comparison closestBed.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_closestbed" name="bedtools ClosestBed" version="@WRAPPER_VERSION@">
    <description>find the closest, potentially non-overlapping interval</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

#end if
-a '$inputA'
#if str($overlap_with.source) == "data_table":
    -b '$overlap_with.table.fields.path'
#else
    #set inputBs = "' '".join([str( $file ) for $file in $overlap_with.inputB])
    -b '$inputBs'
#end if
> '$output'
    ]]></command>
    <inputs>
        <param name="inputA" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
        <!-- overlap with file (inputB) -->
        <conditional name="overlap_with">
            <param name="source" type="select" label="Overlap with: will you select a @STD_BEDTOOLS_INPUT_LABEL@ file from your history or use a built-in GFF file?" help="Built-in GFF files contain full annotation of a reference genome">
                <option value="history" selected="true">Use a @STD_BEDTOOLS_INPUT_LABEL@ file from the history</option>
                <option value="data_table">Use a built-in GFF file</option>

                        <validator type="no_options" message="No files are available"/>
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="inputB" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="Select a @STD_BEDTOOLS_INPUT_LABEL@ file" />
            </when>
        </conditional>

        <param name="ties" type="select"
            label="How ties for closest feature should be handled"

            <option value="all">Report closest records among all databases. (-all)</option>
        </param>
    </inputs>
    <outputs>
        <!-- Would like to use a nicer name, but since there are possibly many inputB datasets, falling back to ${on_string} -->
        <!-- <data format_source="inputA" name="output" metadata_source="inputA" label="Closest regions from ${inputB[0].name} to ${inputA.name}"/> -->
        <data name="output" format_source="inputA" metadata_source="inputA" label="Closest regions from ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="inputA" value="closestBedA.bed" ftype="bed" />

34:dde39ba9c031

<tool id="bedtools_closestbed" name="bedtools ClosestBed" version="@TOOL_VERSION@">
    <description>find the closest, potentially non-overlapping interval</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

#end if
-a '$inputA'
#if str($overlap_with.source) == "data_table":
    -b '$overlap_with.table.fields.path'
#else
    -b
    #for $file in $overlap_with.inputB:
        '$file'
    #end for
#end if
> '$output'
    ]]></command>
    <inputs>
        <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
        <!-- overlap with file (inputB) -->
        <conditional name="overlap_with">
            <param name="source" type="select" label="Overlap with: will you select a @STD_BEDTOOLS_INPUT_LABEL@ file from your history or use a built-in GFF file?" help="Built-in GFF files contain full annotation of a reference genome">
                <option value="history" selected="true">Use a @STD_BEDTOOLS_INPUT_LABEL@ file from the history</option>
                <option value="data_table">Use a built-in GFF file</option>

                        <validator type="no_options" message="No files are available"/>
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="Select a @STD_BEDTOOLS_INPUT_LABEL@ file" />
            </when>
        </conditional>

        <param name="ties" type="select"
            label="How ties for closest feature should be handled"

            <option value="all">Report closest records among all databases. (-all)</option>
        </param>
    </inputs>
    <outputs>
        <!-- Would like to use a nicer name, but since there are possibly many inputB datasets, falling back to ${on_string} -->
        <!-- <data name="output" format_source="inputA" metadata_source="inputA" label="Closest regions from ${inputB[0].name} to ${inputA.name}"/> -->
        <data name="output" format_source="inputA" metadata_source="inputA" label="Closest regions from ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="inputA" value="closestBedA.bed" ftype="bed" />