 87 </xml>
83 <xml name="reads"> 88 <xml name="reads">
153 label="Consensus Slack" 158 label="Consensus Slack"
154 help="The amount of slack allowed in the quasi-mapping consensus mechanism. Normally, a transcript must cover all hits to be considered for mapping. If this is set to a value, X, greater than 0, then a transcript can fail to cover up to X hits before it is discounted as a mapping candidate. The default value of this option is 1 if --validateMappings is given and 0 otherwise."/> 159 help="The amount of slack allowed in the quasi-mapping consensus mechanism. Normally, a transcript must cover all hits to be considered for mapping. If this is set to a value, X, greater than 0, then a transcript can fail to cover up to X hits before it is discounted as a mapping candidate. The default value of this option is 1 if --validateMappings is given and 0 otherwise."/>
155 <param name="dovetail" label="Allow Dovetail" type="boolean" truevalue="--allowDovetail" falsevalue="" checked="False" help="Allow dovetail mappings"/> 160 <param name="dovetail" label="Allow Dovetail" type="boolean" truevalue="--allowDovetail" falsevalue="" checked="False" help="Allow dovetail mappings"/>
156 <param name="recoverOrphans" label="Recover Orphans" type="boolean" truevalue="--recoverOrphans" falsevalue="" checked="False" 161 <param name="recoverOrphans" label="Recover Orphans" type="boolean" truevalue="--recoverOrphans" falsevalue="" checked="False"
157 help="Attempt to recover the mates of orphaned reads. This uses edlib for orphan recovery, and so introduces some computational overhead, but it can improve sensitivity."/> 162 help="Attempt to recover the mates of orphaned reads. This uses edlib for orphan recovery, and so introduces some computational overhead, but it can improve sensitivity."/>
158 <param name="writeMappings" type="boolean" truevalue="--writeMappings=./output/samout.sam" falsevalue="" checked="False" 163 <conditional name="bam_options">
159 label="Write Mappings to Bam File" 164 <param argument="--writeMappings" type="select" label="Write Mappings to BAM File" help="If this option is provided, then the quasi-mapping results will be written out in SAM-compatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead">
160 help="If this option is provided, then the quasi-mapping results will be written out in SAM-compatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead"/> 165 <option value="--writeMappings=./output/samout.sam">Enabled</option>
166 <option value="" selected="true">Disabled</option>
167 </param>
168 <when value="--writeMappings=./output/samout.sam">
169 <param argument="--writeQualities" type="boolean" truevalue="--writeQualities" falsevalue="" checked="false" label="Write qualities" help="If this flag is
170 provided, then the output SAM file will contain quality strings as well as read sequences." />
171 </when>
172 <when value=""/>
173 </conditional>
174 <param name="writeMappings" type="boolean" truevalue="" falsevalue="" checked="False"
175 label="Write Mappings to Bam File"
176 help="If this option is provided, then the quasi-mapping results will be written out in SAM-compatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead"/>
161 <param name="consistentHits" type="boolean" truevalue="--consistentHits" falsevalue="" checked="False" 177 <param name="consistentHits" type="boolean" truevalue="--consistentHits" falsevalue="" checked="False"
162 label="Consistent Hits" 178 label="Consistent Hits"
163 help="Force hits gathered during quasi-mapping to be 'consistent' (i.e. co-linear and approximately the right distance apart)."/> 179 help="Force hits gathered during quasi-mapping to be 'consistent' (i.e. co-linear and approximately the right distance apart)."/>
164 <param name="quasiCoverage" type="integer" optional="True" label="Quasi Coverage" 180 <param name="quasiCoverage" type="integer" optional="True" label="Quasi Coverage"
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."/> 181 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."/>
313 <token name="@bam_sort@"><![CDATA[samtools sort -@ \${GALAXY_SLOTS} --output-fmt=BAM -o ./output/bamout.bam]]></token> 329 <token name="@bam_sort@"><![CDATA[samtools sort -@ \${GALAXY_SLOTS} --output-fmt=BAM -o ./output/bamout.bam]]></token>
314 <token name="@indexing@"><![CDATA[ 330 <token name="@indexing@"><![CDATA[
315 mkdir ./index && 331 mkdir ./index &&
316 mkdir ./output && 332 mkdir ./output &&
317 #if $quant_type.refTranscriptSource.TranscriptSource != "indexed": 333 #if $quant_type.refTranscriptSource.TranscriptSource != "indexed":
334 #if $quant_type.refTranscriptSource.s_index.genome
335 cat '${quant_type.refTranscriptSource.s_index.genome}' | grep "^>" | cut -d " " -f 1 > 'decoys.txt' &&
336 sed -i.bak -e 's/>//g' 'decoys.txt' &&
337 cat '${quant_type.refTranscriptSource.s_index.fasta}' '${quant_type.refTranscriptSource.s_index.genome}' > 'input_index.fasta' &&
338 #else
339 ln -s '${quant_type.refTranscriptSource.s_index.fasta}' 'input_index.fasta' &&
340 #end if
318 salmon index -i ./index 341 salmon index -i ./index
319 --kmerLen '${quant_type.refTranscriptSource.s_index.kmer}' 342 --kmerLen '${quant_type.refTranscriptSource.s_index.kmer}'
320 --gencode 343 --gencode
321 --transcripts '${quant_type.refTranscriptSource.s_index.fasta}' 344 --threads "\${GALAXY_SLOTS:-4}"
345 --transcripts 'input_index.fasta'
346 #if $quant_type.refTranscriptSource.s_index.genome
347 --decoy 'decoys.txt'
348 #end if
322 && 349 &&
323 #set $index_path = './index' 350 #set $index_path = './index'
324 #else 351 #else
325 #set $index_path = $quant_type.refTranscriptSource.index.fields.path 352 #set $index_path = $quant_type.refTranscriptSource.index.fields.path
326 #end if 353 #end if
451 #if $quant_type.consensusSlack: 478 #if $quant_type.consensusSlack:
452 --consensusSlack '${quant_type.consensusSlack}' 479 --consensusSlack '${quant_type.consensusSlack}'
453 #end if 480 #end if
454 ${quant_type.dovetail} 481 ${quant_type.dovetail}
455 ${quant_type.recoverOrphans} 482 ${quant_type.recoverOrphans}
456 ${quant_type.writeMappings} 483 ${quant_type.bam_options.writeMappings}
484 #if $quant_type.bam_options.writeMappings:
485 ${quant_type.bam_options.writeQualities}
486 #end if
457 ${quant_type.consistentHits} 487 ${quant_type.consistentHits}
458 #if $quant_type.quasiCoverage: 488 #if $quant_type.quasiCoverage:
459 --quasiCoverage '${quant_type.quasiCoverage}' 489 --quasiCoverage '${quant_type.quasiCoverage}'
460 #end if 490 #end if
461 ]]> 491 ]]>