view emsar_wrapper.xml @ 0:41e92972b7f1 draft default tip

Fix XML formatting

<tool id="emsar" name="EMSAR" version="1.2j">
    <description></description>

    <command>

    #set rsh_path = $refIndex.fields.rshPath
    #set rsh = $rsh_path + "." + $nRL.__str__() + ".rsh"
    #set libType = ""

    #if $bPaired
        #if $sLT.__str__() == "n"
            #set libType = "ns"
        #end if
        #if $sLT.__str__() == "f"
            #set libType = "ssfr"
        #end if
        #if $sLT.__str__() == "r"
            #set libType = "ssrf"
        #end if
    #else
        #if $sLT.__str__() == "n"
            #set libType = "ns"
        #end if
        #if $sLT.__str__() == "f"
            #set libType = "ssf"
        #end if
        #if $sLT.__str__() == "r"
            #set libType = "ssr"
        #end if
    #end if

    emsar
        -P
        #if $sBS.__str__() == "S"
        -S
        #end if
        #if $sBS.__str__() == "B"
        -B
        #end if
        -p 8
        -h $sHT
        #if $bG
        -g
        #end if
        -s $libType
        -I $rsh
        output
        emsar
        $input_bam
        2> emsar.log

    </command>

    <stdio></stdio>

    <inputs>
        <param format="bam,sam" compression="none" name="input_bam" type="data" label="Bowtie Alignment BAM file" help=""/>
        <param name="refIndex" type="select" label="Select a reference genome" help="">
            <options from_data_table="emsar_indices">
                <filter type="sort_by" column="2"/>
                <validator type="no_options" message="No genomes are available for the selected input dataset"/>
            </options>
        </param>
        <param name="sBS" type="select" label="Input alignment file type ">
            <option value="S">SAM</option>
            <option value="B">BAM</option>
        </param>
        <param name="sHT" type="select" label="Transcriptome header type">
            <option value="R">RefSeq</option>
            <option value="E">Ensembl</option>
        </param>
        <param name="bG" type="boolean" label="Generate list of all segments with their associated sequence-sharing set and transcript(seperated by '+')" value="True" />
        <param name="bPaired" type="boolean" label="Is this paired-end sequenced data ?" value="True" />
        <param name="nRL" type="integer" label="read length" value="101" />
        <param name="sLT" type="select" label="library type">
            <option value="n">Unstranded</option>
            <option value="f">Forward Stranded</option>
            <option value="r">Reverse Stranded</option>
        </param>
    </inputs>

    <outputs>
        <data format="txt" name="fpkm" label="${tool.name} on ${on_string}: FPKM" from_work_dir="output/emsar.0.fpkm" />
        <data format="txt" name="fraglength_stat" label="${tool.name} on ${on_string}: Fracgment Length Effect" from_work_dir="output/emsar.0.fraglength_effect" />
        <data format="txt" name="segments" label="${tool.name} on ${on_string}: Segments" from_work_dir="output/emsar.0.segments" />
    </outputs>

    <help>

    </help>
</tool>