comparison samtools_depth.xml @ 2:2ee8dc1aeda9 draft

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

1:44de678a44c4

<tool id="samtools_depth" name="Samtools depth" version="@TOOL_VERSION@">
    <description>compute the depth at each position or region</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

    -Q $mapquality
#end if
#for $i in range(len( $input_bams )):
    ${i}
#end for
> '${output}'
    ]]></command>
    <inputs>
        <param name="input_bams" type="data" format="bam" multiple="true" label="BAM file(s)" />
        <conditional name="cond_region">

        <param name="minlength" type="integer" argument="-l" min="0" optional="true" label="Ignore reads shorter than" />
        <param name="maxdepth" type="integer" argument="-m" min="0" optional="true" label="Limits the maximum number of considered alignments starting at any sequence position to INT. Note that, the reported depths values might be larger than INT. If 0, depth is set to the maximum integer value, effectively removing any depth limit. (default = 8000)" />

        <param name="basequality" type="integer" argument="-q" min="0" optional="true" label="Only count reads with base quality greater than" />
        <param name="mapquality" type="integer" argument="-Q" min="0" optional="true" label="Only count reads with mapping quality greater than" />
    </inputs>
    <outputs>
        <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <conditional name="cond_region">
                <param name="select_region" value="bed"/>
                <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
            </conditional>
            <param name="input_bams" value="eboVir3.bam" ftype="bam" />
            <output name="output" file="samtools_depth_out1.tab" />
        </test>
        <test>
            <conditional name="cond_region">
                <param name="select_region" value="text"/>
                <param name="region" value="eboVir3:500-1500" />
            </conditional>
            <param name="input_bams" value="eboVir3.bam" ftype="bam" />
            <output name="output" file="samtools_depth_out2.tab" />
        </test>
        <test>
            <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
            <param name="all" value="-a"/>
            <output name="output" file="samtools_depth_out3.tab" />
        </test>
        <test>
            <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
            <param name="minlength" value="10" />
            <!-- Odd thing: I did not expect values > 4 in the output, but there are ... ?
             see https://github.com/samtools/samtools/issues/889 -->
            <param name="maxdepth" value="4" />
            <param name="basequality" value="11"  />
            <param name="mapquality" value="12" />
            <output name="output" file="samtools_depth_out4.tab" />
        </test>
    </tests>
    <help>
**What it does**

2:2ee8dc1aeda9

<tool id="samtools_depth" name="Samtools depth" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>compute the depth at each position or region</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

    -Q $mapquality
#end if
#for $i in range(len( $input_bams )):
    ${i}
#end for
#set $filter = $additional_options.required_flags
@FLAGS@
-g $flags
#set $filter = $additional_options.skipped_flags
@FLAGS@
-G $flags
$additional_options.deletions
$additional_options.single_read
$output_options.header
> '${output}'
    ]]></command>
    <inputs>
        <param name="input_bams" type="data" format="bam" multiple="true" label="BAM file(s)" />
        <conditional name="cond_region">

        <param name="minlength" type="integer" argument="-l" min="0" optional="true" label="Ignore reads shorter than" />
        <param name="maxdepth" type="integer" argument="-m" min="0" optional="true" label="Limits the maximum number of considered alignments starting at any sequence position to INT. Note that, the reported depths values might be larger than INT. If 0, depth is set to the maximum integer value, effectively removing any depth limit. (default = 8000)" />

        <param name="basequality" type="integer" argument="-q" min="0" optional="true" label="Only count reads with base quality greater than" />
        <param name="mapquality" type="integer" argument="-Q" min="0" optional="true" label="Only count reads with mapping quality greater than" />

        <section name="additional_options" title="Additional Filter Options">
            <param name="required_flags" argument="-g" type="select" multiple="True" label="Require that these flags are set.">
                <expand macro="flag_options" />
            </param>

            <param name="skipped_flags" argument="-G" type="select" multiple="True" label="Exclude reads with any of the following flags set (the default set is UNMAP,SECONDARY,QCFAIL,DUP or 0x704).">
                <expand macro="flag_options" s4="true" s256="true" s512="true" s1024="true"/>
            </param>

            <param name="deletions" type="boolean" argument="-J" truevalue="-J" falsevalue="" checked="false" label="Include reads with deletions in depth computation." />
            <param name="single_read" type="boolean" argument="-s" truevalue="-s" falsevalue="" checked="false" label="For the overlapping section of a read pair, count only the bases of a single read." />
        </section>

        <section name="output_options" title="Output Options" expanded="true">
            <param name="header" type="boolean" argument="-H" truevalue="-H" falsevalue="" checked="false" label="Print a file header to file." />
        </section>

    </inputs>
    <outputs>
        <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <!-- 1) -->
        <test>
            <conditional name="cond_region">
                <param name="select_region" value="bed"/>
                <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
            </conditional>
            <param name="input_bams" value="eboVir3.bam" ftype="bam" />
            <output name="output" file="samtools_depth_out1.tab" />
        </test>
        <!-- 2) -->
        <test>
            <conditional name="cond_region">
                <param name="select_region" value="text"/>
                <param name="region" value="eboVir3:500-1500" />
            </conditional>
            <param name="input_bams" value="eboVir3.bam" ftype="bam" />
            <output name="output" file="samtools_depth_out2.tab" />
        </test>
        <!-- 3) -->
        <test>
            <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
            <param name="all" value="-a"/>
            <output name="output" file="samtools_depth_out3.tab" />
        </test>
        <!-- 4) -->
        <test>
            <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
            <param name="minlength" value="10" />
            <!-- Odd thing: I did not expect values > 4 in the output, but there are ... ?
             see https://github.com/samtools/samtools/issues/889 -->
            <param name="maxdepth" value="4" />
            <param name="basequality" value="11"  />
            <param name="mapquality" value="12" />
            <output name="output" file="samtools_depth_out4.tab" />
        </test>
        <!-- 5) Testing argument -H -->
        <test>
            <conditional name="cond_region">
                <param name="select_region" value="bed"/>
                <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
            </conditional>
            <param name="input_bams" value="eboVir3.bam" ftype="bam" />
            <param name="header" value="true" />
            <output name="output" file="samtools_depth_out5.tab" />
        </test>
        <!-- 6) Tetsing argument -g -->
        <test>
            <param name="input_bams" value="eboVir3.bam" ftype="bam" />
            <param name="required_flags" value="2,16,64" />
            <output name="output" file="samtools_depth_out6.tab" />
        </test>
        <!-- 7) Tetsing argument -G -->
        <test>
            <param name="input_bams" value="eboVir3.bam" ftype="bam" />
            <param name="skipped_flags" value="2,16,64" />
            <output name="output" file="samtools_depth_out7.tab" />
        </test>
    </tests>
    <help>
**What it does**