comparison trinity.xml @ 34:8f1c3df4dd49 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ec26c475a013d89b0f973f29250d660e79d4751f

33:9fa24d5aac68

<tool id="trinity" name="Trinity" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>de novo assembly of RNA-Seq data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>

            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' &&
        #end if

        #end if

        ## CPU and butterfly options.
        --CPU \${GALAXY_SLOTS:-4} --max_memory \${GALAXY_MEMORY_GB:-1}G --bflyHeapSpaceMax \${GALAXY_MEMORY_GB:-1}G --bfly_opts '-V 10 --stderr'

        ## > $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>
        <conditional name="pool">
            <param name="pool_mode" type="select" label="Are you pooling sequence datasets?" help="" >
                <option value="No">No</option>

                help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/>
            <param argument="--min_kmer_cov" type="integer" optional="true" value="1" min="1" label="Minimum count for K-mers to be assembled"/>
        </section>
    </inputs>
    <outputs>
        <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir.Trinity.fasta"/>
        <data name="gene_to_trans" format="tabular" label="${tool.name} on ${on_string}: Gene to transcripts map" from_work_dir="trinity_out_dir.Trinity.fasta.gene_trans_map"/>
    </outputs>
    <tests>
        <test>
            <param name="pool_mode" value="No" />
            <param name="paired_or_single" value="unmerged_paired_collection"/>

34:8f1c3df4dd49

<tool id="trinity" name="Trinity" version="@TOOL_VERSION@+galaxy1" profile="21.05">
    <description>de novo assembly of RNA-Seq data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>

            GALAXY_MEMORY_GB=1 ;
        else
            GALAXY_MEMORY_GB=\$((GALAXY_MEMORY_MB / 1024)) ;
        fi ;

        TRINITY_SCRATCH_DIR=\${TRINITY_SCRATCH_DIR:-\${TMPDIR:-\$_GALAXY_JOB_TMP_DIR}}
        workdir=\$(pwd)
        scratchfolder=\$(mktemp -d -p "\$TRINITY_SCRATCH_DIR");
        emptyfolder=\$(mktemp -d -p "\$TRINITY_SCRATCH_DIR");
        cd "\$scratchfolder" ;

        #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' &&
        #end if

        #end if

        ## CPU and butterfly options.
        --CPU \${GALAXY_SLOTS:-4} --max_memory \${GALAXY_MEMORY_GB:-1}G --bflyHeapSpaceMax \${GALAXY_MEMORY_GB:-1}G --bfly_opts '-V 10 --stderr'

        &&

        ## 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
        rsync -a --delete "\$emptyfolder/" "\$scratchfolder/" --exclude=trinity_out_dir.Trinity.fasta --exclude=trinity_out_dir.Trinity.fasta.gene_trans_map;
        mv "\$scratchfolder/trinity_out_dir.Trinity.fasta" '$assembled_transcripts';
        mv "\$scratchfolder/trinity_out_dir.Trinity.fasta.gene_trans_map" '$gene_to_trans';
        cd "\$workdir";
        rmdir "\$emptyfolder" "\$scratchfolder"
    ]]></command>
    <inputs>
        <conditional name="pool">
            <param name="pool_mode" type="select" label="Are you pooling sequence datasets?" help="" >
                <option value="No">No</option>

                help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/>
            <param argument="--min_kmer_cov" type="integer" optional="true" value="1" min="1" label="Minimum count for K-mers to be assembled"/>
        </section>
    </inputs>
    <outputs>
        <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts"/>
        <data name="gene_to_trans" format="tabular" label="${tool.name} on ${on_string}: Gene to transcripts map"/>
    </outputs>
    <tests>
        <test>
            <param name="pool_mode" value="No" />
            <param name="paired_or_single" value="unmerged_paired_collection"/>