comparison trinity.xml @ 29:d5e8807a407d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9f23ced8d1f5a7ddf96e5f6cb608f3de8fc76250"

28:48636f857c4b

<tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@+galaxy1">
    <description>de novo assembly of RNA-Seq data</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive"><![CDATA[
        if [ -z "\$GALAXY_MEMORY_MB" ] ; then
            GALAXY_MEMORY_GB=1 ;
        else
            GALAXY_MEMORY_GB=\$((GALAXY_MEMORY_MB / 1024)) ;
        fi ;

        if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then
            workdir=`pwd` ;
            cd "\$TRINITY_SCRATCH_DIR" ;
        fi ;

        #if $additional_params.guided.is_guided == "yes":
            ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' &&
            ln -s '${$additional_params.guided.genome_guided_bam.metadata.bam_index}' 'localbam.bam.bai' &&

        ## > $trinity_log 2>&1

        &&

        if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then
            mkdir -p "\$workdir/trinity_out_dir";
            cp -p trinity_out_dir/Trinity* "\$workdir/trinity_out_dir";
            cd "\$workdir";
        fi ;

    ]]></command>
    <inputs>

29:d5e8807a407d

<tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@+galaxy2">
    <description>de novo assembly of RNA-Seq data</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="8.32">coreutils</requirement>
        <requirement type="package" version="3.2.3">rsync</requirement>
    </expand>
    <command detect_errors="aggressive"><![CDATA[
        if [ -z "\$GALAXY_MEMORY_MB" ] ; then
            GALAXY_MEMORY_GB=1 ;
        else
            GALAXY_MEMORY_GB=\$((GALAXY_MEMORY_MB / 1024)) ;
        fi ;

        if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then
            workdir=`pwd` ;
            scratchfolder=\$(mktemp -d -p "\$TRINITY_SCRATCH_DIR");
            emptyfolder=\$(mktemp -d -p "\$TRINITY_SCRATCH_DIR");
            cd "\$scratchfolder" ;
        fi ;

        #if $additional_params.guided.is_guided == "yes":
            ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' &&
            ln -s '${$additional_params.guided.genome_guided_bam.metadata.bam_index}' 'localbam.bam.bai' &&

        ## > $trinity_log 2>&1

        &&

        ## Trinity can create millions of files in the same directory, so the cleaning task makes use of rsync
        ## for ensuring better performances.
        ## see: https://web.archive.org/web/20130929001850/http://linuxnote.net/jianingy/en/linux/a-fast-way-to-remove-huge-number-of-files.html
        if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then
            mkdir -p "\$workdir/trinity_out_dir";
            cp -p trinity_out_dir/Trinity* "\$workdir/trinity_out_dir";
            cd "\$TRINITY_SCRATCH_DIR";
            rsync -a --delete "\$emptyfolder/" "\$scratchfolder/";
            rmdir "\$emptyfolder" "\$scratchfolder/";
            cd "\$workdir";
        fi ;

    ]]></command>
    <inputs>