comparison samtools_stats.xml @ 6:47035d167365 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 558d30ff047fe2f62658e8b57e27ebe8db77ede1"

5:5a08c09b9311

<tool id="samtools_stats" name="Samtools stats" version="2.0.2+galaxy1">
    <description>generate statistics for BAM dataset</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="5.2.3">gnuplot</requirement>
        <requirement type="package" version="5.26">perl</requirement>
    </expand>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
        @ADDTHREADS@
        @PREPARE_IDX@

            #end if
            -@ \$addthreads 
            infile
            @REGIONS_MANUAL@
            > '$output'

            #if $cond_plot.select_plot=='yes':
                && plot-bamstats '$output' $cond_plot.log -p '${html_file.files_path}'/
                && mv '${html_file.files_path}'/index.html '${html_file}'
            #end if

            #if $split_output_cond.split_output_selector == "yes":
                #set outputs_to_split = str($split_output_cond.generate_tables).split(',')
                && mkdir split
                #for s in str($split_output_cond.generate_tables).split(','):

        <expand macro="regions_macro"/>

        <param name="sparse" argument="-x/--sparse" type="boolean" truevalue="-x" falsevalue="" checked="False" label="Suppress absence of insertions" help="Suppress outputting IS rows where there are no insertions."/>
        <param name="remove_overlaps" argument="-p/--remove-overlaps" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Remove overlaps of paired-end reads from coverage and base count computations" />
        <param name="cov_threshold" argument="-g/--cov-threshold"  optional="true" type="integer" label="Only bases with coverage above this value will be included in the target percentage computation" />
        <conditional name="cond_plot">
            <param name="select_plot" type="select" label="Generate plots with plot-bamstats">
                <option value="no" selected="True">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no"/>
            <when value="yes">
                <param name="log" argument="-l/--log-y" type="boolean" truevalue="-l" falsevalue="" checked="False" label="log scale insert size plot" help="Set the Y axis scale of the Insert Size plot to log 10"/>
            </when>
        </conditional>
    </inputs>

    <outputs>
        <data name="output" format="tabular" label="${tool.name} on ${on_string}">
            <discover_datasets directory="split" pattern="(?P&lt;designation&gt;.+)\.tab" format="tabular" visible="true" assign_primary_output="true"/>

        </data>
        <collection name="output_collection" type="list" label="${tool.name} on ${on_string}">
            <discover_datasets directory="split" pattern="(?P&lt;designation&gt;.+)\.tab" format="tabular" visible="false"/>
            <filter>split_output_cond['split_output_selector'] == 'yes'</filter>
        </collection>
        <data format="html" name="html_file" label="${tool.name} on ${on_string}: plot-bamstats">
            <filter>cond_plot['select_plot']=='yes'</filter>
        </data>
    </outputs>
    <tests>
        <!-- https://github.com/samtools/samtools/blob/9ce8c64493f7ea3fa69bc5c1ac980b1a8e3dcf1f/test/test.pl#L2402 -->
        <test>
            <param name="input" value="1_map_cigar.sam" ftype="sam" />

            <param name="input" value="samtools_stats_input.bam" ftype="bam" />
            <conditional name="addref_cond">
                <param name="addref_select" value="history" />
                <param name="ref" value="samtools_stats_ref.fa" ftype="fasta" />
            </conditional>
            <conditional name="cond_plot">
                <param name="select_plot" value="yes"/>
            </conditional>
            <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="2" />
        </test>
        <test>
            <param name="input" value="samtools_stats_input.bam" ftype="bam" />
            <conditional name="addref_cond">

    </tests>
    <help><![CDATA[
**What it does**

This tool runs the ``samtools stats`` command.
    ]]></help>
    <expand macro="citations"/>
</tool>

6:47035d167365

<tool id="samtools_stats" name="Samtools stats" version="2.0.2+galaxy2">
    <description>generate statistics for BAM dataset</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
        @ADDTHREADS@
        @PREPARE_IDX@

            #end if
            -@ \$addthreads 
            infile
            @REGIONS_MANUAL@
            > '$output'

            #if $split_output_cond.split_output_selector == "yes":
                #set outputs_to_split = str($split_output_cond.generate_tables).split(',')
                && mkdir split
                #for s in str($split_output_cond.generate_tables).split(','):

        <expand macro="regions_macro"/>

        <param name="sparse" argument="-x/--sparse" type="boolean" truevalue="-x" falsevalue="" checked="False" label="Suppress absence of insertions" help="Suppress outputting IS rows where there are no insertions."/>
        <param name="remove_overlaps" argument="-p/--remove-overlaps" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Remove overlaps of paired-end reads from coverage and base count computations" />
        <param name="cov_threshold" argument="-g/--cov-threshold"  optional="true" type="integer" label="Only bases with coverage above this value will be included in the target percentage computation" />
    </inputs>

    <outputs>
        <data name="output" format="tabular" label="${tool.name} on ${on_string}">
            <discover_datasets directory="split" pattern="(?P&lt;designation&gt;.+)\.tab" format="tabular" visible="true" assign_primary_output="true"/>

        </data>
        <collection name="output_collection" type="list" label="${tool.name} on ${on_string}">
            <discover_datasets directory="split" pattern="(?P&lt;designation&gt;.+)\.tab" format="tabular" visible="false"/>
            <filter>split_output_cond['split_output_selector'] == 'yes'</filter>
        </collection>
    </outputs>
    <tests>
        <!-- https://github.com/samtools/samtools/blob/9ce8c64493f7ea3fa69bc5c1ac980b1a8e3dcf1f/test/test.pl#L2402 -->
        <test>
            <param name="input" value="1_map_cigar.sam" ftype="sam" />

            <param name="input" value="samtools_stats_input.bam" ftype="bam" />
            <conditional name="addref_cond">
                <param name="addref_select" value="history" />
                <param name="ref" value="samtools_stats_ref.fa" ftype="fasta" />
            </conditional>
            <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="2" />
        </test>
        <test>
            <param name="input" value="samtools_stats_input.bam" ftype="bam" />
            <conditional name="addref_cond">

    </tests>
    <help><![CDATA[
**What it does**

This tool runs the ``samtools stats`` command.

The results of samtools stats can be visualized with MultiQC (for this the default of a single output file needs to be selected).
    ]]></help>
    <expand macro="citations"/>
</tool>