Mercurial > repos > iuc > data_manager_star_index_builder

comparison data_manager/macros.xml @ 10:a225487bf618 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
author iuc
date Fri, 17 Feb 2023 20:00:58 +0000
parents c520a52b5174
children d63c1442407f
comparison
equal deleted inserted replaced
9:c520a52b5174 10:a225487bf618
1 <macros> 1 <macros>
2 <!-- REMEMBER to bump the version of rna_star_index_builder_data_manager 2 <!-- REMEMBER to bump the version of @IDX_VERSION_SUFFIX@
3 whenever you make changes to the following two version tokens! 3 whenever you make changes to the @TOOL_VERSION@ token!
4 The data manager uses a symlink to this macro file to keep the STAR and 4 The data manager uses a symlink to this macro file to keep the STAR and
5 the index versions in sync, but you should manually adjust the +galaxy 5 the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->
6 version number. -->
7 <!-- STAR version to be used --> 6 <!-- STAR version to be used -->
8 <token name="@VERSION@">2.7.8a</token> 7 <token name="@TOOL_VERSION@">2.7.10b</token>
8 <token name="@VERSION_SUFFIX@">0</token>
9 <token name="@PROFILE@">21.01</token>
9 <!-- STAR index version compatible with this version of STAR 10 <!-- STAR index version compatible with this version of STAR
10 This is the STAR version that introduced the index structure expected 11 This is the STAR version that introduced the index structure expected
11 by the current version. 12 by the current version.
12 It can be found for any specific version of STAR with: 13 It can be found for any specific version of STAR with:
13 STAR -h | grep versionGenome 14 STAR -h | grep versionGenome
14 or by looking for the versionGenome parameter in source/parametersDefault 15 or by looking for the versionGenome parameter in source/parametersDefault
15 of STAR's source code --> 16 of STAR's source code -->
16 <token name="@IDX_VERSION@">2.7.4a</token> 17 <token name="@IDX_VERSION@">2.7.4a</token>
18 <token name="@IDX_VERSION_SUFFIX@">1</token>
17 <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token> 19 <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token>
18 20
19 <xml name="requirements"> 21 <xml name="requirements">
20 <requirements> 22 <requirements>
21 <requirement type="package" version="@VERSION@">star</requirement> 23 <requirement type="package" version="@TOOL_VERSION@">star</requirement>
22 <requirement type="package" version="1.9">samtools</requirement> 24 <requirement type="package" version="1.16.1">samtools</requirement>
25 <requirement type="package" version="1.12">gzip</requirement>
23 <yield /> 26 <yield />
24 </requirements> 27 </requirements>
25 </xml> 28 </xml>
26 29
27 <xml name="edam"> 30 <xml name="edam">
33 <edam_operation>operation_0292</edam_operation> 36 <edam_operation>operation_0292</edam_operation>
34 </edam_operations> 37 </edam_operations>
35 </xml> 38 </xml>
36 39
37 <xml name="index_selection" token_with_gene_model="0"> 40 <xml name="index_selection" token_with_gene_model="0">
38 <param argument="--genomeDir" name="genomeDir" type="select" 41 <param argument="--genomeDir" type="select"
39 label="Select reference genome" 42 label="Select reference genome"
40 help="If your genome of interest is not listed, contact the Galaxy team"> 43 help="If your genome of interest is not listed, contact the Galaxy team">
41 <options from_data_table="@IDX_DATA_TABLE@"> 44 <options from_data_table="@IDX_DATA_TABLE@">
42 <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" /> 45 <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />
43 <filter type="static_value" column="5" value="@IDX_VERSION@" /> 46 <filter type="static_value" column="5" value="@IDX_VERSION@" />
53 <xml name="citations"> 56 <xml name="citations">
54 <citations> 57 <citations>
55 <citation type="doi">10.1093/bioinformatics/bts635</citation> 58 <citation type="doi">10.1093/bioinformatics/bts635</citation>
56 </citations> 59 </citations>
57 </xml> 60 </xml>
58 <xml name="@SJDBOPTIONS@" token_optional="true"> 61 <xml name="SJDBOPTIONS">
59 <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="@OPTIONAL@" help="Exon junction information for mapping splices"/> 62 <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="false" help="Exon junction information for mapping splices"/>
60 <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/> 63 <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/>
61 </xml> 64 </xml>
62 <xml name="dbKeyActions"> 65 <xml name="dbKeyActions">
63 <actions> 66 <actions>
64 <conditional name="refGenomeSource.geneSource"> 67 <conditional name="refGenomeSource.geneSource">
79 </actions> 82 </actions>
80 </xml> 83 </xml>
81 <token name="@TEMPINDEX@"><![CDATA[ 84 <token name="@TEMPINDEX@"><![CDATA[
82 ## Create temporary index for custom reference 85 ## Create temporary index for custom reference
83 #if str($refGenomeSource.geneSource) == 'history': 86 #if str($refGenomeSource.geneSource) == 'history':
87 #if $refGenomeSource.genomeFastaFiles.ext == "fasta"
88 ln -s '$refGenomeSource.genomeFastaFiles' refgenome.fa &&
89 #else
90 gunzip -c '$refGenomeSource.genomeFastaFiles' > refgenome.fa &&
91 #end if
84 mkdir -p tempstargenomedir && 92 mkdir -p tempstargenomedir &&
85 STAR 93 STAR
86 --runMode genomeGenerate 94 --runMode genomeGenerate
87 --genomeDir 'tempstargenomedir' 95 --genomeDir 'tempstargenomedir'
88 --genomeFastaFiles '${refGenomeSource.genomeFastaFiles}' 96 --genomeFastaFiles refgenome.fa
89 ## Handle difference between indices with/without annotations 97 ## Handle difference between indices with/without annotations
90 #if 'GTFconditional' in $refGenomeSource: 98 #if 'GTFconditional' in $refGenomeSource:
91 ## GTFconditional exists only in STAR, but not STARsolo 99 ## GTFconditional exists only in STAR, but not STARsolo
92 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf': 100 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
93 --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}' 101 --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}'
107 #end if 115 #end if
108 #if str($refGenomeSource.genomeSAindexNbases): 116 #if str($refGenomeSource.genomeSAindexNbases):
109 --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases} 117 --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases}
110 #end if 118 #end if
111 --runThreadN \${GALAXY_SLOTS:-4} 119 --runThreadN \${GALAXY_SLOTS:-4}
120 ## in bytes
121 --limitGenomeGenerateRAM \$((\${GALAXY_MEMORY_MB:-31000} * 1000000))
112 && 122 &&
113 #end if 123 #end if
114 ]]></token> 124 ]]></token>
115 <token name="@REFGENOMEHANDLING@" ><![CDATA[ 125 <token name="@REFGENOMEHANDLING@" ><![CDATA[
116 --runThreadN \${GALAXY_SLOTS:-4} 126 --runThreadN \${GALAXY_SLOTS:-4}
119 #if str($refGenomeSource.geneSource) == 'history': 129 #if str($refGenomeSource.geneSource) == 'history':
120 tempstargenomedir 130 tempstargenomedir
121 #else: 131 #else:
122 '${refGenomeSource.GTFconditional.genomeDir.fields.path}' 132 '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
123 ## Handle difference between indices with/without annotations 133 ## Handle difference between indices with/without annotations
124 #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf': 134 #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf-with-gtf':
125 #if $refGenomeSource.GTFconditional.sjdbGTFfile: 135 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
126 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang 136 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
127 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}' 137 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
128 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3': 138 --sjdbGTFtagExonParentTranscript Parent
129 --sjdbGTFtagExonParentTranscript Parent
130 #end if
131 #end if 139 #end if
132 #end if 140 #end if
133 #end if 141 #end if
134 ]]></token> 142 ]]></token>
135 <token name="@READSHANDLING@" ><![CDATA[ 143 <token name="@READSHANDLING@" ><![CDATA[
136 ## Check that the input pairs are of the same type 144 ## Check that the input pairs are of the same type
137 ## otherwise STARsolo will run for a long time and then error out. 145 ## otherwise STARsolo will run for a long time and then error out.
138 ## We consume either repeats of two inputs R1 + R2 146 ## We consume either repeats of two inputs R1 + R2
139 ## or a collection of paired reads. 147 ## or a collection of paired reads.
159 --soloCBmatchWLtype $sc.soloCBmatchWLtype 167 --soloCBmatchWLtype $sc.soloCBmatchWLtype
160 #if $r1.is_of_type('fastq.gz', 'fastqsanger.gz'): 168 #if $r1.is_of_type('fastq.gz', 'fastqsanger.gz'):
161 @FASTQ_GZ_OPTION@ 169 @FASTQ_GZ_OPTION@
162 #end if 170 #end if
163 ]]></token> 171 ]]></token>
172 <token name="@LIMITS@" ><![CDATA[
173 --limitOutSJoneRead $getVar('algo.params.junction_limits.limitOutSJoneRead', $getVar('solo.junction_limits.limitOutSJoneRead', 1000))
174 --limitOutSJcollapsed $getVar('algo.params.junction_limits.limitOutSJcollapsed', $getVar('solo.junction_limits.limitOutSJcollapsed', 1000000))
175 --limitSjdbInsertNsj $getVar('algo.params.junction_limits.limitSjdbInsertNsj', $getVar('solo.junction_limits.limitSjdbInsertNsj', 1000000))
176 ]]></token>
164 <xml name="ref_selection"> 177 <xml name="ref_selection">
165 <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" /> 178 <param argument="--genomeFastaFiles" type="data" format="fasta,fasta.gz" label="Select a reference genome" />
166 <param argument="--genomeSAindexNbases" type="integer" min="2" max="16" value="14" label="Length of the SA pre-indexing string" help="Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter --genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1)"/> 179 <param argument="--genomeSAindexNbases" type="integer" min="2" max="16" value="14" label="Length of the SA pre-indexing string" help="Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter --genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1)"/>
167 </xml> 180 </xml>
168 <xml name="stdio" > 181 <xml name="stdio" >
169 <stdio> 182 <stdio>
170 <regex match="FATAL error" source="both" level="fatal"/> 183 <regex match="FATAL error" source="both" level="fatal"/>
243 <option value="Hamming" selected="true" >Adapter clipping based on Hamming distance</option> 256 <option value="Hamming" selected="true" >Adapter clipping based on Hamming distance</option>
244 <option value="CellRanger4" >5p and 3p adapter clipping similar to CellRanger4</option> 257 <option value="CellRanger4" >5p and 3p adapter clipping similar to CellRanger4</option>
245 <option value="None" >No adapter clipping</option> 258 <option value="None" >No adapter clipping</option>
246 </param> 259 </param>
247 </xml> 260 </xml>
261 <xml name="common_SAM_attributes">
262 <option value="NH" selected="true">NH (number of reported alignments/hits for the read)</option>
263 <option value="HI" selected="true">HI (query hit index)</option>
264 <option value="AS" selected="true">AS (local alignment score)</option>
265 <option value="nM" selected="true">nM (number of mismatches per (paired) alignment)</option>
266 <option value="NM">NM (edit distance of the aligned read to the reference)</option>
267 <option value="MD">MD (string for mismatching positions)</option>
268 <option value="jM">jM (intron motifs for all junctions)</option>
269 <option value="jI">jI (1-based start and end of introns for all junctions)</option>
270 </xml>
271 <xml name="limits">
272 <section name="junction_limits" title="Junction Limits" expanded="false">
273 <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" />
274 <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" />
275 <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." />
276 </section>
277 </xml>
278 <xml name="outCountActions">
279 <actions>
280 <action name="column_names" type="metadata" default="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" />
281 </actions>
282 </xml>
283 <xml name="outWig">
284 <conditional name="outWig">
285 <param name="outWigType" type="select" label="Compute coverage">
286 <option value="None">No coverage</option>
287 <option value="bedGraph">Yes in bedgraph format</option>
288 <option value="wiggle">Yes in wiggle format</option>
289 </param>
290 <when value="None">
291 <!-- This is necessary for the filtering of output -->
292 <param name="outWigStrand" type="hidden" value="false" />
293 </when>
294 <when value="bedGraph">
295 <expand macro="outWigParams"/>
296 </when>
297 <when value="wiggle">
298 <expand macro="outWigParams"/>
299 </when>
300 </conditional>
301 </xml>
302 <xml name="outWigParams">
303 <param name="outWigTypeSecondWord" type="select" label="Input for coverage">
304 <option value="">Default (everything that mapped)</option>
305 <option value="read_5p">signal from only 5’ of the 1st read</option>
306 <option value="read2">signal from only 2nd read</option>
307 </param>
308 <param argument="--outWigStrand" type="boolean" truevalue="Stranded" falsevalue="Unstranded" checked="true" label="collapse strands (unstranded coverage)" help="By default, the strands are separated."/>
309 <param argument="--outWigReferencesPrefix" type="text" value="-" label="prefix matching reference name" help="For example, set 'chr' if you mapped on an ensembl genome but you want to display on UCSC"/>
310 <param argument="--outWigNorm" type="boolean" truevalue="RPM" falsevalue="None" checked="true" label="Normalize coverage to million of mapped reads (RPM)"/>
311 </xml>
312 <token name="@OUTWIG@"><![CDATA[
313 #if str($outWig.outWigType) != 'None':
314 --outWigType '$outWig.outWigType' '$outWig.outWigTypeSecondWord'
315 --outWigStrand '$outWig.outWigStrand'
316 --outWigReferencesPrefix '$outWig.outWigReferencesPrefix'
317 --outWigNorm '$outWig.outWigNorm'
318 #end if
319 ]]></token>
320 <token name="@OUTWIGOUTPUTS@"><![CDATA[
321 #if str($outWig.outWigType) == "bedGraph":
322 && mv Signal.Unique.str1.out.bg Signal.Unique.str1.out
323 && mv Signal.UniqueMultiple.str1.out.bg Signal.UniqueMultiple.str1.out
324 #if str($outWig.outWigStrand) == "Stranded":
325 && mv Signal.Unique.str2.out.bg Signal.Unique.str2.out
326 && mv Signal.UniqueMultiple.str2.out.bg Signal.UniqueMultiple.str2.out
327 #end if
328 #elif str($outWig.outWigType) == "wiggle":
329 && mv Signal.Unique.str1.out.wig Signal.Unique.str1.out
330 && mv Signal.UniqueMultiple.str1.out.wig Signal.UniqueMultiple.str1.out
331 #if str($outWig.outWigStrand) == "Stranded":
332 && mv Signal.Unique.str2.out.wig Signal.Unique.str2.out
333 && mv Signal.UniqueMultiple.str2.out.wig Signal.UniqueMultiple.str2.out
334 #end if
335 #end if
336 ]]></token>
337 <xml name="outWigOutputs">
338 <data format="bedgraph" name="signal_unique_str1" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 1" from_work_dir="Signal.Unique.str1.out">
339 <filter>outWig['outWigType'] != "None"</filter>
340 <expand macro="dbKeyActions" />
341 <change_format>
342 <when input="outWig.outWigType" value="wiggle" format="wig" />
343 </change_format>
344 </data>
345 <data format="bedgraph" name="signal_uniquemultiple_str1" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 1" from_work_dir="Signal.UniqueMultiple.str1.out">
346 <filter>outWig['outWigType'] != "None"</filter>
347 <expand macro="dbKeyActions" />
348 <change_format>
349 <when input="outWig.outWigType" value="wiggle" format="wig" />
350 </change_format>
351 </data>
352 <data format="bedgraph" name="signal_unique_str2" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 2" from_work_dir="Signal.Unique.str2.out">
353 <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter>
354 <expand macro="dbKeyActions" />
355 <change_format>
356 <when input="outWig.outWigType" value="wiggle" format="wig" />
357 </change_format>
358 </data>
359 <data format="bedgraph" name="signal_uniquemultiple_str2" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 2" from_work_dir="Signal.UniqueMultiple.str2.out">
360 <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter>
361 <expand macro="dbKeyActions" />
362 <change_format>
363 <when input="outWig.outWigType" value="wiggle" format="wig" />
364 </change_format>
365 </data>
366 </xml>
367 <xml name="quantMode">
368 <conditional name="quantmode_output">
369 <param argument="--quantMode" type="select"
370 label="Per gene/transcript output"
371 help="STAR can provide analysis results not only with respect to the reference genome, but also with respect to genes and transcripts described by a gene model. Note: This functionality requires either the selection above of a cached index with a gene model, or a gene model provided alongside the index/reference genome in GTF or GFF3 format!">
372 <option value="-">No per gene or transcript output</option>
373 <option value="GeneCounts">Per gene read counts (GeneCounts)</option>
374 <option value="TranscriptomeSAM">Transcript-based BAM output (TranscriptomeSAM)</option>
375 <option value="TranscriptomeSAM GeneCounts">Both per gene read counts and transcript-based BAM output (TranscriptomeSAM GeneCounts)</option>
376 </param>
377 <when value="-" />
378 <when value="GeneCounts" />
379 <when value="TranscriptomeSAM">
380 <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"
381 label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"
382 help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled." />
383 </when>
384 <when value="TranscriptomeSAM GeneCounts">
385 <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"
386 label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"
387 help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled." />
388 </when>
389 </conditional>
390 </xml>
391 <xml name="quantModeNoGTF">
392 <conditional name="quantmode_output">
393 <param argument="--quantMode" type="select"
394 label="Per gene/transcript output">
395 <option value="-">No per gene or transcript output as no GTF was provided</option>
396 </param>
397 <when value="-" />
398 </conditional>
399 </xml>
248 </macros> 400 </macros>