comparison anndata_operations.xml @ 2:ba18139e7400 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003

1:339d205356c6

<?xml version="1.0" encoding="utf-8"?>
<tool id="anndata_ops" name="AnnData Operations" version="0.0.1+galaxy0">
  <description>modifies metadata and flags genes</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

adata.write('output.h5', compression='gzip')
    </configfile>
</configfiles>

  <inputs>
    <param name="input_obj_file" argument="input-object-file" type="data" format="h5" label="Input object in hdf5 AnnData format"/>
    <repeat name="modifications" title="Change field names in AnnData observations" min="0">
      <param name="from_obs" type="text" label="Original name" help="Name in observations that you want to change">
        <sanitizer>
          <valid initial="string.printable"/>
        </sanitizer>

    </repeat>
    <param name="top_genes" label="Number of top genes" value='50' help="to calculate percentage of the flagged genes in that number of top genes. Used by sc.pp.calculate_qc_metrics (integer)." type="integer"/>
  </inputs>

  <outputs>
    <data name="output" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: anndata with metadata changes."/>
  </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[
=============================

2:ba18139e7400

<?xml version="1.0" encoding="utf-8"?>
<tool id="anndata_ops" name="AnnData Operations" version="0.0.1+galaxy1">
  <description>modifies metadata and flags genes</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

adata.write('output.h5', compression='gzip')
    </configfile>
</configfiles>

  <inputs>
    <param name="input_obj_file" argument="input-object-file" type="data" format="h5,h5ad" label="Input object in hdf5 AnnData format"/>
    <expand macro="output_object_params_no_loom"/>
    <repeat name="modifications" title="Change field names in AnnData observations" min="0">
      <param name="from_obs" type="text" label="Original name" help="Name in observations that you want to change">
        <sanitizer>
          <valid initial="string.printable"/>
        </sanitizer>

    </repeat>
    <param name="top_genes" label="Number of top genes" value='50' help="to calculate percentage of the flagged genes in that number of top genes. Used by sc.pp.calculate_qc_metrics (integer)." type="integer"/>
  </inputs>

  <outputs>
    <expand macro="output_data_obj_no_loom" description="metadata changes on"/>
  </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[
=============================