annotate sccaf_asses.xml @ 0:95670267a5b6 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c

<?xml version="1.0" encoding="utf-8"?>
<tool id="sccaf_asses" name="SCCAF Assesment" version="@TOOL_VERSION@+galaxy0">
  <description>runs an assesment of an SCCAF optimisation result or an existing clustering.</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-assess -i input.h5 --iterations $iterations --cores \${GALAXY_SLOTS:-1}
    -o sccaf_assess.txt
#if $rounds_file
    --slot-for-existing-clustering \$( cat $rounds_file )
#else
    --slot-for-existing-clustering $existing_slot
#end if


]]></command>

  <inputs>
    <expand macro="input_object_params"/>

    <conditional name="slot_source">
      <param type="select" name="source" label="Choose the source of the slot for existing clustering" help="either a round file or an explicit name of a round.">
        <option value="explicit" selected="True">Input the desired round directly</option>
        <option value="file">Input the desired round through a file</option>
      </param>
      <when value="explicit">
        <param type="text" value="" name="existing_slot" label="Specific round to asses" help="Write the slot of the AnnData object that you want assessed."/>
      </when>
      <when value="file">
        <param name="rounds_file" argument="--slot-for-existing-clustering" type="data" format="txt,tsv" label="A file containing a single round to asses in the AnnData file." help="For use with sccaf_distribute_assesment" optional="true"/>
      </when>
    </conditional>
    <param type="integer" value="5" name="iterations" label="Iterations for assesment" help="The number of times that the assesment is internally repeated to achieve a result."/>

  </inputs>

  <outputs>
    <data name="output_table" format="txt" from_work_dir="sccaf_assess.txt" label="${tool.name} on ${on_string} assesment accuracy and cross validation."/>
    <data name="output_png" format="png" from_work_dir="roc-curve.png" label="${tool.name} on ${on_string} ROC-Curve">
      <filter>iterations == 1</filter>
    </data>
  </outputs>

  <tests>
    <test>
      <param name="input_obj_file" value="find_cluster.h5"/>
      <param name="use_tsv" value="true"/>
      <param name="input_tsv" value="find_cluster.tsv"/>
      <output name="output_png" file="run_sccaf.png" ftype="png"/>
    </test>
  </tests>

  <help><![CDATA[
@SCCAF_INTRO@

SCCAF Assesment
===============

This module is used to independently asses either SCCAF Optimisation rounds
results or just any clustering contained in an AnnData object that contains also
UMAP embeddings (necessary for the plots shown). The main purpose of this
independent assesment module is to distribute assesment runs after an optimisation.


]]></help>
  <!-- <expand macro="citations"/> -->
</tool>