| Previous changeset 31:53255f6eecfc (2024-12-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 |
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modified:
macros.xml rg_rnaStar.xml |
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added:
test-data/filtered4_algo_full.bam |
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| diff -r 53255f6eecfc -r de21b616f03a macros.xml --- a/macros.xml Thu Dec 05 06:50:18 2024 +0000 +++ b/macros.xml Sat May 31 19:52:54 2025 +0000 |
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| b'@@ -4,8 +4,8 @@\n The data manager uses a symlink to this macro file to keep the STAR and\n the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->\n <!-- STAR version to be used -->\n- <token name="@TOOL_VERSION@">2.7.11a</token>\n- <token name="@VERSION_SUFFIX@">1</token>\n+ <token name="@TOOL_VERSION@">2.7.11b</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n <token name="@PROFILE@">21.01</token>\n <!-- STAR index version compatible with this version of STAR\n This is the STAR version that introduced the index structure expected\n@@ -121,7 +121,7 @@\n #if str($refGenomeSource.diploidconditional.diploid) == \'Yes\':\n --genomeTransformVCF \'${refGenomeSource.diploidconditional.genomeTransformVCF}\'\n --genomeTransformType Diploid\n- #end if \n+ #end if\n #end if\n --runThreadN \\${GALAXY_SLOTS:-4}\n ## in bytes\n@@ -371,6 +371,13 @@\n </change_format>\n </data>\n </xml>\n+ <xml name="quantTranscriptomeSAMoutput_param">\n+ <param argument="--quantTranscriptomeSAMoutput" type="select" label="Alignment filtering for TranscriptomeSAM output">\n+ <option value="BanSingleEnd_BanIndels_ExtendSoftclip" selected="true">prohibit indels and single-end alignments, extend softclips - compatible with RSEM</option>\n+ <option value="BanSingleEnd">prohibit single-end alignments, allow indels and softclips</option>\n+ <option value="BanSingleEnd_ExtendSoftclip">prohibit single-end alignments, extend softclips, allow indels</option>\n+ </param>\n+ </xml>\n <xml name="quantMode">\n <conditional name="quantmode_output">\n <param argument="--quantMode" type="select" label="Per gene/transcript output" 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!">\n@@ -382,10 +389,10 @@\n <when value="-"/>\n <when value="GeneCounts"/>\n <when value="TranscriptomeSAM">\n- <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend" label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?" 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."/>\n+ <expand macro="quantTranscriptomeSAMoutput_param"/>\n </when>\n <when value="TranscriptomeSAM GeneCounts">\n- <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend" label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?" 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."/>\n+ <expand macro="quantTranscriptomeSAMoutput_param"/>\n </when>\n </conditional>\n </xml>\n@@ -432,4 +439,149 @@\n <when value=""/>\n </conditional>\n </xml>\n+ <xml name="full_algo_params">\n+ <section name="seed" title="Seed parameters" expanded="false">\n+ <param argument="--seedSe'..b'ameter options\n+\n+ ## Seed parameter options\n+ --seedSearchStartLmax ${algo.params.seed.seedSearchStartLmax}\n+ --seedSearchStartLmaxOverLread ${algo.params.seed.seedSearchStartLmaxOverLread}\n+ --seedSearchLmax ${algo.params.seed.seedSearchLmax}\n+ --seedMultimapNmax ${algo.params.seed.seedMultimapNmax}\n+ --seedPerReadNmax ${algo.params.seed.seedPerReadNmax}\n+ --seedPerWindowNmax ${algo.params.seed.seedPerWindowNmax}\n+ --seedNoneLociPerWindow ${algo.params.seed.seedNoneLociPerWindow}\n+\n+ ## Alignment parameter options\n+ --alignIntronMin ${algo.params.align.alignIntronMin}\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+ --alignWindowsPerReadNmax ${algo.params.align.alignWindowsPerReadNmax}\n+ --alignTranscriptsPerWindowNmax ${algo.params.align.alignTranscriptsPerWindowNmax}\n+ --alignTranscriptsPerReadNmax ${algo.params.align.alignTranscriptsPerReadNmax}\n+ --alignEndsType ${algo.params.align.alignEndsType}\n+ --peOverlapNbasesMin ${algo.params.align.peOverlapNbasesMin}\n+ --peOverlapMMp ${algo.params.align.peOverlapMMp}\n+ ## Chimeric alignment parameter options\n+ #if str($chimOutType):\n+ --chimSegmentMin ${algo.params.chim_settings.chimSegmentMin}\n+ --chimScoreMin ${algo.params.chim_settings.chimScoreMin}\n+ --chimScoreDropMax $algo.params.chim_settings.chimScoreDropMax\n+ --chimScoreSeparation $algo.params.chim_settings.chimScoreSeparation\n+ --chimScoreJunctionNonGTAG $algo.params.chim_settings.chimScoreJunctionNonGTAG\n+ --chimSegmentReadGapMax $algo.params.chim_settings.chimSegmentReadGapMax\n+ --chimFilter $algo.params.chim_settings.chimFilter\n+ --chimJunctionOverhangMin $algo.params.chim_settings.chimJunctionOverhangMin\n+ --chimMainSegmentMultNmax $algo.params.chim_settings.chimMainSegmentMultNmax\n+ #if str($chimOutType) == \'Junctions\':\n+ --chimMultimapNmax $algo.params.chim_settings.chimMultimapNmax\n+ #else:\n+ --chimMultimapNmax 0\n+ #end if\n+ --chimMultimapScoreRange $algo.params.chim_settings.chimMultimapScoreRange\n+ #end if\n+\n+ ## Limits\n+ @LIMITS@\n+ ]]></token>\n+ <token name="@ALGO_DEFAULT@"><![CDATA[\n+ ## Go with STAR\'s default algorithmic settings,\n+ ## but we need to provide a reasonable default\n+ ## (taken from STAR-Fusion)\n+ ## for --chimSegmentMin in case the user enabled chimeric\n+ ## alignments (the STAR default is 0, which disables chimeric\n+ ## alignments). For consistency, also set\n+ ## --chimMultimapNmax to 1 when chimeric alignments are reported\n+ ## in Junctions format only.\n+ #if str($chimOutType):\n+ --chimSegmentMin 12\n+ #if str($chimOutType) == \'Junctions\':\n+ --chimMultimapNmax 1\n+ #end if\n+ #end if\n+ ]]></token>\n+\n </macros>\n' |
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| diff -r 53255f6eecfc -r de21b616f03a rg_rnaStar.xml --- a/rg_rnaStar.xml Thu Dec 05 06:50:18 2024 +0000 +++ b/rg_rnaStar.xml Sat May 31 19:52:54 2025 +0000 |
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| b"@@ -69,7 +69,7 @@\n \n --quantMode ${refGenomeSource.GTFconditional.quantmode_output.quantMode}\n #if 'TranscriptomeSAM' in str($refGenomeSource.GTFconditional.quantmode_output.quantMode):\n- --quantTranscriptomeBan ${refGenomeSource.GTFconditional.quantmode_output.quantTranscriptomeBan}\n+ --quantTranscriptomeSAMoutput '${refGenomeSource.GTFconditional.quantmode_output.quantTranscriptomeSAMoutput}'\n #end if\n \n ## Output format parameters\n@@ -98,7 +98,7 @@\n #if 'diploidconditional' in $refGenomeSource:\n #if str($refGenomeSource.diploidconditional.diploid) == 'Yes':\n '${refGenomeSource.diploidconditional.genomeTransformOutput}'\n- #end if \n+ #end if\n #end if\n #end if\n \n@@ -156,7 +156,7 @@\n --chimMultimapScoreRange 10\n --chimMultimapNmax 10\n --chimNonchimScoreDropMin 10\n- \n+\n #elif str( $algo.params.settingsType ) == 'arriba':\n ## Preset parameters for Arriba\n --peOverlapNbasesMin 10\n@@ -171,68 +171,9 @@\n --chimMultimapNmax 50\n \n #elif str( $algo.params.settingsType ) == 'full':\n- ## Extended parameter options\n-\n- ## Seed parameter options\n- --seedSearchStartLmax ${algo.params.seed.seedSearchStartLmax}\n- --seedSearchStartLmaxOverLread ${algo.params.seed.seedSearchStartLmaxOverLread}\n- --seedSearchLmax ${algo.params.seed.seedSearchLmax}\n- --seedMultimapNmax ${algo.params.seed.seedMultimapNmax}\n- --seedPerReadNmax ${algo.params.seed.seedPerReadNmax}\n- --seedPerWindowNmax ${algo.params.seed.seedPerWindowNmax}\n- --seedNoneLociPerWindow ${algo.params.seed.seedNoneLociPerWindow}\n-\n- ## Alignment parameter options\n- --alignIntronMin ${algo.params.align.alignIntronMin}\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- --alignWindowsPerReadNmax ${algo.params.align.alignWindowsPerReadNmax}\n- --alignTranscriptsPerWindowNmax ${algo.params.align.alignTranscriptsPerWindowNmax}\n- --alignTranscriptsPerReadNmax ${algo.params.align.alignTranscriptsPerReadNmax}\n- --alignEndsType ${algo.params.align.alignEndsType}\n- --peOverlapNbasesMin ${algo.params.align.peOverlapNbasesMin}\n- --peOverlapMMp ${algo.params.align.peOverlapMMp}\n- ## Chimeric alignment parameter options\n- #if str($chimOutType):\n- --chimSegmentMin ${algo.params.chim_settings.chimSegmentMin}\n- --chimScoreMin ${algo.params.chim_settings.chimScoreMin}\n- --chimScoreDropMax $algo.params.chim_settings.chimScoreDropMax\n- --chimScoreSeparation $algo.params.chim_settings.chimScoreSeparation\n- --chimScoreJunctionNonGTAG $algo.params.chim_settings.chimScoreJunctionNonGTAG\n- --chimSegmentReadGapMax $algo.params.chim_settings.chimSegmentReadGapMax\n- --chimFilter $algo.params.chim_settings.chimFilter\n- --chimJunctionOverhangMin $algo.params.chim_settings.chimJunctionOverhangMin\n- "..b'="integer" min="1" value="12"\n- label="Minimum length of chimeric segment"\n- help="For small numbers this will cause large number of chimeric alignments. A value of 12 is commonly used." />\n- <param argument="--chimScoreMin" type="integer" min="0" value="0"\n- label="Minimum total (summed) score of chimeric segments"/>\n- <param argument="--chimScoreDropMax" type="integer" min="0" value="20"\n- label="Maximum difference of chimeric score from read length"/>\n- <param argument="--chimScoreSeparation" type="integer" min="0" value="10"\n- label="Minimum difference between the best chimeric score and the next one"/>\n- <param argument="--chimScoreJunctionNonGTAG" type="integer" value="-1"\n- label="Penalty for a non-GT/AG chimeric junction"/>\n- <param argument="--chimJunctionOverhangMin" type="integer" min="0" value="20"\n- label="Minimum overhang for a chimeric junction"/>\n- <param argument="--chimSegmentReadGapMax" type="integer" min="0" value="0"\n- label="Maximum gap in the read sequence between chimeric segments" />\n- <param argument="--chimFilter" type="boolean" truevalue="banGenomicN" falsevalue="None" checked="true"\n- label="Discard chimeric alignments with Ns in the genome sequence around the chimeric junction" />\n- <param argument="--chimMainSegmentMultNmax" type="integer" min="1" value="10"\n- label="Maximum number of multi-alignments for the main chimeric segment."\n- help="A value of 1 prohibits multimapping main segments"/>\n- <param argument="--chimMultimapNmax" type="integer" min="1" value="1"\n- label="Maximum number of chimeric multi-alignments"\n- help="The default value of 1 only considers unique alignments. If you chose to report chimeric alignments alongside regular ones in the BAM output, this setting is ignored and only uniquely mapping chimeric reads get reported. " />\n- <param argument="--chimMultimapScoreRange" type="integer" min="0" value="1"\n- label="Score range for multi-mapping chimeras"\n- help="The threshold below the best chimeric score that a multimapping chimera must have to be output. This is ignored unless --chimMultimapNmax is above 1" />\n- </section>\n- <expand macro="limits" />\n+ <expand macro="full_algo_params"/>\n </when>\n </conditional>\n </section>\n@@ -1215,8 +1081,8 @@\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+ **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@@ -1253,7 +1119,7 @@\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+.. _parameters: https://github.com/suhrig/arriba/wiki/03-Workflow\n ]]></help>\n <expand macro="citations"/>\n </tool>\n' |
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| diff -r 53255f6eecfc -r de21b616f03a test-data/filtered4_algo_full.bam |
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| Binary file test-data/filtered4_algo_full.bam has changed |