comparison genrich.xml @ 2:8353f3cc03db draft default tip

"planemo upload for repository https://github.com/jsh58/Genrich commit 62a6ec655d7743ce084e45ba02b495e8bd2dc06c"

1:db50f51a2952

<tool id="genrich" name="Genrich" version="0.5+galaxy1">
    <description>Detecting sites of genomic enrichment</description>
    <requirements>
        <requirement type="package" version="0.5">genrich</requirement>
        <requirement type="package" version="1.9">samtools</requirement>
    </requirements>

## Input ##
###########

## Treatment File(s)
#if str($treatment.t_multi_select) == "Yes":
    -t ${ ' '.join( [ "'%s'" %  $x for $x in $treatment.input_treatment_file] ) }
#else
    -t '$treatment.input_treatment_file'
#end if

## Control File(s)
#if str($control.c_select) == "Yes":
    #if str($control.c_multiple.c_multi_select) == "Yes":
        -c ${ ' '.join( [ "'%s'" %  $x for $x in $control.c_multiple.input_control_file] ) }
    #else
        -c '$control.c_multiple.input_control_file'
    #end if
#end if

            <output name="outfile" ftype="encodepeak" file="CTCF.encodepeak" />
            <output name="out_bedgraph1" ftype="bedgraph" file="CTCF1.bedgraph" />
            <output name="out_bedgraph2" ftype="bedgraph" file="CTCF2.bedgraph" compare="contains" lines_diff="1" />
            <output name="out_bed" ftype="bed" file="CTCF.bed" />
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

2:8353f3cc03db

<tool id="genrich" name="Genrich" version="0.5+galaxy2">
    <description>Detecting sites of genomic enrichment</description>
    <requirements>
        <requirement type="package" version="0.5">genrich</requirement>
        <requirement type="package" version="1.9">samtools</requirement>
    </requirements>

## Input ##
###########

## Treatment File(s)
#if str($treatment.t_multi_select) == "Yes":
    -t ${ ','.join( [ "'%s'" %  $x for $x in $treatment.input_treatment_file] ) }
#else
    -t '$treatment.input_treatment_file'
#end if

## Control File(s)
#if str($control.c_select) == "Yes":
    #if str($control.c_multiple.c_multi_select) == "Yes":
        -c ${ ','.join( [ "'%s'" %  $x for $x in $control.c_multiple.input_control_file] ) }
    #else
        -c '$control.c_multiple.input_control_file'
    #end if
#end if

            <output name="outfile" ftype="encodepeak" file="CTCF.encodepeak" />
            <output name="out_bedgraph1" ftype="bedgraph" file="CTCF1.bedgraph" />
            <output name="out_bedgraph2" ftype="bedgraph" file="CTCF2.bedgraph" compare="contains" lines_diff="1" />
            <output name="out_bed" ftype="bed" file="CTCF.bed" />
        </test>
        <!-- ChIP Test Data for Pooled Data (Replicates)-->
        <test expect_num_outputs="4">
            <param name="input_treatment_file" ftype="bam" value="CTCF_PE_ChIP_chr22.bam,CTCF_PE_ChIP_chr22_2.bam" />
            <param name="input_control_file" ftype="bam" value="CTCF_PE_CTRL_chr22.bam,CTCF_PE_CTRL_chr22_2.bam" />
            <param name="c_select" value="Yes" />
            <param name="t_multi_select" value="Yes" />
            <param name="c_multi_select" value="Yes" />
            <param name="bedgraph1" value="True" />
            <param name="bedgraph2" value="True" />
            <param name="bed" value="True" />
            <output name="outfile" ftype="encodepeak" file="Pool.encodepeak" />
            <output name="out_bedgraph1" ftype="bedgraph" file="Pool1.bedgraph" />
            <output name="out_bedgraph2" ftype="bedgraph" file="Pool2.bedgraph" compare="contains" lines_diff="2" />
            <output name="out_bed" ftype="bed" file="Pool.bed" />
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark