comparison samtools_bedcov.xml @ 3:e371922c38e8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40

2:21964f813454

<tool id="samtools_bedcov" name="BedCov" version="2.0">
  <description>calculate read depth for a set of genomic intervals</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"></expand>
    <expand macro="stdio"></expand>
    <expand macro="version_command"></expand>
    <command><![CDATA[
        for bamfile in 
        #for dataset in $input_bams:
            "${dataset}"
        #end for
        ; do
            if [ ! -f \$bamfile.bai ] ; then
                ln -s \$bamfile && samtools index `basename \$bamfile` ;
            else
                ln -s \$bamfile && ln -s \$bamfile.bai ;
            fi ;
        done ;
        samtools bedcov "${input_bed}"
        #for dataset in $input_bams:
            `basename "${dataset}"`
        #end for
        > "${output}"
        ]]>
    </command>
    <inputs>
        <param name="input_bed" type="data" format="bed" label="BED file" />
        <param name="input_bams" type="data" format="bam" label="BAM file" multiple="true" />
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
            <param name="input_bams" value="eboVir3.bam" ftype="bam" />

**What it does**

Calculates read depth for regions listed in a BED dataset using ``samtools bedcov`` command::

 samtools bedcov [INPUT BED] [INPUT BAM1] ... [INPUT BAMn] > [OUTPUT]

    </help>
    <expand macro="citations"></expand>
</tool>

3:e371922c38e8

<tool id="samtools_bedcov" name="BedCov" version="2.0.1">
    <description>calculate read depth for a set of genomic intervals</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
        ## Ensure simlinks have unique filenames
        #for $i, $bam in enumerate( $input_bams ):
            ln -s -f '${bam}' '${i}.bam' &&
            ln -s -f '${bam.metadata.bam_index}' '${i}.bam.bai' &&
        #end for

        samtools bedcov
            '${input_bed}'
            #for $i in range(len( $input_bams )):
                '${i}.bam'
            #end for
            > '${output}'
    ]]></command>
    <inputs>
        <param name="input_bed" type="data" format="bed" label="Genemic intervals (in BED format)" />
        <param name="input_bams" type="data" format="bam" multiple="true" label="BAM file(s)" />
    </inputs>
    <outputs>
        <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
            <param name="input_bams" value="eboVir3.bam" ftype="bam" />

**What it does**

Calculates read depth for regions listed in a BED dataset using ``samtools bedcov`` command::

 samtools bedcov [INPUT BED] [INPUT BAM1] ... [INPUT BAMn] > [OUTPUT]
    </help>
    <expand macro="citations"/>
</tool>