diff sccaf_asses_merger.xml @ 0:933fad89b50a draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sccaf_asses_merger.xml	Mon Oct 14 08:11:06 2019 -0400
@@ -0,0 +1,55 @@
+<?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>