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comparison sccaf_asses_merger.xml @ 0:933fad89b50a draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
author ebi-gxa
date Mon, 14 Oct 2019 08:11:06 -0400
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1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="sccaf_asses_merger" name="SCCAF Assesment Merger" version="@TOOL_VERSION@+galaxy0">
3 <description>brings together distributed assesments.</description>
4 <macros>
5 <import>sccaf_macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9
10 mkdir -p asses_results;
11 #for $assesment in $assesments:
12 ln -s '$assesment' asses_results/sccaf_assess_${assesments.index($assesment)}.txt;
13 #end for
14
15 touch rounds.txt;
16 #for $round_file in $round_files
17 cat '$round_file' >> rounds.txt;
18 #end for
19
20 sccaf-assess-merger -i asses_results -r rounds.txt -o report_merge.pdf
21
22 ]]></command>
23
24 <inputs>
25 <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." />
26 <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."/>
27 </inputs>
28
29 <outputs>
30 <data name="accuracy_plot" format="pdf" from_work_dir="report_merge.pdf" label="${tool.name} on ${on_string} assesment report pdf"/>
31 </outputs>
32
33 <tests>
34 <test>
35 <param name="input_obj_file" value="find_cluster.h5"/>
36 <param name="use_tsv" value="true"/>
37 <param name="input_tsv" value="find_cluster.tsv"/>
38 <output name="accuracy_plot" file="report_merge.pdf" ftype="pdf"/>
39 </test>
40 </tests>
41
42 <help><![CDATA[
43 @SCCAF_INTRO@
44
45 The main tool in the SCCAF suite is Run SCCAF. The purpose of this tool is to
46 merge multiple runs of SCCAF Assesment and produce a single plot that compares
47 Test accuracy and Cross Validations, towards deciding on the best solution
48 provided by the optimisation process.
49
50 To produce the required Round files collection, RUN SCCAF needs to be run in
51 optimisation mode and enable the `Produce parameter walk for asessment distribution`
52 option.
53 ]]></help>
54 <!-- <expand macro="citations"/> -->
55 </tool>