comparison mergeBed.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_mergebed" name="bedtools MergeBED" version="@WRAPPER_VERSION@">
    <description>combine overlapping/nearby intervals into a single interval</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        mergeBed
            -i "${input}"
            $strand
            -d $distance
            $header
            @C_AND_O_ARGUMENT@
            > "${output}"
]]>
    </command>
    <inputs>
        <param  name="input" format="bam,@STD_BEDTOOLS_INPUTS@" type="data" label="Sort the following BAM/@STD_BEDTOOLS_INPUT_LABEL@ file"/>
        <param name="strand" type="select" label="Calculation based on strandedness?">
            <option value="" selected="True">Overlaps on either strand</option>
            <option value="-s">Force strandedness. That is, only merge features that are the same strand.</option>
            <option value="-S +">Force merge for forward strand only.</option>
            <option value="-S -">Force merge for reverse strand only.</option>
        </param>
        <param name="distance" type="integer" value="0"
            label="Maximum distance between features allowed for features to be merged"
            help="That is, overlapping and/or book-ended features are merged. (-d)"/>
        <expand macro="print_header" />
        <expand macro="c_and_o_argument">
            <param name="col" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" help="(-c)" />
        </expand>
    </inputs>
    <outputs>
        <data format="bed" name="output" metadata_source="input" label="Merged ${input.name}"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="mergedBed1.bed" ftype="bed" />
            <output name="output" file="mergedBed_result1.bed" ftype="bed" />

                <param name="operation" value="count"/>
            </repeat>
            <output name="output" file="mergedBed_result5.bed" ftype="bed" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

bedtools merge combines overlapping or "book-ended" features in an interval file into a single feature which spans all of the combined features.

  $ bedtools merge -i A.bed -d 1000
  chr1  100  200  1000


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

34:dde39ba9c031

<tool id="bedtools_mergebed" name="bedtools MergeBED" version="@TOOL_VERSION@">
    <description>combine overlapping/nearby intervals into a single interval</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command><![CDATA[
mergeBed
-i '${input}'
$strand
-d $distance
$header
@C_AND_O_ARGUMENT@
> '${output}'
    ]]></command>
    <inputs>
        <param  name="input" argument="-i" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="Sort the following BAM/@STD_BEDTOOLS_INPUT_LABEL@ file"/>
        <param name="strand" type="select" label="Calculation based on strandedness?">
            <option value="" selected="true">Overlaps on either strand</option>
            <option value="-s">Force strandedness. That is, only merge features that are the same strand (-s)</option>
            <option value="-S +">Force merge for forward strand only (-S +)</option>
            <option value="-S -">Force merge for reverse strand only (-S -)</option>
        </param>
        <param name="distance" argument="-d" type="integer" value="0"
            label="Maximum distance between features allowed for features to be merged"
            help="That is, overlapping and/or book-ended features are merged"/>
        <expand macro="print_header" />
        <expand macro="c_and_o_argument">
            <param name="col" argument="-c" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" />
        </expand>
    </inputs>
    <outputs>
        <data name="output" format="bed" metadata_source="input" label="Merged ${input.name}"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="mergedBed1.bed" ftype="bed" />
            <output name="output" file="mergedBed_result1.bed" ftype="bed" />

                <param name="operation" value="count"/>
            </repeat>
            <output name="output" file="mergedBed_result5.bed" ftype="bed" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

bedtools merge combines overlapping or "book-ended" features in an interval file into a single feature which spans all of the combined features.

  $ bedtools merge -i A.bed -d 1000
  chr1  100  200  1000


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