comparison sccaf_regress_out.xml @ 1:5ef0610e9f50 draft default tip

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 7034937deaaf56b2e6f585bb28234a86a5b5fa2e

0:885db50f1bc1

<?xml version="1.0" encoding="utf-8"?>
<tool id="sccaf_regress_out" name="SCCAF mulitple regress out" version="@TOOL_VERSION@+galaxy0">
  <description>with multiple categorical keys on an AnnData object.</description>
  <macros>
    <import>sccaf_macros.xml</import>
  </macros>
  <expand macro="requirements"/>

  ln -s '${input_obj_file}' input.h5 &&
  sccaf-regress-out -i input.h5 -o output.h5 -k '${keys_to_regress}'
  ]]></command>
  <inputs>
    <param name="input_obj_file" argument="input-object-file" type="data" format="h5" label="Input object in hdf5 AnnData format"/>
    <param name="keys_to_regress" label="Keys to regress" help="Comma separated keys for regressing out; they need to exist in the observations part of the AnnData object." type="text"/>
  </inputs>
  <outputs>
    <data name="output" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: regressesed out on ${keys_to_regress}"/>
  </outputs>

  <tests>
    <test>
      <param name="input_obj_file" value="find_cluster.h5"/>
      <param name="input_format" value="anndata"/>
      <param name="color_by" value="louvain"/>
      <output name="output" file="output.h5" ftype="h5" compare="sim_size"/>
    </test>
  </tests>

  <help><![CDATA[
=============================

1:5ef0610e9f50

<?xml version="1.0" encoding="utf-8"?>
<tool id="sccaf_regress_out" name="SCCAF mulitple regress out" version="@TOOL_VERSION@+galaxy1">
  <description>with multiple categorical keys on an AnnData object.</description>
  <macros>
    <import>sccaf_macros.xml</import>
  </macros>
  <expand macro="requirements"/>

  ln -s '${input_obj_file}' input.h5 &&
  sccaf-regress-out -i input.h5 -o output.h5 -k '${keys_to_regress}'
  ]]></command>
  <inputs>
    <param name="input_obj_file" argument="input-object-file" type="data" format="h5" label="Input object in hdf5 AnnData format"/>
    <expand macro="output_object_params"/>
    <param name="keys_to_regress" label="Keys to regress" help="Comma separated keys for regressing out; they need to exist in the observations part of the AnnData object." type="text"/>
  </inputs>
  <outputs>
    <expand macro="output_data_obj" description="regressed out on ${keys_to_regress}"/>
  </outputs>

  <tests>
    <test>
      <param name="input_obj_file" value="find_cluster.h5"/>
      <param name="input_format" value="anndata"/>
      <param name="color_by" value="louvain"/>
      <output name="output_h5ad" file="output.h5" ftype="h5" compare="sim_size"/>
    </test>
  </tests>

  <help><![CDATA[
=============================