Mercurial > repos > bgruening > hicexplorer_hicpca

comparison hicPCA.xml @ 2:97c797606746 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
author iuc
date Wed, 03 Jan 2018 13:32:31 -0500
parents 61165fbb020d
children ea50f7bba657
comparison
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1:d5a86de86846 2:97c797606746
1 <tool id="hicexplorer_hicpca" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hicpca" name="@BINARY@" version="@WRAPPER_VERSION@.1">
2 <description>computes the principal components for A / B compartment analysis</description> 2 <description>computes the principal components for A / B compartment analysis</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicPCA</token> 4 <token name="@BINARY@">hicPCA</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 9
10 hicPCA --matrix '$matrix_h5_cooler' 10 hicPCA --matrix '$matrix_h5_cooler'
11 11
12 #if $outputFormat == 'bigwig' 12 --outputFileName pca1.$outputFormat pca2.$outputFormat
13 --outputFileName 'pca1.bigwig' 'pca2.bigwig' 13 --format $outputFormat
14 --format bigwig 14
15 #elif $outputFormat == 'bedgraph' 15 && mv pca1.$outputFormat pca1
16 --outputFileName 'pca1.bedgraph' 'pca2.bedgraph' 16 && mv pca2.$outputFormat pca2
17 --format bedgraph
18 #end if
19 17
20 ]]> 18 ]]>
21 </command> 19 </command>
22 <inputs> 20 <inputs>
23 <expand macro='matrix_h5_cooler_macro' /> 21 <expand macro='matrix_h5_cooler_macro' />
24 <param name='outputFormat' type='select' label="Output file format"> 22 <param name='outputFormat' type='select' label="Output file format">
25 <option value='bigwig'>bigwig</option> 23 <option value='bigwig' selected="true">bigwig</option>
26 <option value="bedgraph">bedgraph</option> 24 <option value="bedgraph">bedgraph</option>
27 </param> 25 </param>
28 26
29 </inputs> 27 </inputs>
30 <outputs> 28 <outputs>
31 29
32 <data name="pca1_bw" from_work_dir="pca1.bigwig" format="bigwig"> 30 <data name="pca1" from_work_dir="pca1" format="bigwig">
33 <filter>outputFormat == 'bigwig'</filter> 31 <filter>outputFormat == 'bigwig'</filter>
32 <change_format>
33 <when input="outputFormat" value="bedgraph" format="bedgraph" />
34 </change_format>
34 </data> 35 </data>
35 <data name="pca2_bw" from_work_dir="pca2.bigwig" format="bigwig"> 36 <data name="pca2" from_work_dir="pca2" format="bigwig">
36 <filter>outputFormat == 'bigwig'</filter> 37 <change_format>
38 <when input="outputFormat" value="bedgraph" format="bedgraph" />
39 </change_format>
37 </data> 40 </data>
38 41
39 <data name="pca1_bedgraph" from_work_dir="pca1.bedgraph" format="bedgraph">
40 <filter>outputFormat == 'bedgraph'</filter>
41 </data>
42 <data name="pca2_bedgraph" from_work_dir="pca2.bedgraph" format="bedgraph">
43 <filter>outputFormat == 'bedgraph'</filter>
44 </data>
45 42
46 </outputs> 43 </outputs>
47 <tests> 44 <tests>
48 <test> 45 <test>
49 <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/> 46 <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/>
50 <param name="outputFormat" value="bedgraph" /> 47 <param name="outputFormat" value="bedgraph" />
51 <output name="pca1_bedgraph" file="pca1.bedgraph" ftype="bedgraph" compare="sim_size"/> 48 <output name="pca1" file="pca1.bedgraph" ftype="bedgraph" compare="sim_size"/>
52 <output name="pca2_bedgraph" file="pca2.bedgraph" ftype="bedgraph" compare="sim_size"/> 49 <output name="pca2" file="pca2.bedgraph" ftype="bedgraph" compare="sim_size"/>
53 </test> 50 </test>
54 <test> 51 <test>
55 <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/> 52 <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/>
56 53
57 <param name="outputFormat" value="bigwig" /> 54 <param name="outputFormat" value="bigwig" />
58 <output name="pca1_bw" file="pca1.bw" ftype="bigwig" compare="sim_size"/> 55 <output name="pca1" file="pca1.bw" ftype="bigwig" compare="sim_size"/>
59 <output name="pca2_bw" file="pca2.bw" ftype="bigwig" compare="sim_size"/> 56 <output name="pca2" file="pca2.bw" ftype="bigwig" compare="sim_size"/>
60 </test> 57 </test>
61 </tests> 58 </tests>
62 <help><![CDATA[ 59 <help><![CDATA[
63 Principal component analysis 60 Principal component analysis
64 ============================ 61 ============================