comparison salmonKallistoMtxTo10x.xml @ 1:a2aaefceb418 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml commit 3fbbd818012005da4513271beda50df98d3c1cde-dirty

0:fe0fd27aba50

<tool id="_salmon_kallisto_mtx_to_10x" name="salmonKallistoMtxTo10x" version="0.0.1+galaxy0">
    <description>Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data</description>
    <requirements>
      <requirement type="package">scipy</requirement>
      <requirement type="package">pandas</requirement>
    </requirements>
    <command interpreter="python" detect_errors="exit_code"><![CDATA[
        $__tool_directory__/salmonKallistoMtxTo10x.py --cell_prefix "${cell_prefix}" "${mtx_file}" "${genes_file}" "${barcodes_file}" ./
	    ]]></command>

    <inputs>
        <param name="mtx_file" type="data" format="txt" label=".mtx-format matrix" />
        <param name="genes_file" type="data" format="txt" label="Tab-delimited genes file" />
        <param name="barcodes_file" type="data" format="txt" label="Tab-delimited barcodes file" />
        <param name="cell_prefix" type="text" optional='true' value="" label="Prefix to prepend to cell names / barcodes" help="This is useful when multiple matrices from different libraries with overlapping barcodes will be merged"/>
    </inputs>

    <outputs>
        <data name="genes_out" format="txt" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: genes"/>
        <data name="barcodes_out" format="txt" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: barcodes"/>
        <data name="matrix_out" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: matrix" />
    </outputs>
    
    <help><![CDATA[
.. class:: infomark

1:a2aaefceb418

<tool id="_salmon_kallisto_mtx_to_10x" name="salmonKallistoMtxTo10x" version="0.0.1+galaxy1">
    <description>Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data</description>
    <requirements>
      <requirement type="package">scipy</requirement>
      <requirement type="package">pandas</requirement>
    </requirements>
    <command interpreter="python" detect_errors="exit_code"><![CDATA[
        $__tool_directory__/salmonKallistoMtxTo10x.py --cell_prefix "${cell_prefix}" "${mtx_file}" "${genes_file}" "${barcodes_file}" ./
	    ]]></command>

    <inputs>
        <param name="mtx_file" type="data" format="mtx" label=".mtx-format matrix" />
        <param name="genes_file" type="data" format="txt" label="Tab-delimited genes file" />
        <param name="barcodes_file" type="data" format="txt" label="Tab-delimited barcodes file" />
        <param name="cell_prefix" type="text" optional='true' value="" label="Prefix to prepend to cell names / barcodes" help="This is useful when multiple matrices from different libraries with overlapping barcodes will be merged"/>
    </inputs>

    <outputs>
        <data name="genes_out" format="txt" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: genes"/>
        <data name="barcodes_out" format="txt" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: barcodes"/>
        <data name="matrix_out" format="mtx" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: matrix" />
    </outputs>
    
    <help><![CDATA[
.. class:: infomark