comparison groot.xml @ 3:4d5cf5a423d5 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 90b5334805ccaec1ede5dc1b25a2b45d772a69f8

2:c15e34e39e09

<tool id="groot" name="Groot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description> align reads to references and weight variation graphs and generate report</description>
    <macros>
        <token name="@TOOL_VERSION@">1.1.2</token>
        <token name="@VERSION_SUFFIX@">1</token>
        <token name="@PROFILE@">22.05</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">groot</xref>
    </xrefs>

    --minKmerCov $minKmerCov
    $noAlign
    --processors "\${GALAXY_SLOTS:-1}"

| groot report
    --covCutoff '$covCutoff'
    $lowCov
    > '$report_out'

]]></command>
    <inputs>
        <param argument="--fastq" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ file(s) to align"/>

            <param argument="--sketchSize" type="integer" min="0" value="21" label="Size of MinHash sketch" />
        </section>
        <section name="align" title="Align">
            <param argument="--contThresh" type="float" min="0" max="1.0" value="0.99" label="Containment threshold for the LSH ensemble" />
            <param argument="--minKmerCov" type="integer" min="0" value="1" label="Minimum number of k-mers covering each base of a graph segment" />
            <param argument="--noAlign" type="boolean" truevalue="" falsevalue="--noAlign" label="Perform exact alignment?" 
                help="If not, graphs will still be weighted using approximate read mappings"/>
        </section>
        <section name="report" title="Report">
            <param argument="--covCutoff" type="float" min="0" max="1.0" value="0.97" label="Coverage cutoff for reporting ARGs" />
            <param argument="--lowCov" type="boolean" checked="false" truevalue="--lowCov" falsevalue="" label="Report ARGs which may not be covered at the 5'/3' ends" 
                help="If 'Yes', overrides --covCutoff option"/>
        </section>
    </inputs>
    <outputs>
        <data name="report_out" format="tabular" label="${tool.name} on ${on_string}: Report"/>
    </outputs>

                <param name="sketchSize" value="20"/>
            </section>
            <section name="align">
                <param name="contThresh" value="0.99"/>
                <param name="minKmerCov" value="1" />
                <param name="noAlign" value=""/>
            </section>
            <section name="report">
                <conditional name="arg_report">
                    <param name="criteria" value="cutoff" />
                    <param name="covCutoff" value="0.97" />
                </conditional>
            </section>
            <output name="report_out" ftype="tabular">
                <assert_contents>

                <param name="sketchSize" value="21"/>
            </section>
            <section name="align">
                <param name="contThresh" value="0.99"/>
                <param name="minKmerCov" value="1" />
                <param name="noAlign" value=""/>
            </section>
            <section name="report">
                <param name="covCutoff" value="0.97" />
                <param name="lowCov" value="True"/>
            </section>
            <output name="report_out" ftype="tabular">
                <assert_contents>
                    <has_text text="argannot~~~(Bla)VIM-9~~~AY524988:1-801"/>
                    <has_text text="argannot~~~(Bla)VIM-20~~~GQ414736:1-801"/>

3:4d5cf5a423d5

<tool id="groot" name="Groot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description> align reads to references and weight variation graphs and generate report</description>
    <macros>
        <token name="@TOOL_VERSION@">1.1.2</token>
        <token name="@VERSION_SUFFIX@">2</token>
        <token name="@PROFILE@">22.05</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">groot</xref>
    </xrefs>

    --minKmerCov $minKmerCov
    $noAlign
    --processors "\${GALAXY_SLOTS:-1}"

| groot report
    #if str($coverage.mode) == "cutoff"
    --covCutoff '$covCutoff'
    #elif str($coverage.mode) == "lowcov"
    --lowCov
    #end if
    > '$report_out'

]]></command>
    <inputs>
        <param argument="--fastq" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ file(s) to align"/>

            <param argument="--sketchSize" type="integer" min="0" value="21" label="Size of MinHash sketch" />
        </section>
        <section name="align" title="Align">
            <param argument="--contThresh" type="float" min="0" max="1.0" value="0.99" label="Containment threshold for the LSH ensemble" />
            <param argument="--minKmerCov" type="integer" min="0" value="1" label="Minimum number of k-mers covering each base of a graph segment" />
            <param argument="--noAlign" type="boolean" checked="true" truevalue="" falsevalue="--noAlign" label="Perform exact alignment?" 
                help="If 'No', --noAlign will be set, no exact alignment will be performed and graphs will still be weighted using approximate read mappings"/>
        </section>
        <section name="report" title="Report">
            <conditional name="coverage">
                <param name="mode" type="select" label="Choose your coverage mode" help="" >
                    <option value="cutoff" selected="true">Choose your coverage cutoff</option>
                    <option value="lowcov">Low coverage (will report ARGs which may not be covered at the 5’/3’ ends)</option>
                </param>
                <when value="cutoff">
                    <param argument="--covCutoff" type="float" min="0" max="1.0" value="0.97" label="Coverage cutoff for reporting ARGs" />
                </when>
                <when value="lowcov"/>
            </conditional>
        </section>
    </inputs>
    <outputs>
        <data name="report_out" format="tabular" label="${tool.name} on ${on_string}: Report"/>
    </outputs>

                <param name="sketchSize" value="20"/>
            </section>
            <section name="align">
                <param name="contThresh" value="0.99"/>
                <param name="minKmerCov" value="1" />
            </section>
            <section name="report">
                <conditional name="coverage">
                    <param name="mode" value="cutoff"/>
                    <param name="covCutoff" value="0.97" />
                </conditional>
            </section>
            <output name="report_out" ftype="tabular">
                <assert_contents>

                <param name="sketchSize" value="21"/>
            </section>
            <section name="align">
                <param name="contThresh" value="0.99"/>
                <param name="minKmerCov" value="1" />
                <param name="noAlign" value="true"/>
            </section>
            <section name="report">
                <conditional name="coverage">
                    <param name="mode" value="lowcov"/>
                </conditional>
            </section>
            <output name="report_out" ftype="tabular">
                <assert_contents>
                    <has_text text="argannot~~~(Bla)VIM-9~~~AY524988:1-801"/>
                    <has_text text="argannot~~~(Bla)VIM-20~~~GQ414736:1-801"/>