comparison dexseq.xml @ 8:2872c633f07e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit d6fb005b0dbf26037aab1748d9b5df12876c674d"

7:62adf13b86ea

<tool id="dexseq" name="DEXSeq" version="@VERSION@+galaxy1">
    <description>Determines differential exon usage from count tables</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.20.2">r-getopt</requirement>

        <param name="rds" type="boolean" truevalue="True" falsevalue="False" checked="false"
            label="Output rds file for plotDEXSeq?" help="Can be used to generate plots for individual genes with plotDEXSeq" />
        <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.05" label="All the genes under this FDR threshold will be shown in the html report"/>
    </inputs>
    <outputs>
        <data name="dexseq_out" format="tabular" label="DEXSeq result file on ${on_string}" />
        <data name="htmlreport" format="html" label="DEXSeq report on ${on_string}">
            <filter>report is True</filter>
        </data>
        <data name="rds_out" format="rdata" from_work_dir="DEXSeqResults.rds" label="DEXSeq rds file on ${on_string}">
            <filter>rds is True</filter>
        </data>
    </outputs>
    <tests>
        <!-- Ensure default output works-->

            </repeat>
            <param name="report" value="False"/>
            <param name="rds" value="True"/>
            <param name="fdr_cutoff" value="0.05"/>
            <output name="dexseq_out" ftype="tabular" file="dexseq_result.tabular" compare="sim_size"/>
            <output name="rds_out" ftype="rdata" file="dexseq.rds" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

8:2872c633f07e

<tool id="dexseq" name="DEXSeq" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
    <description>Determines differential exon usage from count tables</description>
    <xrefs>
        <xref type="bio.tools">dexseq</xref>
    </xrefs>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.20.2">r-getopt</requirement>

        <param name="rds" type="boolean" truevalue="True" falsevalue="False" checked="false"
            label="Output rds file for plotDEXSeq?" help="Can be used to generate plots for individual genes with plotDEXSeq" />
        <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.05" label="All the genes under this FDR threshold will be shown in the html report"/>
    </inputs>
    <outputs>
        <data name="dexseq_out" format="tabular" label="${tool.name} on ${on_string}: result" />
        <data name="htmlreport" format="html" label="${tool.name} on ${on_string}: report">
            <filter>report is True</filter>
        </data>
        <data name="rds_out" format="rds" from_work_dir="DEXSeqResults.rds" label="${tool.name} on ${on_string}: rds file">
            <filter>rds is True</filter>
        </data>
    </outputs>
    <tests>
        <!-- Ensure default output works-->

            </repeat>
            <param name="report" value="False"/>
            <param name="rds" value="True"/>
            <param name="fdr_cutoff" value="0.05"/>
            <output name="dexseq_out" ftype="tabular" file="dexseq_result.tabular" compare="sim_size"/>
            <output name="rds_out" ftype="rds" file="dexseq.rds" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark