comparison samtools_view.xml @ 2:02afb5ea2fce draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8

1:6ade12d94f9a

<tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@">
    <description>reformat, filter, or subsample</description>
    <macros>
    <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
        @ADDTHREADS@
        ## prepare reference data
        @PREPARE_FASTA_IDX@
        @PREPARE_IDX@

        ##call samtools view
        samtools view
        -@ \$addthreads

        #if $outtype == 'count':

            #end if
            #for $i, $s in enumerate($cond_filter.readtags)
                -x '${s.readtag}'
            #end for
        #end if
        #if $cond_subsample.select_subsample == 'yes':
            #set fraction=str($cond_subsample.subsample).split('.')[1]
            #if str($cond_subsample.seed) == '':
                -s "\${RANDOM}".$fraction
            #else
                -s $cond_subsample.seed.$fraction
            #end if
        #end if

        ## output options
        $adv_output.header

            </when>
            <when value="no"/>
        </conditional>
        <conditional name="cond_subsample">
            <param name="select_subsample" type="select" argument="-s" label="Subsample alignment">
                <option value="yes">Yes</option>
                <option value="no" selected="True">No</option>
            </param>
            <when value="yes">
                <param name="subsample" type="float" optional="False" value="0.5" min="0" max="1" label="Subsampling fraction" help="sets the fraction of templates/pairs to subsample." />
                <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." />
            </when>
            <when value="no"/>
        </conditional>
        <conditional name="addref_cond">
            <param name="addref_select" type="select" label="Reference data">

            <conditional name="cond_region">
                <param name="select_region" value="no"/>
            </conditional>
            <output name="outputsam" file="sam_to_bam_out2.bam" ftype="bam" />
        </test>
    </tests>
    <help>
**What it does**

Samtools view can: 

2:02afb5ea2fce

<tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@">
    <description>reformat, filter, or subsample</description>
    <macros>
    <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package">gawk</requirement>
    </expand>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
        @ADDTHREADS@
        ## prepare reference data
        @PREPARE_FASTA_IDX@
        @PREPARE_IDX@
        #if $cond_subsample.select_subsample == 'target':
            ##this must be done before the main command because we don't know the total # reads until execution time
            #if str($cond_subsample.seed) == '':
                #set seed_expr="int(rand() * 32768)"
            #else
                #set seed_expr=$cond_subsample.seed
            #end if
            #if $input.is_of_type('sam'):
                sample_fragment=`samtools view -c infile | awk '{s=\$1} END {frac=$cond_subsample.target/s; print(frac < 1 ? "-s "  $seed_expr+frac : "")}'` &&
            #else
                sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {frac=$cond_subsample.target/s; print(frac < 1 ? "-s " $seed_expr+frac : "")}'` &&
            #end if
        #end if
        ##call samtools view
        samtools view
        -@ \$addthreads

        #if $outtype == 'count':

            #end if
            #for $i, $s in enumerate($cond_filter.readtags)
                -x '${s.readtag}'
            #end for
        #end if
        #if $cond_subsample.select_subsample != 'no':
            #if $cond_subsample.select_subsample == "target":
                ##this is calculated at execution time before the main samtools command
                "\${sample_fragment}"
            #else
                #set fraction=str($cond_subsample.fraction).split('.')[1]
                #if  str($cond_subsample.seed) == '':
                    -s "\${RANDOM}".$fraction
                #else
                    -s $cond_subsample.seed.$fraction
                #end if
            #end if
        #end if

        ## output options
        $adv_output.header

            </when>
            <when value="no"/>
        </conditional>
        <conditional name="cond_subsample">
            <param name="select_subsample" type="select" argument="-s" label="Subsample alignment">
                <option value="fraction">Specify a fraction to keep</option>
                <option value="target">Specify a target # of reads</option>
                <option value="no" selected="True">No downsampling</option>
            </param>
            <when value="fraction">
                <param name="fraction" type="float" optional="False" value="0.5" min="0" max="1" label="Subsampling fraction" help="sets the fraction of templates/pairs to subsample." />
                <expand macro="seed_input" />
            </when>
            <when value='target'>
                <param name="target" type="integer" optional="False" value="" min="0"  label="Target # of reads" help="sets the target number of reads to subsample." />
                <expand macro="seed_input" />
            </when>
            <when value="no"/>
        </conditional>
        <conditional name="addref_cond">
            <param name="addref_select" type="select" label="Reference data">

            <conditional name="cond_region">
                <param name="select_region" value="no"/>
            </conditional>
            <output name="outputsam" file="sam_to_bam_out2.bam" ftype="bam" />
        </test>
        <!-- sampling options-->
        <test>
            <param name="input" value="test.sam" ftype="sam" />
            <param name="outtype" value="sam" />
            <conditional name="cond_subsample">
                <param name="select_subsample" value="target" />
                <param name="target" value="2" />
            </conditional>
            <output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="6" />
        </test>
        <test>
            <param name="input" value="test.sam" ftype="sam" />
            <param name="outtype" value="sam" />
            <conditional name="cond_subsample">
                <param name="select_subsample" value="target" />
                <param name="seed" value="7" />
                <param name="target" value="2" />
            </conditional>
            <output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="4" />
        </test>
        <test>
            <param name="input" value="test.bam" ftype="bam" />
            <param name="outtype" value="bam" />
            <conditional name="cond_subsample">
                <param name="select_subsample" value="target" />
                <param name="seed" value="7" />
                <param name="target" value="2" />
            </conditional>
            <output name="outputsam" file="test_ds.bam" ftype="bam" />
        </test>        
        <test>
            <param name="input" value="test.bam" ftype="bam" />
            <param name="outtype" value="bam" />
            <conditional name="cond_subsample">
                <param name="select_subsample" value="fraction" />
                <param name="seed" value="7" />
                <param name="fraction" value=".2" />
            </conditional>
            <output name="outputsam" file="test_ds.bam" ftype="bam" />
        </test>        
    </tests>
    <help>
**What it does**

Samtools view can: