comparison kallisto_pseudo.xml @ 6:a157781cddd7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 168993a4e148506b1d3998c536caa2e501c36ccf

5:87c11c05d238

<?xml version="1.0"?>
<tool id="kallisto_pseudo" name="Kallisto pseudo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
    <description>- run pseudoalignment on RNA-Seq transcripts</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
        <![CDATA[
        #if $reference_transcriptome.reference_transcriptome_source == "history":
            ln -s '$reference_transcriptome.reference' reference.fa &&

                <option value="single" selected="true">Single-end</option>
                <option value="paired">Paired</option>
            </param>
            <when value="single">
                <param name="reads" type="data" format="fastq,fastq.gz" multiple="True" label="Reads in FASTQ format" />
                <param name="fragment_length" argument="--fragment-length" type="integer" value="200" label="Average fragment length" />
                <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" />
            </when>
            <when value="paired">
                <conditional name="collection">
                    <param name="collection_selector" type="select" label="Collection or individual datasets">

        <test>
            <param name="reference_transcriptome_source" value="cached" />
            <param name="single_paired_selector" value="paired" />
            <param name="collection_selector" value="datasets" />
            <param name="umi" value="yes" />
            <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM.umi" />
            <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" />
            <output name="sample">
                <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out6.tab" ftype="tabular" />
                <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out6.ec" ftype="tabular" />
                <discovered_dataset designation="Matrix.cells" file="kallisto_pseudo_out6.cells" ftype="tabular" />

6:a157781cddd7

<?xml version="1.0"?>
<tool id="kallisto_pseudo" name="Kallisto pseudo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
    <description>run pseudoalignment on RNA-Seq transcripts</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <xrefs>
        <xref type="bio.tools">kallisto</xref>
    </xrefs>

    <expand macro="requirements" />
    <command detect_errors="exit_code">
        <![CDATA[
        #if $reference_transcriptome.reference_transcriptome_source == "history":
            ln -s '$reference_transcriptome.reference' reference.fa &&

                <option value="single" selected="true">Single-end</option>
                <option value="paired">Paired</option>
            </param>
            <when value="single">
                <param name="reads" type="data" format="fastq,fastq.gz" multiple="True" label="Reads in FASTQ format" />
                <param argument="--fragment-length" type="integer" value="200" label="Average fragment length" />
                <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" />
            </when>
            <when value="paired">
                <conditional name="collection">
                    <param name="collection_selector" type="select" label="Collection or individual datasets">

        <test>
            <param name="reference_transcriptome_source" value="cached" />
            <param name="single_paired_selector" value="paired" />
            <param name="collection_selector" value="datasets" />
            <param name="umi" value="yes" />
            <param name="forward" ftype="tabular" dbkey="sacCer2" value="sacCer2_chrM.umi" />
            <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" />
            <output name="sample">
                <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out6.tab" ftype="tabular" />
                <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out6.ec" ftype="tabular" />
                <discovered_dataset designation="Matrix.cells" file="kallisto_pseudo_out6.cells" ftype="tabular" />