| Previous changeset 9:c520a52b5174 (2021-09-10) Next changeset 11:d63c1442407f (2023-04-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 |
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modified:
data_manager/macros.xml data_manager/rna_star_index_builder.xml |
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| diff -r c520a52b5174 -r a225487bf618 data_manager/macros.xml --- a/data_manager/macros.xml Fri Sep 10 16:44:59 2021 +0000 +++ b/data_manager/macros.xml Fri Feb 17 20:00:58 2023 +0000 |
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| b'@@ -1,11 +1,12 @@\n <macros>\n- <!-- REMEMBER to bump the version of rna_star_index_builder_data_manager\n- whenever you make changes to the following two version tokens!\n+ <!-- REMEMBER to bump the version of @IDX_VERSION_SUFFIX@\n+ whenever you make changes to the @TOOL_VERSION@ token!\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 adjust the +galaxy\n- version number. -->\n+ the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->\n <!-- STAR version to be used -->\n- <token name="@VERSION@">2.7.8a</token>\n+ <token name="@TOOL_VERSION@">2.7.10b</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 by the current version.\n@@ -14,12 +15,14 @@\n or by looking for the versionGenome parameter in source/parametersDefault\n of STAR\'s source code -->\n <token name="@IDX_VERSION@">2.7.4a</token>\n+ <token name="@IDX_VERSION_SUFFIX@">1</token>\n <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token>\n \n <xml name="requirements">\n <requirements>\n- <requirement type="package" version="@VERSION@">star</requirement>\n- <requirement type="package" version="1.9">samtools</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">star</requirement>\n+ <requirement type="package" version="1.16.1">samtools</requirement>\n+ <requirement type="package" version="1.12">gzip</requirement>\n <yield />\n </requirements>\n </xml>\n@@ -35,7 +38,7 @@\n </xml>\n \n <xml name="index_selection" token_with_gene_model="0">\n- <param argument="--genomeDir" name="genomeDir" type="select"\n+ <param argument="--genomeDir" type="select"\n label="Select reference genome"\n help="If your genome of interest is not listed, contact the Galaxy team">\n <options from_data_table="@IDX_DATA_TABLE@">\n@@ -55,8 +58,8 @@\n <citation type="doi">10.1093/bioinformatics/bts635</citation>\n </citations>\n </xml>\n- <xml name="@SJDBOPTIONS@" token_optional="true">\n- <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="@OPTIONAL@" help="Exon junction information for mapping splices"/>\n+ <xml name="SJDBOPTIONS">\n+ <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"/>\n <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"/>\n </xml>\n <xml name="dbKeyActions">\n@@ -81,11 +84,16 @@\n <token name="@TEMPINDEX@"><![CDATA[\n ## Create temporary index for custom reference\n #if str($refGenomeSource.geneSource) == \'history\':\n+ #if $refGenomeSource.genomeFastaFiles.ext == "fasta"\n+ ln -s \'$refGenomeSource.genomeFastaFiles\' refgenome.fa &&\n+ #else\n+ gunzip -c \'$refGenomeSource.genomeFastaFiles\' > refgenome.fa &&\n+ #end if\n mkdir -p tempstargenomedir &&\n STAR\n --runMode genomeGenerate\n --genomeDir \'tempstargenomedir\'\n- --genomeFastaFiles \'${refGenomeSource.genomeFastaFiles}\'\n+ --genomeFastaFiles refgenome.fa\n ## Handle difference between indices with/without annotations\n #if \'GTFconditional\' in $refGenomeSource:\n ## GTFconditional exists only in STAR, but not STARsolo\n@@ -109,6 +117,8 @@\n --genomeSAindexNbases ${refGenomeSource'..b' <expand macro="dbKeyActions" />\n+ <change_format>\n+ <when input="outWig.outWigType" value="wiggle" format="wig" />\n+ </change_format>\n+ </data>\n+ <data format="bedgraph" name="signal_unique_str2" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 2" from_work_dir="Signal.Unique.str2.out">\n+ <filter>outWig[\'outWigType\'] != "None" and outWig[\'outWigStrand\']</filter>\n+ <expand macro="dbKeyActions" />\n+ <change_format>\n+ <when input="outWig.outWigType" value="wiggle" format="wig" />\n+ </change_format>\n+ </data>\n+ <data format="bedgraph" name="signal_uniquemultiple_str2" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 2" from_work_dir="Signal.UniqueMultiple.str2.out">\n+ <filter>outWig[\'outWigType\'] != "None" and outWig[\'outWigStrand\']</filter>\n+ <expand macro="dbKeyActions" />\n+ <change_format>\n+ <when input="outWig.outWigType" value="wiggle" format="wig" />\n+ </change_format>\n+ </data>\n+ </xml>\n+ <xml name="quantMode">\n+ <conditional name="quantmode_output">\n+ <param argument="--quantMode" type="select"\n+ label="Per gene/transcript output"\n+ 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+ <option value="-">No per gene or transcript output</option>\n+ <option value="GeneCounts">Per gene read counts (GeneCounts)</option>\n+ <option value="TranscriptomeSAM">Transcript-based BAM output (TranscriptomeSAM)</option>\n+ <option value="TranscriptomeSAM GeneCounts">Both per gene read counts and transcript-based BAM output (TranscriptomeSAM GeneCounts)</option>\n+ </param>\n+ <when value="-" />\n+ <when value="GeneCounts" />\n+ <when value="TranscriptomeSAM">\n+ <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"\n+ label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"\n+ 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+ </when>\n+ <when value="TranscriptomeSAM GeneCounts">\n+ <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"\n+ label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"\n+ 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+ </when>\n+ </conditional>\n+ </xml>\n+ <xml name="quantModeNoGTF">\n+ <conditional name="quantmode_output">\n+ <param argument="--quantMode" type="select"\n+ label="Per gene/transcript output">\n+ <option value="-">No per gene or transcript output as no GTF was provided</option>\n+ </param>\n+ <when value="-" />\n+ </conditional>\n+ </xml>\n </macros>\n' |
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| diff -r c520a52b5174 -r a225487bf618 data_manager/rna_star_index_builder.xml --- a/data_manager/rna_star_index_builder.xml Fri Sep 10 16:44:59 2021 +0000 +++ b/data_manager/rna_star_index_builder.xml Fri Feb 17 20:00:58 2023 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="rna_star_index_builder_data_manager" name="rnastar index versioned" tool_type="manage_data" version="@IDX_VERSION@" profile="19.05"> +<tool id="rna_star_index_builder_data_manager" name="rnastar index versioned" tool_type="manage_data" version="@IDX_VERSION@+galaxy@IDX_VERSION_SUFFIX@" profile="19.05"> <description>builder</description> <macros> |