annotate 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

<?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"/>
  <command detect_errors="exit_code"><![CDATA[
  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[
=============================
Operations on AnnData objects
=============================

Performs the following operations:

* Change observation fields, mostly for downstreaming processes convenience. Multiple fields can be changed as one.
* Flag genes that start with a certain text: useful for flagging mitochondrial, spikes or other groups of genes.
* For the flags created, calculates qc metrics (pct_<flag>_counts).
* Calculates `n_genes`, `n_counts` for cells and `n_cells`, `n_counts` for genes.
* For top <N> genes specified, calculate qc metrics (pct_counts_in_top_<N>_genes).

This functionality will probably be added in the future to a larger package.
]]></help>
  <!-- <expand macro="citations"/> -->
</tool>