| Previous changeset 21:381a32c51141 (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_rnaStarSolo.xml |
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added:
test-data/filtered4_algo_full.bam |
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| diff -r 381a32c51141 -r a00cceb45700 macros.xml --- a/macros.xml Thu Dec 05 06:50:56 2024 +0000 +++ b/macros.xml Sat May 31 19:53:27 2025 +0000 |
| [ |
| 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 381a32c51141 -r a00cceb45700 rg_rnaStarSolo.xml --- a/rg_rnaStarSolo.xml Thu Dec 05 06:50:56 2024 +0000 +++ b/rg_rnaStarSolo.xml Sat May 31 19:53:27 2025 +0000 |
| [ |
| @@ -131,8 +131,12 @@ $solo.outSAMunmapped ## Read MAPQ --outSAMmapqUnique ${solo.outSAMmapqUnique} - ## Limits - @LIMITS@ + + #if str( $algo.params.settingsType ) == 'full': + @ALGO_FULL@ + #else: + @ALGO_DEFAULT@ + #end if ##outWig: @OUTWIG@ @@ -273,7 +277,7 @@ <option value="MultiGeneUMI" >Remove lower-count UMIs that map to more than one gene</option> <option value="MultiGeneUMI_All" >Remove all UMIs that map to more than one gene</option> <option value="MultiGeneUMI_CR" >Remove lower-count UMIs that map to more than one gene, matching CellRanger > 3.0.0</option> - </param> + </param> </when> </conditional> <param argument="--soloCBmatchWLtype" type="select" label="Matching the Cell Barcodes to the WhiteList" help="Exact: only exact matches allowed; 1MM: only one match in whitelist with 1 mismatched base allowed. Allowed @@ -320,7 +324,7 @@ <option value="MultiGeneUMI" >Remove lower-count UMIs that map to more than one gene</option> <option value="MultiGeneUMI_All" >Remove all UMIs that map to more than one gene</option> <option value="MultiGeneUMI_CR" >Remove lower-count UMIs that map to more than one gene, matching CellRanger > 3.0.0</option> - </param> + </param> </when> </conditional> <param argument="--soloCBmatchWLtype" type="select" label="Matching the Cell Barcodes to the WhiteList" help="Exact: only exact matches allowed; 1MM: only one match in whitelist with 1 mismatched base allowed. Allowed @@ -414,8 +418,20 @@ <param name="quantModeGene" type="boolean" truevalue="GeneCounts" falsevalue="" checked="false" label="Output global gene count" help="Can be used by MultiQC" /> <param argument="--outSAMunmapped" type="boolean" truevalue="--outSAMunmapped Within" falsevalue="--outSAMunmapped None" checked="false" label="Output unmapped reads in the BAM" /> <expand macro="outSAMmapqUnique"/> - <expand macro="limits" /> </section> + <section name="algo" title="Algorithmic settings" expanded="true"> + <conditional name="params"> + <param name="settingsType" type="select" label="Configure seed, alignment and limits options"> + <option value="default" selected="true">Use Defaults</option> + <option value="full">Extended parameter list</option> + </param> + <when value="default"/> + <when value="full"> + <expand macro="full_algo_params"/> + </when> + </conditional> + </section> + <expand macro="chim_params"/> <expand macro="outWig"/> </inputs> <outputs> @@ -1381,6 +1397,93 @@ <metadata name="column_names" value="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" /> </output> </test> + <test expect_num_outputs="7"> + <!-- test 14 --> + <conditional name="refGenomeSource"> + <param name="geneSource" value="history" /> + <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" /> + <param name="genomeSAindexNbases" value="4" /> + <param name="sjdbOverhang" value="100" /> + <param name="sjdbGTFfile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf" ftype="gtf"/> + </conditional> + <conditional name="sc" > + <param name="solo_type" value="CB_UMI_Simple" /> + <conditional name="input_types"> + <param name="use" value="repeat" /> + <param name="input1" value="pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" /> + <param name="input2" value="pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" /> + </conditional> + <param name="soloCBwhitelist" value="filtered.barcodes.txt" /> + <conditional name="params"> + <param name="chemistry" value="Cv3" /> + </conditional> + <conditional name="umidedup"> + <param name="soloUMIdedup" value="1MM_All" /> + </conditional> + </conditional> + <section name="solo" > + <conditional name="filter"> + <param name="filter_type" value="no_filter" /> + </conditional> + <param name="soloStrand" value="Forward" /> + <param name="soloFeatures" value="Gene" /> + <param name="quantModeGene" value="true" /> + <conditional name="wasp_conditional"> + <param name="waspOutputMode" value="wasp_mode"/> + <param name="varVCFfile" value="filtered3.vcf" ftype="vcf" /> + </conditional> + </section> + <section name="algo"> + <conditional name="params"> + <param name="settingsType" value="full" /> + <section name="seed"> + <param name="seed_select" value="yes" /> + <param name="seedSearchStartLmax" value="25" /> + <param name="seedSearchStartLmax" value="25" /> + </section> + <section name="align"> + <param name="alignIntronMax" value="100" /> + <param name="alignEndsType" value="EndToEnd" /> + </section> + </conditional> + </section> + <output name="output_barcodes" > + <assert_contents> + <!-- first and last line --> + <has_line line="AAACCTGAGCGCTCCA" /> + <has_line line="TTTGGTTAGTGGGCTA" /> + <has_n_lines n="394" /> + </assert_contents> + </output> + <output name="output_genes"> + <assert_contents> + <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Gene\s+Expression" /> + <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Gene\s+Expression" /> + <has_n_lines n="14" /> + </assert_contents> + </output> + <output name="output_matrix" > + <assert_contents> + <has_line_matching expression="14\s+394\s+6" /> + <has_line_matching expression="4\s+284\s+1" /> + <has_n_lines n="9" /> + </assert_contents> + </output> + <output name="output_stats" > + <assert_contents> + <has_line_matching expression="\s+noUnmapped\s+6040" /> + <has_line_matching expression="\s+yesUMIs\s+6" /> + </assert_contents> + </output> + <output name="output_BAM" value="filtered4_algo_full.bam" ftype="bam" lines_diff="6"/> + <output name="reads_per_gene" > + <assert_contents> + <has_line_matching expression="ENSG00000279493\s+0\s+0\s+0" /> + <has_line_matching expression="ENSG00000275464\s+5\s+0\s+5" /> + </assert_contents> + <metadata name="column_names" value="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" /> + </output> + </test> </tests> <help><![CDATA[ **What it does** |
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| diff -r 381a32c51141 -r a00cceb45700 test-data/filtered4_algo_full.bam |
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| Binary file test-data/filtered4_algo_full.bam has changed |