comparison scanpy_macros.xml @ 2:77f16c784c19 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"

1:ada6d9bd638d

    <requirements>
      <requirement type="package" version="0.0.5">scanpy-scripts</requirement>
      <yield/>
    </requirements>
  </xml>
  <token name="@VERSION_HISTORY@"><![CDATA[
**Version history**

1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home  at
EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
    ]]></token>
  <xml name="citations">

    <param name="edges" argument="--edges" type="boolean" checked="false" label="Show edges"/>
    <param name="arrows" argument="--arrows" type="boolean" checked="false" label="Show arrows"/>
    <param name="sort_order" argument="--no-sort-order" type="boolean" checked="true" label="Element with high color-by value plot on top"/>
    <param name="frameoff" argument="--frameoff" type="boolean" checked="false" label="Omit frame"/>
  </xml>
</macros>

2:77f16c784c19

    <requirements>
      <requirement type="package" version="0.0.5">scanpy-scripts</requirement>
      <yield/>
    </requirements>
  </xml>
  <token name="@EXPORT_MTX_OPTS@">
      ${export_mtx}
  </token>
  <token name="@VERSION_HISTORY@"><![CDATA[
**Version history**

1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files.

1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home  at
EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
    ]]></token>
  <xml name="citations">

    <param name="edges" argument="--edges" type="boolean" checked="false" label="Show edges"/>
    <param name="arrows" argument="--arrows" type="boolean" checked="false" label="Show arrows"/>
    <param name="sort_order" argument="--no-sort-order" type="boolean" checked="true" label="Element with high color-by value plot on top"/>
    <param name="frameoff" argument="--frameoff" type="boolean" checked="false" label="Omit frame"/>
  </xml>
  <xml name="export_mtx_params">
    <param name="export_mtx" argument="--export-mtx" type="boolean" truevalue="--export-mtx ./" falsevalue="" checked="false" label="Save normalised data to 10x format" help="If enabled, it will generate in addition to the main output in Loom or AnnData an export in 10x format of the normalised data."/>
  </xml>
  <xml name="export_mtx_outputs">
    <data name="matrix_10x" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: 10x matrix">
      <filter>export_mtx</filter>
    </data>
    <data name="genes_10x" format="tsv" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: 10x genes">
      <filter>export_mtx</filter>
    </data>
    <data name="barcodes_10x" format="tsv" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: 10x barcodes">
      <filter>export_mtx</filter>
    </data>
  </xml>
</macros>