comparison unionBedGraphs.xml @ 34:dde39ba9c031 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95

33:87ee588b3d45

<tool id="bedtools_unionbedgraph" name="bedtools Merge BedGraph files" version="@WRAPPER_VERSION@">
    <description>combines coverage intervals from multiple BEDGRAPH files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
    unionBedGraphs
        $header
        -filler "${filler}"
        $empty.empty_selector
        @GENOME_FILE_UNION@

        #if str($tag.tag_select) == "tag":
            #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] )
            -i "${files}"
        #else:
            -i
            #for $bg in $tag.bedgraphs:
                "${bg.input}"
            #end for
            -names
            #for $bg in $tag.bedgraphs:
                "${bg.custom_name}"
            #end for
        #end if
        > "${output}"
]]>
    </command>
    <inputs>
        <conditional name="tag">
            <param name="tag_select" type="select" label="Sample name">
                <option value="tag" selected="true">Use input's tag</option>
                <option value="custom">Enter custom name per file</option>
            </param>
            <when value="tag">
                <param name="inputs" format="bedgraph" type="data" multiple="True" label="BedGraph files" />
            </when>
            <when value="custom">
                <repeat name="bedgraphs" title="Add BedGraph files" min="2" >
                    <param name="input" format="bedgraph" type="data" multiple="True" label="BedGraph file" />
                    <param name="custom_name" type="text" area="false" label="Custom sample name" />
                </repeat>
            </when>
        </conditional>
        <conditional name="empty">
            <param name="empty_selector" argument="-empty" type="select" label="Report empty regions" help="Include regions that have zero coverage in all BedGraph datasets">

            <when value="-empty">
                <expand macro="input_conditional_genome_file" />
            </when>
            <when value="" />
        </conditional>
        <param name="filler" type="text" value="N/A"
            label="Text to use for no-coverage value"
            help="Can be 0.0, N/A, - or any other value. (-filler)" />
        <expand macro="print_header" />
    </inputs>
    <outputs>
        <data name="output" format="bedgraph" />
    </outputs>

            <param name="genome_file_opts_selector" value="hist" />
            <param name="genome" value="unionBedGraphs1.len" />
            <output name="output" file="unionBedGraphs_result4.bg" ftype="bedgraph" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

This tool merges multiple BedGraph files, allowing direct and fine-scale coverage comparisons among many samples/files. The BedGraph files need not represent the same intervals; the tool will identify both common and file-specific intervals. In addition, the BedGraph values need not be numeric: one can use any text as the BedGraph value and the tool will compare the values from multiple files.

.. class:: warningmark

    chr1   450    530    0         0.43
    chr1   530    600    Sample2   0.43
    chr1   600    700    0         0.43

@REFERENCES@
]]>
    </help>
    <expand macro="citations" />
</tool>

34:dde39ba9c031

<tool id="bedtools_unionbedgraph" name="bedtools Merge BedGraph files" version="@TOOL_VERSION@">
    <description>combines coverage intervals from multiple BEDGRAPH files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command><![CDATA[
unionBedGraphs
$header
-filler '${filler}'
$empty.empty_selector
@GENOME_FILE_UNION@

#if str($tag.tag_select) == "tag":
    -i
    #for $file in $tag.inputs:
        '${file}'
    #end for
#else:
    -i
    #for $bg in $tag.bedgraphs:
        '${bg.input}'
    #end for
    -names
    #for $bg in $tag.bedgraphs:
        '${bg.custom_name}'
    #end for
#end if
> '${output}'
    ]]></command>
    <inputs>
        <conditional name="tag">
            <param name="tag_select" type="select" label="Sample name">
                <option value="tag" selected="true">Use input's tag</option>
                <option value="custom">Enter custom name per file</option>
            </param>
            <when value="tag">
                <param name="inputs" argument="-i" type="data" format="bedgraph" multiple="true" label="BedGraph files" />
            </when>
            <when value="custom">
                <repeat name="bedgraphs" title="Add BedGraph files" min="2">
                    <param name="input" argument="-i" type="data" format="bedgraph" multiple="true" label="BedGraph file" />
                    <param name="custom_name" argument="-names" type="text" area="false" label="Custom sample name" />
                </repeat>
            </when>
        </conditional>
        <conditional name="empty">
            <param name="empty_selector" argument="-empty" type="select" label="Report empty regions" help="Include regions that have zero coverage in all BedGraph datasets">

            <when value="-empty">
                <expand macro="input_conditional_genome_file" />
            </when>
            <when value="" />
        </conditional>
        <param argument="-filler" type="text" value="N/A"
            label="Text to use for no-coverage value"
            help="Can be 0.0, N/A, - or any other value" />
        <expand macro="print_header" />
    </inputs>
    <outputs>
        <data name="output" format="bedgraph" />
    </outputs>

            <param name="genome_file_opts_selector" value="hist" />
            <param name="genome" value="unionBedGraphs1.len" />
            <output name="output" file="unionBedGraphs_result4.bg" ftype="bedgraph" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

This tool merges multiple BedGraph files, allowing direct and fine-scale coverage comparisons among many samples/files. The BedGraph files need not represent the same intervals; the tool will identify both common and file-specific intervals. In addition, the BedGraph values need not be numeric: one can use any text as the BedGraph value and the tool will compare the values from multiple files.

.. class:: warningmark

    chr1   450    530    0         0.43
    chr1   530    600    Sample2   0.43
    chr1   600    700    0         0.43

@REFERENCES@
    ]]></help>
    <expand macro="citations" />
</tool>