comparison askor_de.xml @ 1:ea4a79798dcf draft

planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/askor commit dea4b3dfc2393e4f5b9945099cfec37afe471283

0:d24096d4c002

<tool id="askor_de" name="AskoR DE" version="0.1">
    <description>EdgeR for AskOmics</description>
    <requirements>
        <requirement type="package" version="3.34.6">bioconductor-limma</requirement>
        <requirement type="package" version="1.4.30">r-statmod</requirement>
        <requirement type="package" version="3.20.7">bioconductor-edger</requirement>

          #if $adv.nh
            --nh ${adv.nh}
          #end if
    ]]></command>
    <inputs>
        <param format="csv" name="fileofcounts" type="data" label="File of counts" />
        <param format="tsv" name="samples" type="data" label="Descriptions of the samples" />
        <param format="tsv" name="contrasts" type="data" label="Descriptions of the contrasts" />
        <section name="adv" title="Format options" expanded="false">
            <param name="colgenes" type="integer" label="Column of the genes" value="1" optional="true" />
            <!--param name="sep" type="text" label="Field separator" value="\t" optional="true" /-->
            <param name="palette" type="text" label="Color palette (Rcolorbrewer)" value="Set2" optional="true" />
            <param name="organism" type="text" label="Organism" value="Asko" optional="true" />

            </param>
        </section>
    </inputs>
    <outputs>
        <data format="pdf" name="out_pdf" label="${tool.name} on ${on_string}: Graphics" />
        <data name="output" format="tsv" label="${tool.name} on ${on_string}">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" ext="tsv" visible="true" directory="askor_output" />
        </data>
    </outputs>
    <tests>
        <test>
            <param name="fileofcounts" ftype="csv" value="counts.csv" />
            <param name="samples" ftype="tsv" value="Samples.txt" />
            <param name="contrasts" ftype="tsv" value="Contrasts.txt" />
            <section name="adv">
                <param name="colgenes" value="3" />
            </section>
            <section name="thresholds">
                <param name="th_cpm" value="10" />
            </section>
            <output name="out_pdf" file="out.pdf" compare="sim_size"/>
            <output name="output">
                <discovered_dataset designation="AskoAvsK" ftype="tsv" file="AskoAvsK.txt" compare="sim_size" />
                <discovered_dataset designation="AskoT1AvsT1K" ftype="tsv" file="AskoT1AvsT1K.txt" compare="sim_size" />
                <discovered_dataset designation="AskoT1vsT0" ftype="tsv" file="AskoT1vsT0.txt" compare="sim_size" />
                <discovered_dataset designation="AskoT1vsT2" ftype="tsv" file="AskoT1vsT2.txt" compare="sim_size" />
                <discovered_dataset designation="condition.asko" ftype="tsv" file="condition.asko.txt" compare="sim_size" />
                <discovered_dataset designation="context.asko" ftype="tsv" file="context.asko.txt" compare="sim_size" />
                <discovered_dataset designation="contrast.asko" ftype="tsv" file="contrast.asko.txt" compare="sim_size" />
            </output>
        </test>
    </tests>
    <help><![CDATA[
This tools generates a list of differential genes from various contrasts in an AskOmics format (https://askomics.github.io/).

1:ea4a79798dcf

<tool id="askor_de" name="AskoR DE" version="0.2">
    <description>EdgeR for AskOmics</description>
    <requirements>
        <requirement type="package" version="3.34.6">bioconductor-limma</requirement>
        <requirement type="package" version="1.4.30">r-statmod</requirement>
        <requirement type="package" version="3.20.7">bioconductor-edger</requirement>

          #if $adv.nh
            --nh ${adv.nh}
          #end if
    ]]></command>
    <inputs>
        <param format="tabular,csv" name="fileofcounts" type="data" label="File of counts" />
        <param format="tabular,tsv" name="samples" type="data" label="Descriptions of the samples" />
        <param format="tabular,tsv" name="contrasts" type="data" label="Descriptions of the contrasts" />
        <section name="adv" title="Format options" expanded="false">
            <param name="colgenes" type="integer" label="Column of the genes" value="1" optional="true" />
            <!--param name="sep" type="text" label="Field separator" value="\t" optional="true" /-->
            <param name="palette" type="text" label="Color palette (Rcolorbrewer)" value="Set2" optional="true" />
            <param name="organism" type="text" label="Organism" value="Asko" optional="true" />

            </param>
        </section>
    </inputs>
    <outputs>
        <data format="pdf" name="out_pdf" label="${tool.name} on ${on_string}: Graphics" />
        <data name="output" format="tabular" label="${tool.name} on ${on_string}">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" ext="tabular" visible="true" directory="askor_output" />
        </data>
    </outputs>
    <tests>
        <test>
            <param name="fileofcounts" ftype="csv" value="counts.csv" />
            <param name="samples" ftype="tabular" value="Samples.txt" />
            <param name="contrasts" ftype="tabular" value="Contrasts.txt" />
            <section name="adv">
                <param name="colgenes" value="3" />
            </section>
            <section name="thresholds">
                <param name="th_cpm" value="10" />
            </section>
            <output name="out_pdf" file="out.pdf" compare="sim_size"/>
            <output name="output">
                <discovered_dataset designation="AskoAvsK" ftype="tabular" file="AskoAvsK.txt" compare="sim_size" />
                <discovered_dataset designation="AskoT1AvsT1K" ftype="tabular" file="AskoT1AvsT1K.txt" compare="sim_size" />
                <discovered_dataset designation="AskoT1vsT0" ftype="tabular" file="AskoT1vsT0.txt" compare="sim_size" />
                <discovered_dataset designation="AskoT1vsT2" ftype="tabular" file="AskoT1vsT2.txt" compare="sim_size" />
                <discovered_dataset designation="condition.asko" ftype="tabular" file="condition.asko.txt" compare="sim_size" />
                <discovered_dataset designation="context.asko" ftype="tabular" file="context.asko.txt" compare="sim_size" />
                <discovered_dataset designation="contrast.asko" ftype="tabular" file="contrast.asko.txt" compare="sim_size" />
            </output>
        </test>
    </tests>
    <help><![CDATA[
This tools generates a list of differential genes from various contrasts in an AskOmics format (https://askomics.github.io/).