| Previous changeset 21:4074fc1940e2 (2021-09-10) Next changeset 23:a2b0feda6933 (2023-02-17) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb |
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modified:
rg_rnaStar.xml |
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| diff -r 4074fc1940e2 -r 980d2a2e1180 rg_rnaStar.xml --- a/rg_rnaStar.xml Fri Sep 10 16:45:37 2021 +0000 +++ b/rg_rnaStar.xml Tue Nov 01 16:56:55 2022 +0000 |
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| b'@@ -1,13 +1,13 @@\n-<tool id="rna_star" name="RNA STAR" version="@VERSION@+galaxy0" profile="20.01" license="MIT">\n+<tool id="rna_star" name="RNA STAR" version="@VERSION@+galaxy1" profile="20.01" license="MIT">\n <description>Gapped-read mapper for RNA-seq data</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="edam"/>\n <xrefs>\n <xref type="bio.tools">star</xref>\n </xrefs>\n- <macros>\n- <import>macros.xml</import>\n- </macros>\n <expand macro="requirements"/>\n- <expand macro="edam"/>\n <expand macro="stdio" />\n \n <!--\n@@ -145,6 +145,19 @@\n --chimMultimapScoreRange 10\n --chimMultimapNmax 10\n --chimNonchimScoreDropMin 10\n+ \n+ #elif str( $algo.params.settingsType ) == \'arriba\':\n+ ## Preset parameters for Arriba\n+ --peOverlapNbasesMin 10\n+ --alignSplicedMateMapLminOverLmate 0.5\n+ --alignSJstitchMismatchNmax 5 -1 5 5\n+ --chimSegmentMin 10\n+ --chimJunctionOverhangMin 10\n+ --chimScoreDropMax 30\n+ --chimScoreJunctionNonGTAG 0\n+ --chimScoreSeparation 1\n+ --chimSegmentReadGapMax 3\n+ --chimMultimapNmax 50\n \n #elif str( $algo.params.settingsType ) == \'full\':\n ## Extended parameter options\n@@ -163,6 +176,7 @@\n --alignIntronMax ${algo.params.align.alignIntronMax}\n --alignMatesGapMax ${algo.params.align.alignMatesGapMax}\n --alignSJoverhangMin ${algo.params.align.alignSJoverhangMin}\n+ --alignSJstitchMismatchNmax ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax1} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax2} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax3} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax4}\n --alignSJDBoverhangMin ${algo.params.align.alignSJDBoverhangMin}\n --alignSplicedMateMapLmin ${algo.params.align.alignSplicedMateMapLmin}\n --alignSplicedMateMapLminOverLmate ${algo.params.align.alignSplicedMateMapLminOverLmate}\n@@ -349,7 +363,9 @@\n <option value="">Don\'t report chimeric alignments</option>\n <option value="Junctions">As separate tabular "Junctions" output (Junctions)</option>\n <option value="WithinBAM">Within the BAM output (together with regular alignments; WithinBAM)</option>\n- <option value="WithinBAM Junctions">In both forms (WithinBAM Junctions)</option>\n+ <option value="WithinBAM HardClip">Within the BAM output (together with regular alignments; WithinBAM HardClip) hard-clipping in the CIGAR for supplemental chimeric alignments</option>\n+ <option value="WithinBAM SoftClip">Within the BAM output (together with regular alignments; WithinBAM SoftClip) soft-clipping in the CIGAR for supplemental chimeric alignments</option>\n+ <option value="WithinBAM Junctions">Deprecated: In both forms (WithinBAM Junctions)</option>\n </param>\n \n <section name="oformat" title="BAM output format specification" expanded="true">\n@@ -433,11 +449,13 @@\n <param name="settingsType" type="select" label="Configure seed, alignment and limits options">\n <option value="default" selected="true">Use Defaults</option>\n <option value="star_fusion">Use parameters suggested for STAR-Fusion</option>\n+ <option value="arriba">Use parameters suggested for Arriba</option>\n <option value="full">Extended parameter list</option>\n </param>\n <when value="default"/>\n <!-- Set STAR-fusion parameters in command section -->\n <when value="star_fusion"/>\n+ <when value="arriba"/>\n \n <when value="full">\n <section name="seed'..b'integer" min="0" value="0" label="Maximum intron size"/>\n <param argument="--alignMatesGapMax" type="integer" min="0" value="0" label="Maximum gap between two mates"/>\n <param argument="--alignSJoverhangMin" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments"/>\n+ <section name="alignSJstitchMismatchNmax" title="Maximum number of mismatches for stitching of the splice junctions (-1: no limit)" expanded="true">\n+ <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax1" type="integer" min="-1" value="0" label="Non-canonical motifs"/>\n+ <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax2" type="integer" min="-1" value="-1" label="GT/AG and CT/AC motif"/>\n+ <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax3" type="integer" min="-1" value="0" label="GC/AG and CT/GC motif"/>\n+ <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax4" type="integer" min="-1" value="0" label="AT/AC and GT/AT motif"/>\n+ </section>\n <param argument="--alignSJDBoverhangMin" type="integer" min="1" value="3" label="Minimum overhang for annotated spliced alignments"/>\n <param argument="--alignSplicedMateMapLmin" type="integer" min="0" value="0" label="Minimum mapped length for a read mate that is spliced"/>\n <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"/>\n@@ -654,7 +678,7 @@\n <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />\n <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>\n <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />\n- <output name="transcriptome_mapped_reads" file="rnastar_test_transcriptome_mapped_reads.bam" />\n+ <output name="transcriptome_mapped_reads" file="rnastar_test_transcriptome_mapped_reads.bam" compare="sim_size" delta="634" />\n </test>\n <test expect_num_outputs="3">\n <conditional name="singlePaired">\n@@ -989,6 +1013,23 @@\n - under *Algorithmic settings*, **Configure seed, alignment and limits options**:\n `use parameters suggested for STAR-Fusion`.\n \n+*Arriba*\n+\n+Arriba_ can use the BAM with chimeric junctions or both files separately, generated by STAR, as input, but you\n+need to enable **chimeric alignment detection** by STAR for those datasets to be\n+generated. Hence, be sure to select either:\n+\n+**Report chimeric alignments?**: `As separate tabular "Junctions" output (Junctions)` or **Report chimeric alignments?**: `Within the BAM output (together with regular alignments; WithinBAM)`.\n+\n+In addition, the following parameters_ related to chimeric alignment are recommended for improved sensitivity\n+\n+- under *Output filter criteria*,\n+ **Would you like to set additional output filters?**: select `Yes\' to set \n+ **Maximum number of alignments to output a read\'s alignment results, plus 1** to 50 \n+\n+- under *Algorithmic settings*, **Configure seed, alignment and limits options**:\n+ `use parameters suggested for Arriba`.\n+\n *Cufflinks*\n \n .. class:: infomark\n@@ -1019,7 +1060,9 @@\n \n .. _STAR: https://github.com/alexdobin/STAR\n .. _STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion\n+.. _Arriba: https://github.com/suhrig/arriba\n .. _recommended: https://github.com/STAR-Fusion/STAR-Fusion/wiki#alternatively-kickstart-mode-running-star-yourself-and-then-running-star-fusion-using-the-existing-outputs\n+.. _parameters: https://arriba.readthedocs.io/en/latest/workflow/\n ]]></help>\n <expand macro="citations"/>\n </tool>\n' |