<?xml version="1.0" encoding="utf-8"?>
<tool id="sccaf_asses_merger" name="SCCAF Assesment Merger" version="@TOOL_VERSION@+galaxy0">
  <description>brings together distributed assesments.</description>
  <macros>
    <import>sccaf_macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[

mkdir -p asses_results;
#for $assesment in $assesments:
  ln -s '$assesment' asses_results/sccaf_assess_${assesments.index($assesment)}.txt;
#end for

touch rounds.txt;
#for $round_file in $round_files
  cat '$round_file' >> rounds.txt;
#end for

sccaf-assess-merger -i asses_results -r rounds.txt -o report_merge.pdf

]]></command>

  <inputs>
    <param type="data" name="assesments" label="Assesment results" format="txt" multiple="true" help="A collection of results of SCCAF Assesment for the same or different rounds of the Run SCCAF optimisation process." />
    <param type="data" name="round_files" label="Files containing names of rounds executed, produced by run-scaff" format="txt" multiple="true" help="Round files collection from Run SCCAF."/>
  </inputs>

  <outputs>
    <data name="accuracy_plot" format="pdf" from_work_dir="report_merge.pdf" label="${tool.name} on ${on_string} assesment report pdf"/>
  </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="accuracy_plot" file="report_merge.pdf" ftype="pdf"/>
    </test>
  </tests>

  <help><![CDATA[
@SCCAF_INTRO@

The main tool in the SCCAF suite is Run SCCAF. The purpose of this tool is to
merge multiple runs of SCCAF Assesment and produce a single plot that compares
Test accuracy and Cross Validations, towards deciding on the best solution
provided by the optimisation process.

To produce the required Round files collection, RUN SCCAF needs to be run in
optimisation mode and enable the `Produce parameter walk for asessment distribution`
option. 
]]></help>
  <!-- <expand macro="citations"/> -->
</tool>