comparison macros.xml @ 2:3a1253ee137b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"

1:e613048778d9

            #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

        <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="without-gtf" selected='true'>use genome reference without builtin gene-model</option>
                        <option value="with-gtf">use genome reference with builtin gene-model</option>
                    </param>
                    <when value="with-gtf">
                        <expand macro="index_selection" with_gene_model="1" />
                        <expand macro="@SJDBOPTIONS@" />
                    </when>
                    <when value="without-gtf">
                        <expand macro="index_selection" with_gene_model="0" />
                    </when>
                </conditional>
            </when>
            <when value="history">
                <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />

2:3a1253ee137b

            #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) == 'without-gtf':
            #if $refGenomeSource.GTFconditional.sjdbGTFfile:
                --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
                --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
                #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
                    --sjdbGTFtagExonParentTranscript Parent

        <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"/>
            <yield />
        </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="without-gtf" selected='true'>use genome reference without builtin gene-model</option>
                        <option value="with-gtf">use genome reference with builtin gene-model</option>
                    </param>
                    <when value="with-gtf">
                        <expand macro="index_selection" with_gene_model="1" />
                    </when>
                    <when value="without-gtf">
                        <expand macro="index_selection" with_gene_model="0" />
                        <expand macro="@SJDBOPTIONS@" />
                    </when>
                </conditional>
            </when>
            <when value="history">
                <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />