comparison fgsea.xml @ 1:101b208a3e1a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea commit a8ec42c929d1f96af3cfe6aeaf229190a0a0717a

0:9bb7943b5263

<tool id="fgsea" name="fgsea" version="1.6.0">
    <description>- fast preranked gene set enrichment analysis</description>
    <requirements>
        <requirement type="package" version="1.6.0">bioconductor-fgsea</requirement>
        <requirement type="package" version="1.6.0">r-optparse</requirement>
    </requirements>
    <version_command><![CDATA[
echo $(R --version | grep version | grep -v GNU)", fgsea version" $(R --vanilla --slave -e "library(fgsea); cat(sessionInfo()\$otherPkgs\$fgsea\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
    ]]></version_command>

                <assert_contents>
                    <has_text_matching expression="pathway.*pval.*padj.*ES.*NES.*nMoreExtreme.*size.*leadingEdge" />
                    <has_text_matching expression="HALLMARK_TNFA_SIGNALING_VIA_NFKB.*0.001" />
                </assert_contents>
            </output>
            <output name="out_pdf" value="out_t47d.pdf" compare="sim_size" delta="12000"/>
        </test>
        <test>
            <param name="rnk_file" ftype="tabular" value="t47d_entrez_ids.rnk" />
            <param name="sets_file" ftype="rdata" value="human_H_v5p2.rdata"/>
            <param name="plot_opt" value="True"/>

1:101b208a3e1a

<tool id="fgsea" name="fgsea" version="1.8.0">
    <description>- fast preranked gene set enrichment analysis</description>
    <requirements>
        <requirement type="package" version="1.8.0">bioconductor-fgsea</requirement>
        <requirement type="package" version="1.6.0">r-optparse</requirement>
    </requirements>
    <version_command><![CDATA[
echo $(R --version | grep version | grep -v GNU)", fgsea version" $(R --vanilla --slave -e "library(fgsea); cat(sessionInfo()\$otherPkgs\$fgsea\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
    ]]></version_command>

                <assert_contents>
                    <has_text_matching expression="pathway.*pval.*padj.*ES.*NES.*nMoreExtreme.*size.*leadingEdge" />
                    <has_text_matching expression="HALLMARK_TNFA_SIGNALING_VIA_NFKB.*0.001" />
                </assert_contents>
            </output>
            <output name="out_pdf" value="out_t47d.pdf" compare="sim_size"/>
        </test>
        <test>
            <param name="rnk_file" ftype="tabular" value="t47d_entrez_ids.rnk" />
            <param name="sets_file" ftype="rdata" value="human_H_v5p2.rdata"/>
            <param name="plot_opt" value="True"/>