comparison scanpy-run-diffmap.xml @ 12:26e1a99e3c0f draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"

11:f10df597ed6d

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_run_diffmap" name="Scanpy DiffusionMap" version="@TOOL_VERSION@+galaxy11" profile="@PROFILE@">
  <description>calculate diffusion components</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-cli embed diffmap
    --n-comps ${n_comps}
#if $use_graph
    --use-graph '${use_graph}'
#end if
#if $key_added
    --key-added '${key_added}'
#end if
    $export_embed

    <param name="n_comps" argument="--n-comps" type="integer" min="2" value="10"
           label="Number of diffusion components to calculate"/>
    <param name="export_embed" argument="--export-embedding" type="boolean" checked="false"
           truevalue="--export-embedding embed.tsv" falsevalue=""
           label="Export embeddings as a tab-separated text table"/>
    <param name="use_graph" argument="--use-graph" value="neighbors" type="text"
           label="Name of the slot that holds the KNN graph"/>
    <param name="key_added" argument="--key-added" type="text" optional="true"
           label="Additional suffix to the name of the slot to save the calculated diffusion map"/>
  </inputs>

    </data>
  </outputs>

  <tests>
    <test>
      <param name="input_obj_file" value="diffmap.h5"/>
      <param name="input_format" value="anndata"/>
      <param name="output_format" value="anndata"/>
      <param name="n_dcs" value="10"/>
      <param name="root_attr" value="leiden"/>
      <param name="root_value" value="1"/>
      <param name="use_graph" value="neighbors"/>
      <output name="output_h5" file="paga.h5" ftype="h5" compare="sim_size"/>
    </test>
  </tests>

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

12:26e1a99e3c0f

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_run_diffmap" name="Scanpy DiffusionMap" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
  <description>calculate diffusion components</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-cli embed diffmap
    --n-comps ${n_comps}
#if $use_graph
    --neighbors-key '${use_graph}'
#end if
#if $key_added
    --key-added '${key_added}'
#end if
    $export_embed

    <param name="n_comps" argument="--n-comps" type="integer" min="2" value="10"
           label="Number of diffusion components to calculate"/>
    <param name="export_embed" argument="--export-embedding" type="boolean" checked="false"
           truevalue="--export-embedding embed.tsv" falsevalue=""
           label="Export embeddings as a tab-separated text table"/>
    <param name="use_graph" argument="--neighbors-key" value="neighbors" type="text"
           label="Name of the slot that holds the KNN graph"/>
    <param name="key_added" argument="--key-added" type="text" optional="true"
           label="Additional suffix to the name of the slot to save the calculated diffusion map"/>
  </inputs>

    </data>
  </outputs>

  <tests>
    <test>
      <param name="input_obj_file" value="find_cluster.h5"/>
      <param name="input_format" value="anndata"/>
      <param name="output_format" value="anndata"/>
      <param name="n_dcs" value="10"/>
      <param name="root_attr" value="louvain"/>
      <param name="root_value" value="1"/>
      <param name="use_graph" value="neighbors"/>
      <output name="output_h5" file="diffmap.h5" ftype="h5" compare="sim_size"/>
    </test>
  </tests>

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