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comparison data_manager/macros.xml @ 11:d63c1442407f 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 08:31:33 +0000
parents a225487bf618
children 71c994a11f71
comparison
equal deleted inserted replaced
10:a225487bf618 11:d63c1442407f
3 whenever you make changes to the @TOOL_VERSION@ token! 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 update @IDX_VERSION_SUFFIX@ --> 5 the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->
6 <!-- STAR version to be used --> 6 <!-- STAR version to be used -->
7 <token name="@TOOL_VERSION@">2.7.10b</token> 7 <token name="@TOOL_VERSION@">2.7.10b</token>
8 <token name="@VERSION_SUFFIX@">0</token> 8 <token name="@VERSION_SUFFIX@">3</token>
9 <token name="@PROFILE@">21.01</token> 9 <token name="@PROFILE@">21.01</token>
10 <!-- STAR index version compatible with this version of STAR 10 <!-- STAR index version compatible with this version of STAR
11 This is the STAR version that introduced the index structure expected 11 This is the STAR version that introduced the index structure expected
12 by the current version. 12 by the current version.
13 It can be found for any specific version of STAR with: 13 It can be found for any specific version of STAR with:
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"/> 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"/>
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"/> 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"/>
64 </xml> 64 </xml>
65 <xml name="dbKeyActions"> 65 <xml name="dbKeyActions">
66 <actions> 66 <actions>
67 <conditional name="refGenomeSource.geneSource"> 67 <expand macro="dbKeyAction"/>
68 <when value="indexed">
69 <action type="metadata" name="dbkey">
70 <option type="from_data_table" name="@IDX_DATA_TABLE@" column="1" offset="0">
71 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
72 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
73 </option>
74 </action>
75 </when>
76 <when value="history">
77 <action type="metadata" name="dbkey">
78 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
79 </action>
80 </when>
81 </conditional>
82 </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>
83 </xml> 86 </xml>
84 <token name="@TEMPINDEX@"><![CDATA[ 87 <token name="@TEMPINDEX@"><![CDATA[
85 ## Create temporary index for custom reference 88 ## Create temporary index for custom reference
86 #if str($refGenomeSource.geneSource) == 'history': 89 #if str($refGenomeSource.geneSource) == 'history':
87 #if $refGenomeSource.genomeFastaFiles.ext == "fasta" 90 #if $refGenomeSource.genomeFastaFiles.ext == "fasta"
217 <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" />
218 </when> 221 </when>
219 </conditional> 222 </conditional>
220 </xml> 223 </xml>
221 <xml name="umidedup_options"> 224 <xml name="umidedup_options">
222 <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>
223 <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>
224 <option value="1MM_Directional" >Directional with stringent UMI deduplication</option> 227 <option value="1MM_Directional" >Directional with stringent UMI deduplication</option>
225 </xml> 228 </xml>
226 <xml name="anchor_types"> 229 <xml name="anchor_types">
227 <option value="0">Read start</option> 230 <option value="0">Read start</option>
229 <option value="2">Adapter start</option> 232 <option value="2">Adapter start</option>
230 <option value="3">Adapter end</option> 233 <option value="3">Adapter end</option>
231 </xml> 234 </xml>
232 <xml name="cb_match_wl_common"> 235 <xml name="cb_match_wl_common">
233 <option value="Exact" >Exact</option> 236 <option value="Exact" >Exact</option>
234 <option value="1MM" >Single match</option> 237 <option value="1MM" >Single match (1MM)</option>
235 </xml> 238 </xml>
236 <xml name="cb_match_wl_cellranger"> 239 <xml name="cb_match_wl_cellranger">
237 <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>
238 <option value="1MM_multi_pseudocounts" >Multiple matches (CellRanger 3)</option> 241 <option value="1MM_multi_pseudocounts" >Multiple matches (CellRanger 3, 1MM_multi_pseudocounts)</option>
239 <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>
240 </xml> 243 </xml>
241 <xml name="solo_adapter_params"> 244 <xml name="solo_adapter_params">
242 <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." >
243 <sanitizer> 246 <sanitizer>
244 <valid initial="string.digits"> 247 <valid initial="string.digits">
276 </section> 279 </section>
277 </xml> 280 </xml>
278 <xml name="outCountActions"> 281 <xml name="outCountActions">
279 <actions> 282 <actions>
280 <action name="column_names" type="metadata" default="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" /> 283 <action name="column_names" type="metadata" default="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" />
284 <expand macro="dbKeyAction"/>
281 </actions> 285 </actions>
282 </xml> 286 </xml>
283 <xml name="outWig"> 287 <xml name="outWig">
284 <conditional name="outWig"> 288 <conditional name="outWig">
285 <param name="outWigType" type="select" label="Compute coverage"> 289 <param name="outWigType" type="select" label="Compute coverage">
303 <param name="outWigTypeSecondWord" type="select" label="Input for coverage"> 307 <param name="outWigTypeSecondWord" type="select" label="Input for coverage">
304 <option value="">Default (everything that mapped)</option> 308 <option value="">Default (everything that mapped)</option>
305 <option value="read_5p">signal from only 5’ of the 1st read</option> 309 <option value="read_5p">signal from only 5’ of the 1st read</option>
306 <option value="read2">signal from only 2nd read</option> 310 <option value="read2">signal from only 2nd read</option>
307 </param> 311 </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."/> 312 <param argument="--outWigStrand" type="boolean" truevalue="Stranded" falsevalue="Unstranded" checked="true" label="Generate a coverage for each strand (stranded coverage)"/>
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"/> 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"/>
310 <param argument="--outWigNorm" type="boolean" truevalue="RPM" falsevalue="None" checked="true" label="Normalize coverage to million of mapped reads (RPM)"/> 314 <param argument="--outWigNorm" type="boolean" truevalue="RPM" falsevalue="None" checked="true" label="Normalize coverage to million of mapped reads (RPM)"/>
311 </xml> 315 </xml>
312 <token name="@OUTWIG@"><![CDATA[ 316 <token name="@OUTWIG@"><![CDATA[
313 #if str($outWig.outWigType) != 'None': 317 #if str($outWig.outWigType) != 'None':
395 <option value="-">No per gene or transcript output as no GTF was provided</option> 399 <option value="-">No per gene or transcript output as no GTF was provided</option>
396 </param> 400 </param>
397 <when value="-" /> 401 <when value="-" />
398 </conditional> 402 </conditional>
399 </xml> 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>
400 </macros> 413 </macros>