comparison raceid_clustering.xml @ 4:ee0bbc160cb1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"

3:d4646ce659b4

<tool id="raceid_clustering" name="Clustering using RaceID" version="@VERSION_RACEID@.@VERSION_PACKAGE@.1" >
    <description>performs clustering, outlier detection, dimensional reduction</description>
    <macros>
        <import>macros.xml</import>
        <import>macros_cluster.xml</import>
    </macros>
    <expand macro="requirements" />
    <version_command><![CDATA[
Rscript '$__tool_directory__/scripts/cluster.R' @GET_VERSION@
]]></version_command>

    <command detect_errors="exit_code"><![CDATA[
#set bin = 'cluster.R'
Rscript '$__tool_directory__/scripts/$bin' '$userconf' 2>&1 > '$outlog'
    ]]></command>

    <configfiles>
        <configfile name="userconf" ><![CDATA[
@STRING2VECTOR@

@CLUSTER_CHEETAH@

]]></configfile>
    </configfiles>
    <inputs>
        <param name="inputrds" type="data" format="rdata" label="Input RaceID RDS" help="Requires the RDS output from the normalisation stage" />
        <section name="clust" title="Clustering" expanded="true" >
            <!-- CompDist -->
            <param name="metric" type="select" label="Distance Metric" >

        </section>
    </inputs>
    <outputs>
        <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
        <data name="outrdat" format="rdata" label="${tool.name} on ${on_string}: RDS" />
        <data name="outgenelist" format="tabular" label="${tool.name} on ${on_string}: Cluster - Genes per Cluster" />
        <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" >
            <filter>use_log</filter>
        </data>
    </outputs>

    <tests>
        <test>
            <param name="inputrds" value="matrix.filter.rdat" />
            <output name="outgenelist" value="matrix2.genelist" />
            <output name="outrdat" value="matrix2.rdat" compare="sim_size" delta="15" />
            <output name="outpdf" value="matrix2.pdf" compare="sim_size" delta="10" />
        </test>
        <test>
            <!-- defaults, but manually specified. No opts, no CC. Generates identical to above -->
            <param name="inputrds" value="matrix.filter.rdat" />
            <section name="clust" >

4:ee0bbc160cb1

<tool id="raceid_clustering" name="Clustering using RaceID" version="@VERSION_RACEID@.@VERSION_WRAPPER@" >
    <description>performs clustering, outlier detection, dimensional reduction</description>
    <macros>
        <import>macros.xml</import>
        <import>macros_cheetah.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command_config" prog="cluster.R" cheetah="CLUSTER_CHEETAH" out="&#38;&#62; '$outlog'" />

    <inputs>
        <param name="inputrds" type="data" format="rdata" label="Input RaceID RDS" help="Requires the RDS output from the normalisation stage" />
        <section name="clust" title="Clustering" expanded="true" >
            <!-- CompDist -->
            <param name="metric" type="select" label="Distance Metric" >

        </section>
    </inputs>
    <outputs>
        <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
        <data name="outrdat" format="rdata" label="${tool.name} on ${on_string}: RDS" />
        <data name="outassignments" format="tabular" label="${tool.name} on ${on_string}: Cell-to-Cluster assignments" />
        <data name="outgenelist" format="tabular" label="${tool.name} on ${on_string}: Cluster - Genes per Cluster" />
        <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" >
            <filter>use_log</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="inputrds" value="matrix.filter.rdat" />
            <output name="outgenelist" value="matrix2.genelist" />
            <output name="outrdat" value="matrix2.rdat" compare="sim_size" delta="15" />
            <output name="outpdf" value="matrix2.pdf" compare="sim_size" delta="10" />
            <output name="outassignments" >
                <assert_contents>
                    <has_line_matching expression="P1_B1_ATCCAC\s1\s1\sFALSE" />
                </assert_contents>
            </output>
        </test>
        <test>
            <!-- defaults, but manually specified. No opts, no CC. Generates identical to above -->
            <param name="inputrds" value="matrix.filter.rdat" />
            <section name="clust" >