comparison trinity.xml @ 15:e65e640e6196 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933

14:2161c7d8daef

<tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@.0">
    <description>de novo assembly of RNA-Seq data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.1.2">bowtie</requirement>
        <requirement type="set_environment">TRINITY_MEM_OPTIONS</requirement>
    </expand>
    <expand macro="stdio"/>
    <command><![CDATA[
       Trinity

        ## Inputs.
        #if $inputs.paired_or_single == "paired":

            --left ${ ','.join(['"%s"' % x for x in $inputs.left_input]) }

        #if $additional_params.min_kmer_cov:
            --min_kmer_cov $additional_params.min_kmer_cov
        #end if

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

        ## > $trinity_log 2>&1

    ]]></command>
    <inputs>
        <conditional name="inputs">
            <param name="paired_or_single" type="select" label="Paired or Single-end data?">
                <option value="paired">Paired</option>

15:e65e640e6196

<tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@.0">
    <description>de novo assembly of RNA-Seq data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive"><![CDATA[
       Trinity --no_version_check

        ## Inputs.
        #if $inputs.paired_or_single == "paired":

            --left ${ ','.join(['"%s"' % x for x in $inputs.left_input]) }

        #if $additional_params.min_kmer_cov:
            --min_kmer_cov $additional_params.min_kmer_cov
        #end if

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

        ## > $trinity_log 2>&1
    ]]></command>
    <inputs>
        <conditional name="inputs">
            <param name="paired_or_single" type="select" label="Paired or Single-end data?">
                <option value="paired">Paired</option>