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comparison rg_rnaStar.xml @ 22:980d2a2e1180 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
author iuc
date Tue, 01 Nov 2022 16:56:55 +0000
parents 91e0f03268ca
children a2b0feda6933
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21:4074fc1940e2 22:980d2a2e1180
1 <tool id="rna_star" name="RNA STAR" version="@VERSION@+galaxy0" profile="20.01" license="MIT"> 1 <tool id="rna_star" name="RNA STAR" version="@VERSION@+galaxy1" profile="20.01" license="MIT">
2 <description>Gapped-read mapper for RNA-seq data</description> 2 <description>Gapped-read mapper for RNA-seq data</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="edam"/>
3 <xrefs> 7 <xrefs>
4 <xref type="bio.tools">star</xref> 8 <xref type="bio.tools">star</xref>
5 </xrefs> 9 </xrefs>
6 <macros>
7 <import>macros.xml</import>
8 </macros>
9 <expand macro="requirements"/> 10 <expand macro="requirements"/>
10 <expand macro="edam"/>
11 <expand macro="stdio" /> 11 <expand macro="stdio" />
12 12
13 <!-- 13 <!--
14 important quote (https://groups.google.com/forum/#!topic/rna-star/q4zGzlPgwXY): 14 important quote (https://groups.google.com/forum/#!topic/rna-star/q4zGzlPgwXY):
15 Hi Gary, 15 Hi Gary,
143 --peOverlapNbasesMin 12 143 --peOverlapNbasesMin 12
144 --peOverlapMMp 0.1 144 --peOverlapMMp 0.1
145 --chimMultimapScoreRange 10 145 --chimMultimapScoreRange 10
146 --chimMultimapNmax 10 146 --chimMultimapNmax 10
147 --chimNonchimScoreDropMin 10 147 --chimNonchimScoreDropMin 10
148
149 #elif str( $algo.params.settingsType ) == 'arriba':
150 ## Preset parameters for Arriba
151 --peOverlapNbasesMin 10
152 --alignSplicedMateMapLminOverLmate 0.5
153 --alignSJstitchMismatchNmax 5 -1 5 5
154 --chimSegmentMin 10
155 --chimJunctionOverhangMin 10
156 --chimScoreDropMax 30
157 --chimScoreJunctionNonGTAG 0
158 --chimScoreSeparation 1
159 --chimSegmentReadGapMax 3
160 --chimMultimapNmax 50
148 161
149 #elif str( $algo.params.settingsType ) == 'full': 162 #elif str( $algo.params.settingsType ) == 'full':
150 ## Extended parameter options 163 ## Extended parameter options
151 164
152 ## Seed parameter options 165 ## Seed parameter options
161 ## Alignment parameter options 174 ## Alignment parameter options
162 --alignIntronMin ${algo.params.align.alignIntronMin} 175 --alignIntronMin ${algo.params.align.alignIntronMin}
163 --alignIntronMax ${algo.params.align.alignIntronMax} 176 --alignIntronMax ${algo.params.align.alignIntronMax}
164 --alignMatesGapMax ${algo.params.align.alignMatesGapMax} 177 --alignMatesGapMax ${algo.params.align.alignMatesGapMax}
165 --alignSJoverhangMin ${algo.params.align.alignSJoverhangMin} 178 --alignSJoverhangMin ${algo.params.align.alignSJoverhangMin}
179 --alignSJstitchMismatchNmax ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax1} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax2} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax3} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax4}
166 --alignSJDBoverhangMin ${algo.params.align.alignSJDBoverhangMin} 180 --alignSJDBoverhangMin ${algo.params.align.alignSJDBoverhangMin}
167 --alignSplicedMateMapLmin ${algo.params.align.alignSplicedMateMapLmin} 181 --alignSplicedMateMapLmin ${algo.params.align.alignSplicedMateMapLmin}
168 --alignSplicedMateMapLminOverLmate ${algo.params.align.alignSplicedMateMapLminOverLmate} 182 --alignSplicedMateMapLminOverLmate ${algo.params.align.alignSplicedMateMapLminOverLmate}
169 --alignWindowsPerReadNmax ${algo.params.align.alignWindowsPerReadNmax} 183 --alignWindowsPerReadNmax ${algo.params.align.alignWindowsPerReadNmax}
170 --alignTranscriptsPerWindowNmax ${algo.params.align.alignTranscriptsPerWindowNmax} 184 --alignTranscriptsPerWindowNmax ${algo.params.align.alignTranscriptsPerWindowNmax}
347 label="Report chimeric alignments?" 361 label="Report chimeric alignments?"
348 help="Choose if and how chimeric alignments should be reported. STAR-Fusion users should select the 'Junctions' option and use the resulting tabular dataset as input to STAR-Fusion. Everyone else: note that selecting 'WithinBAM' or 'WithinBAM Junctions' disables the --chimMultimapNmax setting in the algorithmic parameters section below (the tool will only consider uniquely mapped reads in the search for chimeric alignments). If you disable the reporting of chimeric alignments here, then all chimeric alignment settings in the algorithmic parameters section below will be ignored."> 362 help="Choose if and how chimeric alignments should be reported. STAR-Fusion users should select the 'Junctions' option and use the resulting tabular dataset as input to STAR-Fusion. Everyone else: note that selecting 'WithinBAM' or 'WithinBAM Junctions' disables the --chimMultimapNmax setting in the algorithmic parameters section below (the tool will only consider uniquely mapped reads in the search for chimeric alignments). If you disable the reporting of chimeric alignments here, then all chimeric alignment settings in the algorithmic parameters section below will be ignored.">
349 <option value="">Don't report chimeric alignments</option> 363 <option value="">Don't report chimeric alignments</option>
350 <option value="Junctions">As separate tabular "Junctions" output (Junctions)</option> 364 <option value="Junctions">As separate tabular "Junctions" output (Junctions)</option>
351 <option value="WithinBAM">Within the BAM output (together with regular alignments; WithinBAM)</option> 365 <option value="WithinBAM">Within the BAM output (together with regular alignments; WithinBAM)</option>
352 <option value="WithinBAM Junctions">In both forms (WithinBAM Junctions)</option> 366 <option value="WithinBAM HardClip">Within the BAM output (together with regular alignments; WithinBAM HardClip) hard-clipping in the CIGAR for supplemental chimeric alignments</option>
367 <option value="WithinBAM SoftClip">Within the BAM output (together with regular alignments; WithinBAM SoftClip) soft-clipping in the CIGAR for supplemental chimeric alignments</option>
368 <option value="WithinBAM Junctions">Deprecated: In both forms (WithinBAM Junctions)</option>
353 </param> 369 </param>
354 370
355 <section name="oformat" title="BAM output format specification" expanded="true"> 371 <section name="oformat" title="BAM output format specification" expanded="true">
356 <param argument="--outSAMattributes" type="select" display="checkboxes" multiple="true" optional="true" 372 <param argument="--outSAMattributes" type="select" display="checkboxes" multiple="true" optional="true"
357 label="Read alignment tags to include in the BAM output" 373 label="Read alignment tags to include in the BAM output"
431 <section name="algo" title="Algorithmic settings" expanded="true"> 447 <section name="algo" title="Algorithmic settings" expanded="true">
432 <conditional name="params"> 448 <conditional name="params">
433 <param name="settingsType" type="select" label="Configure seed, alignment and limits options"> 449 <param name="settingsType" type="select" label="Configure seed, alignment and limits options">
434 <option value="default" selected="true">Use Defaults</option> 450 <option value="default" selected="true">Use Defaults</option>
435 <option value="star_fusion">Use parameters suggested for STAR-Fusion</option> 451 <option value="star_fusion">Use parameters suggested for STAR-Fusion</option>
452 <option value="arriba">Use parameters suggested for Arriba</option>
436 <option value="full">Extended parameter list</option> 453 <option value="full">Extended parameter list</option>
437 </param> 454 </param>
438 <when value="default"/> 455 <when value="default"/>
439 <!-- Set STAR-fusion parameters in command section --> 456 <!-- Set STAR-fusion parameters in command section -->
440 <when value="star_fusion"/> 457 <when value="star_fusion"/>
458 <when value="arriba"/>
441 459
442 <when value="full"> 460 <when value="full">
443 <section name="seed" title="Seed parameters" expanded="false"> 461 <section name="seed" title="Seed parameters" expanded="false">
444 <param argument="--seedSearchStartLmax" type="integer" min="1" value="50" label="Search start point through the read"/> 462 <param argument="--seedSearchStartLmax" type="integer" min="1" value="50" label="Search start point through the read"/>
445 <param argument="--seedSearchStartLmaxOverLread" type="float" min="0" value="1.0" label="Search start point through the read, normalized to read length"/> 463 <param argument="--seedSearchStartLmaxOverLread" type="float" min="0" value="1.0" label="Search start point through the read, normalized to read length"/>
453 <section name="align" title="Alignment parameters" expanded="false"> 471 <section name="align" title="Alignment parameters" expanded="false">
454 <param argument="--alignIntronMin" name="alignIntronMin" type="integer" min="0" value="21" label="Minimum intron size"/> 472 <param argument="--alignIntronMin" name="alignIntronMin" type="integer" min="0" value="21" label="Minimum intron size"/>
455 <param argument="--alignIntronMax" type="integer" min="0" value="0" label="Maximum intron size"/> 473 <param argument="--alignIntronMax" type="integer" min="0" value="0" label="Maximum intron size"/>
456 <param argument="--alignMatesGapMax" type="integer" min="0" value="0" label="Maximum gap between two mates"/> 474 <param argument="--alignMatesGapMax" type="integer" min="0" value="0" label="Maximum gap between two mates"/>
457 <param argument="--alignSJoverhangMin" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments"/> 475 <param argument="--alignSJoverhangMin" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments"/>
476 <section name="alignSJstitchMismatchNmax" title="Maximum number of mismatches for stitching of the splice junctions (-1: no limit)" expanded="true">
477 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax1" type="integer" min="-1" value="0" label="Non-canonical motifs"/>
478 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax2" type="integer" min="-1" value="-1" label="GT/AG and CT/AC motif"/>
479 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax3" type="integer" min="-1" value="0" label="GC/AG and CT/GC motif"/>
480 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax4" type="integer" min="-1" value="0" label="AT/AC and GT/AT motif"/>
481 </section>
458 <param argument="--alignSJDBoverhangMin" type="integer" min="1" value="3" label="Minimum overhang for annotated spliced alignments"/> 482 <param argument="--alignSJDBoverhangMin" type="integer" min="1" value="3" label="Minimum overhang for annotated spliced alignments"/>
459 <param argument="--alignSplicedMateMapLmin" type="integer" min="0" value="0" label="Minimum mapped length for a read mate that is spliced"/> 483 <param argument="--alignSplicedMateMapLmin" type="integer" min="0" value="0" label="Minimum mapped length for a read mate that is spliced"/>
460 <param argument="--alignSplicedMateMapLminOverLmate" type="float" min="0" value="0.66" label="Minimum mapped length for a read mate that is spliced, normalized to mate length"/> 484 <param argument="--alignSplicedMateMapLminOverLmate" type="float" min="0" value="0.66" label="Minimum mapped length for a read mate that is spliced, normalized to mate length"/>
461 <param argument="--alignWindowsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of windows per read"/> 485 <param argument="--alignWindowsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of windows per read"/>
462 <param argument="--alignTranscriptsPerWindowNmax" type="integer" min="1" value="100" label="Maximum number of transcripts per window"/> 486 <param argument="--alignTranscriptsPerWindowNmax" type="integer" min="1" value="100" label="Maximum number of transcripts per window"/>
652 </section> 676 </section>
653 677
654 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" /> 678 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
655 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/> 679 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
656 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" /> 680 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
657 <output name="transcriptome_mapped_reads" file="rnastar_test_transcriptome_mapped_reads.bam" /> 681 <output name="transcriptome_mapped_reads" file="rnastar_test_transcriptome_mapped_reads.bam" compare="sim_size" delta="634" />
658 </test> 682 </test>
659 <test expect_num_outputs="3"> 683 <test expect_num_outputs="3">
660 <conditional name="singlePaired"> 684 <conditional name="singlePaired">
661 <param name="sPaired" value="single" /> 685 <param name="sPaired" value="single" />
662 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> 686 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
986 additional tag to generate (this is the equivalent of using 1010 additional tag to generate (this is the equivalent of using
987 `--outSAMstrandField intronMotif` on the command line) 1011 `--outSAMstrandField intronMotif` on the command line)
988 1012
989 - under *Algorithmic settings*, **Configure seed, alignment and limits options**: 1013 - under *Algorithmic settings*, **Configure seed, alignment and limits options**:
990 `use parameters suggested for STAR-Fusion`. 1014 `use parameters suggested for STAR-Fusion`.
1015
1016 *Arriba*
1017
1018 Arriba_ can use the BAM with chimeric junctions or both files separately, generated by STAR, as input, but you
1019 need to enable **chimeric alignment detection** by STAR for those datasets to be
1020 generated. Hence, be sure to select either:
1021
1022 **Report chimeric alignments?**: `As separate tabular "Junctions" output (Junctions)` or **Report chimeric alignments?**: `Within the BAM output (together with regular alignments; WithinBAM)`.
1023
1024 In addition, the following parameters_ related to chimeric alignment are recommended for improved sensitivity
1025
1026 - under *Output filter criteria*,
1027 **Would you like to set additional output filters?**: select `Yes' to set
1028 **Maximum number of alignments to output a read's alignment results, plus 1** to 50
1029
1030 - under *Algorithmic settings*, **Configure seed, alignment and limits options**:
1031 `use parameters suggested for Arriba`.
991 1032
992 *Cufflinks* 1033 *Cufflinks*
993 1034
994 .. class:: infomark 1035 .. class:: infomark
995 1036
1017 the creative commons 1058 the creative commons
1018 `BY-NC_ND 3.0 license <http://creativecommons.org/licenses/by-nc-nd/3.0/>`__. 1059 `BY-NC_ND 3.0 license <http://creativecommons.org/licenses/by-nc-nd/3.0/>`__.
1019 1060
1020 .. _STAR: https://github.com/alexdobin/STAR 1061 .. _STAR: https://github.com/alexdobin/STAR
1021 .. _STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion 1062 .. _STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion
1063 .. _Arriba: https://github.com/suhrig/arriba
1022 .. _recommended: https://github.com/STAR-Fusion/STAR-Fusion/wiki#alternatively-kickstart-mode-running-star-yourself-and-then-running-star-fusion-using-the-existing-outputs 1064 .. _recommended: https://github.com/STAR-Fusion/STAR-Fusion/wiki#alternatively-kickstart-mode-running-star-yourself-and-then-running-star-fusion-using-the-existing-outputs
1065 .. _parameters: https://arriba.readthedocs.io/en/latest/workflow/
1023 ]]></help> 1066 ]]></help>
1024 <expand macro="citations"/> 1067 <expand macro="citations"/>
1025 </tool> 1068 </tool>