comparison bamToBed.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_bamtobed" name="bedtools BAM to BED" version="@WRAPPER_VERSION@">
    <description>converter</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
    </expand>
    <expand macro="stdio" />
    <command>
<![CDATA[

        #if $input.extension == 'bam' and $option == "-bedpe":
            samtools sort -n "${input}" ./input &&
        #else
            ln -s "${input}" ./input.bam &&
        #end if

        bedtools bamtobed
        $option
        $ed_score
        $split
        #if $tag and str($tag).strip():
          -tag "${tag}"
        #end if
        -i ./input.bam
        > "${output}"
]]>
    </command>
    <inputs>
        <param format="bam" name="input" type="data" label="Convert the following BAM file to BED"/>
        <param name="option" type="select" label="What type of BED output would you like">
            <option value="">Create a 6-column BED file</option>
            <option value="-bed12">Create a full, 12-column "blocked" BED file</option>
            <option value="-bedpe">Create a paired-end, BEDPE format</option>
        </param>
        <expand macro="split" />
        <param name="ed_score" type="boolean" truevalue="-ed" falsevalue="" checked="false"
            label="Use alignment's edit-distance for BED score" help="(-ed)" />
        <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"
            help="(-tag)"/>
    </inputs>
    <outputs>
        <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="srma_in3.bam" ftype="bam" />
            <param name="option" value="" />

            <param name="option" value="" />
            <param name="tag" value="NM" />
            <output name="output" file="bamToBed_result2.bed" ftype="bed" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records.

.. class:: infomark

If using a custom BAM alignment TAG as the BED score, note that this must be a numeric tag (e.g., type "i" as in NM:i:0).


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

34:dde39ba9c031

<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@">
    <description>converter</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
    </expand>
    <expand macro="stdio" />
    <command><![CDATA[
#if $input.extension == 'bam' and $option == "-bedpe":
    samtools sort -n '${input}' ./input &&
#else
    ln -s '${input}' ./input.bam &&
#end if

bedtools bamtobed
$option
$ed_score
$split
#if $tag and str($tag).strip():
    -tag '${tag}'
#end if
-i ./input.bam
> '${output}'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="bam" label="Convert the following BAM file to BED"/>
        <param name="option" type="select" label="What type of BED output would you like">
            <option value="">Create a 6-column BED file</option>
            <option value="-bed12">Create a full, 12-column "blocked" BED file</option>
            <option value="-bedpe">Create a paired-end, BEDPE format</option>
        </param>
        <expand macro="split" />
        <param name="ed_score" argument="-ed" type="boolean" truevalue="-ed" falsevalue="" checked="false"
            label="Use alignment's edit-distance for BED score" />
        <param argument="-tag" type="text" optional="true"
            label="Use other NUMERIC BAM alignment tag as the BED score" />
    </inputs>
    <outputs>
        <data name="output" format="bed" metadata_source="input" label="${input.name} (as BED)"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="srma_in3.bam" ftype="bam" />
            <param name="option" value="" />

            <param name="option" value="" />
            <param name="tag" value="NM" />
            <output name="output" file="bamToBed_result2.bed" ftype="bed" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records.

.. class:: infomark

If using a custom BAM alignment TAG as the BED score, note that this must be a numeric tag (e.g., type "i" as in NM:i:0).


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