view seurat_macros.xml @ 0:2890cec5229f draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit fc12e1e90bdc675bd81cf50528afd64ff3dc5c08

<?xml version="1.0"?>
<macros>

    <token name="@VERSION@">0.0.5</token>

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">seurat-scripts</requirement>
        </requirements>
    </xml>

    <xml name="version">
    	<version_command><![CDATA[
echo $(R --version | grep version | grep -v GNU)", seurat version" $(R --vanilla --slave -e "library(seurat); cat(sessionInfo()\$otherPkgs\$seurat\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
    ]]></version_command>
    </xml>

    <xml name="genes-use-input">
      <param name="genes_use" argument="--genes-use" optional="true" type="data" format="tsv, txt" label="Genes to use" help="A file with gene names to use in construction of SNN graph if building directly based on expression data rather than a dimensionally reduced representation (i.e. PCs)."/>
    </xml>
    <xml name="dims-use-input">
      <param name="dims_use" argument="--dims-use" min="1" optional="true" type="integer" label="PCA Dimensions to use" help="Number of PCs (dimensions) to use in construction of the SNN graph."/>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1038/nbt.4096</citation>
        </citations>
    </xml>
</macros>