comparison samtools_slice_bam.xml @ 4:344fc91e1bfd draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"

3:a4a10c7924d1

<tool id="samtools_slice_bam" name="Slice" version="2.0.1">
    <description>BAM by genomic regions</description>
    <macros>
        <import>macros.xml</import>
    </macros>

    <command><![CDATA[
    ln -s '${input_bam}' temp_input.bam &&
    ln -s '${input_bam.metadata.bam_index}' temp_input.bam.bai &&

    #if str($slice_method.slice_method_selector) == "bed":
        samtools view -@ \${GALAXY_SLOTS:-1} -b -L "${input_interval}" -o unsorted_output.bam temp_input.bam && 
    #elif str($slice_method.slice_method_selector) == "chr":
        samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam 
        ${ ' '.join( map( lambda x:'"%s"' % ( x ), str( $slice_method.refs ).split(",") ) ) } &&
    #elif str($slice_method.slice_method_selector) == "man":
        samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam 

        #for $region in $slice_method.regions:
            "${region.chrom}:${region.start}-${region.end}"
        #end for
        &&
    #end if

    samtools sort
        -O bam
        -T sorted
        -@ \${GALAXY_SLOTS:-1}
        -o '${output_bam}'
        unsorted_output.bam
    ]]></command>
    <inputs>

    <tests>
        <test>
            <param name="input_bam" ftype="bam" value="bam-slice-input.bam" />
            <param name="slice_method_selector" value="bed"/>
            <param name="input_interval" ftype="bed" value="bam-slice.bed" />
            <output name="output_bam" file="bam-slice-test1.bam" ftype="bam" />
        </test>
        <test>
            <param name="input_bam" ftype="bam" value="bam-slice-input.bam" />
            <param name="slice_method_selector" value="chr"/>
            <param name="refs" value="chrM" />
            <output name="output_bam" file="bam-slice-test2.bam" ftype="bam" />
        </test>
        <test>
            <param name="input_bam" ftype="bam" value="bam-slice-input.bam" />
            <param name="slice_method_selector" value="man"/>
            <param name="chrom" value="chrM" />
            <param name="start" value="1" />
            <param name="end" value="1000" />
            <output name="output_bam" file="bam-slice-test3.bam" ftype="bam" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Allows to restrict (slice) input BAM dataset to a list of intervals defined in a BED file, individual chromosomes, or manually set list of coordinates.
BED datasets can be obtained from **Get Data -> UCSC Main**.

This tool is based on ``samtools view`` command. 

@no-chrom-options@
    ]]></help>
    <expand macro="citations"/>
</tool>

4:344fc91e1bfd

<tool id="samtools_slice_bam" name="Slice" version="2.0.2" profile="@PROFILE@">
    <description>BAM by genomic regions</description>
    <macros>
        <import>macros.xml</import>
    </macros>

    <command><![CDATA[
    ln -s '${input_bam}' temp_input.bam &&
    ln -s '${input_bam.metadata.bam_index}' temp_input.bam.bai &&

    #if str($slice_method.slice_method_selector) == "bed":
        samtools view -@ \${GALAXY_SLOTS:-1} -b -L "${input_interval}" -o unsorted_output.bam temp_input.bam &&
    #elif str($slice_method.slice_method_selector) == "chr":
        samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam
        ${ ' '.join( map( lambda x:'"%s"' % ( x ), str( $slice_method.refs ).split(",") ) ) } &&
    #elif str($slice_method.slice_method_selector) == "man":
        samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam

        #for $region in $slice_method.regions:
            "${region.chrom}:${region.start}-${region.end}"
        #end for
        &&
    #end if

    samtools sort
        -O bam
        -T "\${TMPDIR:-.}"
        -@ \${GALAXY_SLOTS:-1}
        -o '${output_bam}'
        unsorted_output.bam
    ]]></command>
    <inputs>

    <tests>
        <test>
            <param name="input_bam" ftype="bam" value="bam-slice-input.bam" />
            <param name="slice_method_selector" value="bed"/>
            <param name="input_interval" ftype="bed" value="bam-slice.bed" />
            <output name="output_bam" file="bam-slice-test1.bam" ftype="bam" lines_diff="4" />
        </test>
        <test>
            <param name="input_bam" ftype="bam" value="bam-slice-input.bam" />
            <param name="slice_method_selector" value="chr"/>
            <param name="refs" value="chrM" />
            <output name="output_bam" file="bam-slice-test2.bam" ftype="bam" lines_diff="4" />
        </test>
        <test>
            <param name="input_bam" ftype="bam" value="bam-slice-input.bam" />
            <param name="slice_method_selector" value="man"/>
            <param name="chrom" value="chrM" />
            <param name="start" value="1" />
            <param name="end" value="1000" />
            <output name="output_bam" file="bam-slice-test3.bam" ftype="bam" lines_diff="4"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Allows to restrict (slice) input BAM dataset to a list of intervals defined in a BED file, individual chromosomes, or manually set list of coordinates.
BED datasets can be obtained from **Get Data -> UCSC Main**.

This tool is based on ``samtools view`` command.

@no-chrom-options@
    ]]></help>
    <expand macro="citations"/>
</tool>