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comparison data_manager/macros.xml @ 11:c6f957c373d3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
author iuc
date Sun, 16 Apr 2023 08:28:41 +0000
parents f639ff7dea45
children 66a8edd52132
comparison
equal deleted inserted replaced
10:f639ff7dea45 11:c6f957c373d3
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@">3</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 <expand macro="dbKeyAction"/>
65 <when value="indexed">
66 <action type="metadata" name="dbkey">
67 <option type="from_data_table" name="@IDX_DATA_TABLE@" column="1" offset="0">
68 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
69 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
70 </option>
71 </action>
72 </when>
73 <when value="history">
74 <action type="metadata" name="dbkey">
75 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
76 </action>
77 </when>
78 </conditional>
79 </actions> 68 </actions>
69 </xml>
70 <xml name="dbKeyAction">
71 <conditional name="refGenomeSource.geneSource">
72 <when value="indexed">
73 <action type="metadata" name="dbkey">
74 <option type="from_data_table" name="@IDX_DATA_TABLE@" column="1" offset="0">
75 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
76 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
77 </option>
78 </action>
79 </when>
80 <when value="history">
81 <action type="metadata" name="dbkey">
82 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
83 </action>
84 </when>
85 </conditional>
80 </xml> 86 </xml>
81 <token name="@TEMPINDEX@"><![CDATA[ 87 <token name="@TEMPINDEX@"><![CDATA[
82 ## Create temporary index for custom reference 88 ## Create temporary index for custom reference
83 #if str($refGenomeSource.geneSource) == 'history': 89 #if str($refGenomeSource.geneSource) == 'history':
90 #if $refGenomeSource.genomeFastaFiles.ext == "fasta"
91 ln -s '$refGenomeSource.genomeFastaFiles' refgenome.fa &&
92 #else
93 gunzip -c '$refGenomeSource.genomeFastaFiles' > refgenome.fa &&
94 #end if
84 mkdir -p tempstargenomedir && 95 mkdir -p tempstargenomedir &&
85 STAR 96 STAR
86 --runMode genomeGenerate 97 --runMode genomeGenerate
87 --genomeDir 'tempstargenomedir' 98 --genomeDir 'tempstargenomedir'
88 --genomeFastaFiles '${refGenomeSource.genomeFastaFiles}' 99 --genomeFastaFiles refgenome.fa
89 ## Handle difference between indices with/without annotations 100 ## Handle difference between indices with/without annotations
90 #if 'GTFconditional' in $refGenomeSource: 101 #if 'GTFconditional' in $refGenomeSource:
91 ## GTFconditional exists only in STAR, but not STARsolo 102 ## GTFconditional exists only in STAR, but not STARsolo
92 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf': 103 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
93 --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}' 104 --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}'
107 #end if 118 #end if
108 #if str($refGenomeSource.genomeSAindexNbases): 119 #if str($refGenomeSource.genomeSAindexNbases):
109 --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases} 120 --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases}
110 #end if 121 #end if
111 --runThreadN \${GALAXY_SLOTS:-4} 122 --runThreadN \${GALAXY_SLOTS:-4}
123 ## in bytes
124 --limitGenomeGenerateRAM \$((\${GALAXY_MEMORY_MB:-31000} * 1000000))
112 && 125 &&
113 #end if 126 #end if
114 ]]></token> 127 ]]></token>
115 <token name="@REFGENOMEHANDLING@" ><![CDATA[ 128 <token name="@REFGENOMEHANDLING@" ><![CDATA[
116 --runThreadN \${GALAXY_SLOTS:-4} 129 --runThreadN \${GALAXY_SLOTS:-4}
119 #if str($refGenomeSource.geneSource) == 'history': 132 #if str($refGenomeSource.geneSource) == 'history':
120 tempstargenomedir 133 tempstargenomedir
121 #else: 134 #else:
122 '${refGenomeSource.GTFconditional.genomeDir.fields.path}' 135 '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
123 ## Handle difference between indices with/without annotations 136 ## Handle difference between indices with/without annotations
124 #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf': 137 #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf-with-gtf':
125 #if $refGenomeSource.GTFconditional.sjdbGTFfile: 138 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
126 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang 139 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
127 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}' 140 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
128 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3': 141 --sjdbGTFtagExonParentTranscript Parent
129 --sjdbGTFtagExonParentTranscript Parent
130 #end if
131 #end if 142 #end if
132 #end if 143 #end if
133 #end if 144 #end if
134 ]]></token> 145 ]]></token>
135 <token name="@READSHANDLING@" ><![CDATA[ 146 <token name="@READSHANDLING@" ><![CDATA[
136 ## Check that the input pairs are of the same type 147 ## Check that the input pairs are of the same type
137 ## otherwise STARsolo will run for a long time and then error out. 148 ## otherwise STARsolo will run for a long time and then error out.
138 ## We consume either repeats of two inputs R1 + R2 149 ## We consume either repeats of two inputs R1 + R2
139 ## or a collection of paired reads. 150 ## or a collection of paired reads.
159 --soloCBmatchWLtype $sc.soloCBmatchWLtype 170 --soloCBmatchWLtype $sc.soloCBmatchWLtype
160 #if $r1.is_of_type('fastq.gz', 'fastqsanger.gz'): 171 #if $r1.is_of_type('fastq.gz', 'fastqsanger.gz'):
161 @FASTQ_GZ_OPTION@ 172 @FASTQ_GZ_OPTION@
162 #end if 173 #end if
163 ]]></token> 174 ]]></token>
175 <token name="@LIMITS@" ><![CDATA[
176 --limitOutSJoneRead $getVar('algo.params.junction_limits.limitOutSJoneRead', $getVar('solo.junction_limits.limitOutSJoneRead', 1000))
177 --limitOutSJcollapsed $getVar('algo.params.junction_limits.limitOutSJcollapsed', $getVar('solo.junction_limits.limitOutSJcollapsed', 1000000))
178 --limitSjdbInsertNsj $getVar('algo.params.junction_limits.limitSjdbInsertNsj', $getVar('solo.junction_limits.limitSjdbInsertNsj', 1000000))
179 ]]></token>
164 <xml name="ref_selection"> 180 <xml name="ref_selection">
165 <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" /> 181 <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)"/> 182 <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> 183 </xml>
168 <xml name="stdio" > 184 <xml name="stdio" >
169 <stdio> 185 <stdio>
170 <regex match="FATAL error" source="both" level="fatal"/> 186 <regex match="FATAL error" source="both" level="fatal"/>
204 <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of paired-end FASTQ files" /> 220 <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of paired-end FASTQ files" />
205 </when> 221 </when>
206 </conditional> 222 </conditional>
207 </xml> 223 </xml>
208 <xml name="umidedup_options"> 224 <xml name="umidedup_options">
209 <option value="1MM_All" selected="true">Collapse all UMIs with 1 mismatch distance to each other</option> 225 <option value="1MM_All" selected="true">Collapse all UMIs with 1 mismatch distance to each other (1MM_All)</option>
210 <option value="1MM_Directional_UMItools" >Directional method from the UMI-tool</option> 226 <option value="1MM_Directional_UMItools" >Directional method from the UMI-tool</option>
211 <option value="1MM_Directional" >Directional with stringent UMI deduplication</option> 227 <option value="1MM_Directional" >Directional with stringent UMI deduplication</option>
212 </xml> 228 </xml>
213 <xml name="anchor_types"> 229 <xml name="anchor_types">
214 <option value="0">Read start</option> 230 <option value="0">Read start</option>
216 <option value="2">Adapter start</option> 232 <option value="2">Adapter start</option>
217 <option value="3">Adapter end</option> 233 <option value="3">Adapter end</option>
218 </xml> 234 </xml>
219 <xml name="cb_match_wl_common"> 235 <xml name="cb_match_wl_common">
220 <option value="Exact" >Exact</option> 236 <option value="Exact" >Exact</option>
221 <option value="1MM" >Single match</option> 237 <option value="1MM" >Single match (1MM)</option>
222 </xml> 238 </xml>
223 <xml name="cb_match_wl_cellranger"> 239 <xml name="cb_match_wl_cellranger">
224 <option value="1MM_multi" selected="true" >Multiple matches (CellRanger 2)</option> 240 <option value="1MM_multi" selected="true" >Multiple matches (CellRanger 2, 1MM_multi)</option>
225 <option value="1MM_multi_pseudocounts" >Multiple matches (CellRanger 3)</option> 241 <option value="1MM_multi_pseudocounts" >Multiple matches (CellRanger 3, 1MM_multi_pseudocounts)</option>
226 <option value="1MM_multi_Nbase_pseudocounts" >Multimatching to WL is allowed for CBs with N-bases (CellRanger 3)</option> 242 <option value="1MM_multi_Nbase_pseudocounts" >Multimatching to WL is allowed for CBs with N-bases (CellRanger 3, 1MM_multi_Nbase_pseudocounts)</option>
227 </xml> 243 </xml>
228 <xml name="solo_adapter_params"> 244 <xml name="solo_adapter_params">
229 <param argument="--soloAdapterSequence" type="text" value="-" label="Adapter sequence to anchor barcodes." > 245 <param argument="--soloAdapterSequence" type="text" value="-" label="Adapter sequence to anchor barcodes." >
230 <sanitizer> 246 <sanitizer>
231 <valid initial="string.digits"> 247 <valid initial="string.digits">
243 <option value="Hamming" selected="true" >Adapter clipping based on Hamming distance</option> 259 <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> 260 <option value="CellRanger4" >5p and 3p adapter clipping similar to CellRanger4</option>
245 <option value="None" >No adapter clipping</option> 261 <option value="None" >No adapter clipping</option>
246 </param> 262 </param>
247 </xml> 263 </xml>
264 <xml name="common_SAM_attributes">
265 <option value="NH" selected="true">NH (number of reported alignments/hits for the read)</option>
266 <option value="HI" selected="true">HI (query hit index)</option>
267 <option value="AS" selected="true">AS (local alignment score)</option>
268 <option value="nM" selected="true">nM (number of mismatches per (paired) alignment)</option>
269 <option value="NM">NM (edit distance of the aligned read to the reference)</option>
270 <option value="MD">MD (string for mismatching positions)</option>
271 <option value="jM">jM (intron motifs for all junctions)</option>
272 <option value="jI">jI (1-based start and end of introns for all junctions)</option>
273 </xml>
274 <xml name="limits">
275 <section name="junction_limits" title="Junction Limits" expanded="false">
276 <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" />
277 <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" />
278 <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." />
279 </section>
280 </xml>
281 <xml name="outCountActions">
282 <actions>
283 <action name="column_names" type="metadata" default="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" />
284 <expand macro="dbKeyAction"/>
285 </actions>
286 </xml>
287 <xml name="outWig">
288 <conditional name="outWig">
289 <param name="outWigType" type="select" label="Compute coverage">
290 <option value="None">No coverage</option>
291 <option value="bedGraph">Yes in bedgraph format</option>
292 <option value="wiggle">Yes in wiggle format</option>
293 </param>
294 <when value="None">
295 <!-- This is necessary for the filtering of output -->
296 <param name="outWigStrand" type="hidden" value="false" />
297 </when>
298 <when value="bedGraph">
299 <expand macro="outWigParams"/>
300 </when>
301 <when value="wiggle">
302 <expand macro="outWigParams"/>
303 </when>
304 </conditional>
305 </xml>
306 <xml name="outWigParams">
307 <param name="outWigTypeSecondWord" type="select" label="Input for coverage">
308 <option value="">Default (everything that mapped)</option>
309 <option value="read_5p">signal from only 5’ of the 1st read</option>
310 <option value="read2">signal from only 2nd read</option>
311 </param>
312 <param argument="--outWigStrand" type="boolean" truevalue="Stranded" falsevalue="Unstranded" checked="true" label="Generate a coverage for each strand (stranded coverage)"/>
313 <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"/>
314 <param argument="--outWigNorm" type="boolean" truevalue="RPM" falsevalue="None" checked="true" label="Normalize coverage to million of mapped reads (RPM)"/>
315 </xml>
316 <token name="@OUTWIG@"><![CDATA[
317 #if str($outWig.outWigType) != 'None':
318 --outWigType '$outWig.outWigType' '$outWig.outWigTypeSecondWord'
319 --outWigStrand '$outWig.outWigStrand'
320 --outWigReferencesPrefix '$outWig.outWigReferencesPrefix'
321 --outWigNorm '$outWig.outWigNorm'
322 #end if
323 ]]></token>
324 <token name="@OUTWIGOUTPUTS@"><![CDATA[
325 #if str($outWig.outWigType) == "bedGraph":
326 && mv Signal.Unique.str1.out.bg Signal.Unique.str1.out
327 && mv Signal.UniqueMultiple.str1.out.bg Signal.UniqueMultiple.str1.out
328 #if str($outWig.outWigStrand) == "Stranded":
329 && mv Signal.Unique.str2.out.bg Signal.Unique.str2.out
330 && mv Signal.UniqueMultiple.str2.out.bg Signal.UniqueMultiple.str2.out
331 #end if
332 #elif str($outWig.outWigType) == "wiggle":
333 && mv Signal.Unique.str1.out.wig Signal.Unique.str1.out
334 && mv Signal.UniqueMultiple.str1.out.wig Signal.UniqueMultiple.str1.out
335 #if str($outWig.outWigStrand) == "Stranded":
336 && mv Signal.Unique.str2.out.wig Signal.Unique.str2.out
337 && mv Signal.UniqueMultiple.str2.out.wig Signal.UniqueMultiple.str2.out
338 #end if
339 #end if
340 ]]></token>
341 <xml name="outWigOutputs">
342 <data format="bedgraph" name="signal_unique_str1" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 1" from_work_dir="Signal.Unique.str1.out">
343 <filter>outWig['outWigType'] != "None"</filter>
344 <expand macro="dbKeyActions" />
345 <change_format>
346 <when input="outWig.outWigType" value="wiggle" format="wig" />
347 </change_format>
348 </data>
349 <data format="bedgraph" name="signal_uniquemultiple_str1" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 1" from_work_dir="Signal.UniqueMultiple.str1.out">
350 <filter>outWig['outWigType'] != "None"</filter>
351 <expand macro="dbKeyActions" />
352 <change_format>
353 <when input="outWig.outWigType" value="wiggle" format="wig" />
354 </change_format>
355 </data>
356 <data format="bedgraph" name="signal_unique_str2" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 2" from_work_dir="Signal.Unique.str2.out">
357 <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter>
358 <expand macro="dbKeyActions" />
359 <change_format>
360 <when input="outWig.outWigType" value="wiggle" format="wig" />
361 </change_format>
362 </data>
363 <data format="bedgraph" name="signal_uniquemultiple_str2" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 2" from_work_dir="Signal.UniqueMultiple.str2.out">
364 <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter>
365 <expand macro="dbKeyActions" />
366 <change_format>
367 <when input="outWig.outWigType" value="wiggle" format="wig" />
368 </change_format>
369 </data>
370 </xml>
371 <xml name="quantMode">
372 <conditional name="quantmode_output">
373 <param argument="--quantMode" type="select"
374 label="Per gene/transcript output"
375 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!">
376 <option value="-">No per gene or transcript output</option>
377 <option value="GeneCounts">Per gene read counts (GeneCounts)</option>
378 <option value="TranscriptomeSAM">Transcript-based BAM output (TranscriptomeSAM)</option>
379 <option value="TranscriptomeSAM GeneCounts">Both per gene read counts and transcript-based BAM output (TranscriptomeSAM GeneCounts)</option>
380 </param>
381 <when value="-" />
382 <when value="GeneCounts" />
383 <when value="TranscriptomeSAM">
384 <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"
385 label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"
386 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." />
387 </when>
388 <when value="TranscriptomeSAM GeneCounts">
389 <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"
390 label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"
391 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." />
392 </when>
393 </conditional>
394 </xml>
395 <xml name="quantModeNoGTF">
396 <conditional name="quantmode_output">
397 <param argument="--quantMode" type="select"
398 label="Per gene/transcript output">
399 <option value="-">No per gene or transcript output as no GTF was provided</option>
400 </param>
401 <when value="-" />
402 </conditional>
403 </xml>
404 <xml name="outSAMmapqUnique">
405 <!-- MAPQ 255 is the default in STAR (coming from tophat behaviour and compatibility for Cufflinks) but it is a problematic value
406 - according to SAM/BAM specs it means "undefined".
407 - Using 255 as the max mapq causes problem with modern downstream tools like mutect2: https://sites.duke.edu/workblog/2021/08/18/star-rnaseq-gatk-mutect2/ and 60 has become an inofficial replacement for 255. -->
408 <param argument="--outSAMmapqUnique" type="integer" value="60" min="0" max="255"
409 label="MAPQ value for unique mappers"
410 help="STAR bases the mapping quality scores of alignment records in its BAM output on the number of alternative mappings for the read. If a read maps to multiple locations on the reference genome, the following MAPQ scoring scheme is
411 used: >=5 mappings => MAPQ=0; 3-4 mappings => MAPQ=1; 2 mappings => MAPQ=3. This setting lets you control the MAPQ used for reads mapped to a single location. Set to 255 for compatibility with Cufflink (default in STAR) but keep to 60 for modern downstream tools like mutect2." />
412 </xml>
248 </macros> 413 </macros>