comparison jaccardBed.xml @ 46:64e2edfe7a2c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4

45:a1a923cd89e8

<tool id="bedtools_jaccard" name="bedtools JaccardBed" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>calculate the distribution of relative distances between two files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools" />
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command><![CDATA[
bedtools jaccard
$strand
$split
$reciprocal

> '$output'
    ]]></command>
    <inputs>
        <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
        <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
        <expand macro="overlap" />
        <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/>
        <expand macro="reciprocal" />
        <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
            label="Force strandedness"
            help="That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand." />
        <expand macro="strand2" />
        <expand macro="split" />
    </inputs>
    <outputs>
        <data name="output" format_source="inputA" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}" />
    </outputs>
    <tests>
        <test>
            <param name="inputA" value="jaccardBed1.bed" ftype="bed" />
            <param name="inputB" value="jaccardBed2.bed" ftype="bed" />
            <output name="output" file="jaccardBed_result1.bed" ftype="bed" />
        </test>
        <test>
            <param name="inputA" value="jaccardBed1.bed" ftype="bed" />
            <param name="inputB" value="jaccardBed2.bed" ftype="bed" />
            <param name="overlap" value="0.1" />
            <output name="output" file="jaccardBed_result2.bed" ftype="bed" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

The jaccard tool requires that your data is pre-sorted by chromosome and then by start position (e.g., sort -k1,1 -k2,2n in.bed > in.sorted.bed for BED files).

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

46:64e2edfe7a2c

<tool id="bedtools_jaccard" name="bedtools JaccardBed" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>calculate the distribution of relative distances between two files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[
bedtools jaccard
$strand
$split
$reciprocal

> '$output'
    ]]></command>
    <inputs>
        <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
        <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
        <expand macro="overlap"/>
        <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/>
        <expand macro="reciprocal"/>
        <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Force strandedness" help="That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand."/>
        <expand macro="split"/>
    </inputs>
    <outputs>
        <data name="output" format_source="inputA" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}"/>
    </outputs>
    <tests>
        <test>
            <param name="inputA" value="jaccardBed1.bed" ftype="bed"/>
            <param name="inputB" value="jaccardBed2.bed" ftype="bed"/>
            <output name="output" file="jaccardBed_result1.bed" ftype="bed"/>
        </test>
        <test>
            <param name="inputA" value="jaccardBed1.bed" ftype="bed"/>
            <param name="inputB" value="jaccardBed2.bed" ftype="bed"/>
            <param name="overlap" value="0.1"/>
            <output name="output" file="jaccardBed_result2.bed" ftype="bed"/>
        </test>
        <test>
            <param name="inputA" value="jaccardBed1.bed" ftype="bed"/>
            <param name="inputB" value="jaccardBed2.bed" ftype="bed"/>
            <param name="overlap" value="0.1"/>
            <param name="strand" value="true"/>
            <output name="output" file="jaccardBed_strand_result2.bed" ftype="bed"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

The jaccard tool requires that your data is pre-sorted by chromosome and then by start position (e.g., sort -k1,1 -k2,2n in.bed > in.sorted.bed for BED files).

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