comparison salmonKallistoMtxTo10x.xml @ 8:5675dc87bb8d 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 bf9021c853da640771202920cde38f77cdeaf368"

7:60fa6080f86f

<tool id="_salmon_kallisto_mtx_to_10x" name="salmonKallistoMtxTo10x" version="0.0.1+galaxy3">
    <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 detect_errors="exit_code"><![CDATA[
        file $mtx_file | grep 'gzip compressed' > /dev/null;
        if [ $? -eq 0 ]; then
            matrixfile=matrix.mtx.gz;

    <outputs>
        <data name="genes_out" format="tabular" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: genes"/>
        <data name="barcodes_out" format="tabular" from_work_dir="barcodes.tsv" label="${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

**What it does**

**Inputs**

MTX and row and gene labels from the relevant tool. For Alevin this will be

 * Matrix file: quants_mat.mtx.gz 
 * Genes file: quants_mat_cols.txt
 * Barcodes file: quants_mat_rows.txt

For Kallisto it will be:

 * Matrix file: [name].mtx.gz 
 * Genes file: [name].genes.txt
 * Barcodes file: [name].barcodes.txt

-----

8:5675dc87bb8d

<tool id="_salmon_kallisto_mtx_to_10x" name="salmonKallistoMtxTo10x" version="0.0.1+galaxy4" profile="18.01">
    <description>Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data</description>
    <requirements>
      <requirement type="package" version="1.4.1">scipy</requirement>
      <requirement type="package" version="1.0.1">pandas</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        file $mtx_file | grep 'gzip compressed' > /dev/null;
        if [ $? -eq 0 ]; then
            matrixfile=matrix.mtx.gz;

    <outputs>
        <data name="genes_out" format="tabular" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: genes"/>
        <data name="barcodes_out" format="tabular" from_work_dir="barcodes.tsv" label="${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

**What it does**

**Inputs**

MTX and row and gene labels from the relevant tool. For Alevin this will be

 * Matrix file: quants_mat.mtx.gz
 * Genes file: quants_mat_cols.txt
 * Barcodes file: quants_mat_rows.txt

For Kallisto it will be:

 * Matrix file: [name].mtx.gz
 * Genes file: [name].genes.txt
 * Barcodes file: [name].barcodes.txt

-----