comparison samtools_view.xml @ 4:fdc58a0cc1d4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 640b53919bfc0ae4b895451218e919a52ac14b9d

3:b91e0f76afe9

        #end if

        ## filter options (regions filter is the last parameter)
        #if $cond_filter.select_filter == 'yes':
            #if $cond_filter.cond_region.select_region == 'bed' and str( $cond_filter.cond_region.bedfile ) != 'None'
                -L '$cond_filter.bedfile'
            #end if
            #if $cond_filter.cond_rg.select_rg == 'text':
                -r '$cond_filter.cond_rg.readgr'
            #else if $cond_filter.cond_rg.select_rg == 'file':
                -R '$cond_filter.cond_rg.rgfile'

                <when input="outtype" value="sam" format="sam" />
                <when input="outtype" value="bam" format="bam" />
                <when input="outtype" value="cram" format="cram" />
            </change_format>
        </data>
        <data name="outputcnt" format="txt" from_work_dir="sam" label="${tool.name} on ${on_string}: Counts">
            <filter>outtype == 'count'</filter>
        </data>
    </outputs>
    <tests>
        <!-- sam to bam (copied from the sam_to_bam tool) -->

                <conditional name="cond_region">
                    <param name="select_region" value="no"/>
                </conditional>
            </conditional>
            <output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" />
        </test>
        <test>
            <param name="input" value="test.sam" ftype="sam" />
            <param name="outtype" value="cram" />
            <conditional name="addref_cond">

            <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">

4:fdc58a0cc1d4

        #end if

        ## filter options (regions filter is the last parameter)
        #if $cond_filter.select_filter == 'yes':
            #if $cond_filter.cond_region.select_region == 'bed' and str( $cond_filter.cond_region.bedfile ) != 'None'
                -L '$cond_filter.cond_region.bedfile'
            #end if
            #if $cond_filter.cond_rg.select_rg == 'text':
                -r '$cond_filter.cond_rg.readgr'
            #else if $cond_filter.cond_rg.select_rg == 'file':
                -R '$cond_filter.cond_rg.rgfile'

                <when input="outtype" value="sam" format="sam" />
                <when input="outtype" value="bam" format="bam" />
                <when input="outtype" value="cram" format="cram" />
            </change_format>
        </data>
        <data name="outputcnt" format="txt" from_work_dir="outfile" label="${tool.name} on ${on_string}: Counts">
            <filter>outtype == 'count'</filter>
        </data>
    </outputs>
    <tests>
        <!-- sam to bam (copied from the sam_to_bam tool) -->

                <conditional name="cond_region">
                    <param name="select_region" value="no"/>
                </conditional>
            </conditional>
            <output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" />
        </test>
       <!-- count alignments -->
       <test>
            <param name="input" value="test.bam" ftype="bam" />
            <param name="outtype" value="count" />
            <output name="outputcnt" file="test_counts.tab" ftype="txt" />
        </test>
        <test>
            <param name="input" value="test.sam" ftype="sam" />
            <param name="outtype" value="cram" />
            <conditional name="addref_cond">

            <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="6" />
        </test>
        <test>
            <param name="input" value="test.bam" ftype="bam" />
            <param name="outtype" value="bam" />
            <conditional name="cond_subsample">