Mercurial > repos > iuc > data_manager_star_index_builder
changeset 7:9a231bb19a3b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
| author | iuc |
|---|---|
| date | Thu, 15 Aug 2019 11:28:53 -0400 |
| parents | 54cddd903437 |
| children | d2f4bfcf269a |
| files | data_manager/macros.xml |
| diffstat | 1 files changed, 96 insertions(+), 1 deletions(-) [+] |
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--- a/data_manager/macros.xml Thu Jul 11 11:35:38 2019 -0400 +++ b/data_manager/macros.xml Thu Aug 15 11:28:53 2019 -0400 @@ -4,7 +4,7 @@ The data manager uses a symlink to this macro file to keep the versions in sync. --> <!-- STAR version to be used --> - <token name="@VERSION@">2.7.1a</token> + <token name="@VERSION@">2.7.2a</token> <!-- STAR index version compatible with this version of STAR This is the STAR version that introduced the index structure expected by the current version. @@ -65,4 +65,99 @@ </conditional> </actions> </xml> + <token name="@TEMPINDEX@"><![CDATA[ + ## Create temporary index for custom reference + #if str($refGenomeSource.geneSource) == 'history': + mkdir -p tempstargenomedir && + STAR + --runMode genomeGenerate + --genomeDir 'tempstargenomedir' + --genomeFastaFiles '${refGenomeSource.genomeFastaFiles}' + ## Handle difference between indices with/without annotations + #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf': + --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}' + --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}' + #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3': + --sjdbGTFtagExonParentTranscript Parent + #end if + #end if + #if str($refGenomeSource.genomeSAindexNbases): + --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases} + #end if + --runThreadN \${GALAXY_SLOTS:-4} + && + #end if + ]]></token> + <token name="@REFGENOMEHANDLING" ><![CDATA[ + --runThreadN \${GALAXY_SLOTS:-4} + --genomeLoad NoSharedMemory + --genomeDir + #if str($refGenomeSource.geneSource) == 'history': + tempstargenomedir + #else: + '${refGenomeSource.GTFconditional.genomeDir.fields.path}' + ## Handle difference between indices with/without annotations + #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf': + #if $refGenomeSource.GTFconditional.sjdbGTFfile: + --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang + --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}' + #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3': + --sjdbGTFtagExonParentTranscript Parent + #end if + #end if + #end if + #end if + ]]></token> + <xml name="stdio" > + <stdio> + <regex match="FATAL error" source="both" level="fatal"/> + <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/> + <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/> + <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/> + </stdio> + </xml> + <xml name="refgenomehandling" > + <conditional name="refGenomeSource"> + <param name="geneSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options"> + <option value="indexed" selected="true">Use a built-in index</option> + <option value="history">Use reference genome from history and create temporary index</option> + </param> + <when value="indexed"> + <conditional name="GTFconditional"> + <param name="GTFselect" type="select" + label="Reference genome with or without an annotation" + help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions."> + <option value="without-gtf">use genome reference with builtin gene-model</option> + <option value="with-gtf">use genome reference without builtin gene-model</option> + </param> + <when value="with-gtf"> + <expand macro="index_selection" with_gene_model="0" /> + <expand macro="@SJDBOPTIONS@" /> + </when> + <when value="without-gtf"> + <expand macro="index_selection" with_gene_model="1" /> + </when> + </conditional> + </when> + <when value="history"> + <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" /> + <!-- Currently, this parameter is not exposed in the wrapper, + but used only in the tests to avoid excessive index sizes for + the tiny test genomes. --> + <param name="genomeSAindexNbases" type="hidden" value="" /> + <conditional name="GTFconditional"> + <param name="GTFselect" type="select" + label="Build index with our without known splice junctions annotation" + help="To build an index with known splice junctions annotated, you will have to provide a GTF or GFF3 dataset that describes the gene models (the location of genes, transcripts and exons) known for the reference genome."> + <option value="without-gtf">build index without gene-model</option> + <option value="with-gtf">build index with gene-model</option> + </param> + <when value="with-gtf"> + <expand macro="@SJDBOPTIONS@" optional="false"/> + </when> + <when value="without-gtf" /> + </conditional> + </when> + </conditional> + </xml> </macros>