Mercurial > repos > bgruening > hicexplorer_hictransform

comparison hicTransform.xml @ 2:3106dcd651f5 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 13:31:00 -0500
parents 369f6cb43a86
children 303558d3bc11
comparison
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1:0c13bd882a1a 2:3106dcd651f5
1 <tool id="hicexplorer_hictransform" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hictransform" name="@BINARY@" version="@WRAPPER_VERSION@.1">
2 <description>transforms a matrix to a obs_exp, pearson and covariance matrix</description> 2 <description>transforms a matrix to a obs_exp, pearson and covariance matrix</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicTransform</token> 4 <token name="@BINARY@">hicTransform</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 9
10 10
11 hicTransform --matrix '$matrix_h5_cooler' 11 hicTransform --matrix '$matrix_h5_cooler'
12 --method all 12 --method all
13 13 --outFileName matrix.$outputFormat
14 #if $outputFormat == 'h5' 14 && mv obs_exp_matrix.$outputFormat obs_exp_matrix
15 --outFileName matrix.h5 15 && mv pearson_matrix.$outputFormat pearson_matrix
16 #elif $outputFormat == 'cool' 16 && mv covariance_matrix.$outputFormat covariance_matrix
17 --outFileName matrix.cool
18 #end if
19
20 ]]> 17 ]]>
21 </command> 18 </command>
22 <inputs> 19 <inputs>
23 <expand macro='matrix_h5_cooler_macro' /> 20 <expand macro='matrix_h5_cooler_macro' />
24 <param name='outputFormat' type='select' label="Output file format"> 21 <param name='outputFormat' type='select' label="Output file format">
26 <option value="cool">cool</option> 23 <option value="cool">cool</option>
27 </param> 24 </param>
28 25
29 </inputs> 26 </inputs>
30 <outputs> 27 <outputs>
31 <data name="obs_exp_h5" from_work_dir="obs_exp_matrix.h5" format="h5"> 28 <data name="obs_exp" from_work_dir="obs_exp_matrix" format="h5">
32 <filter>outputFormat == 'h5'</filter> 29 <change_format>
30 <when input="outputFormat" value="cool" format="cool" />
31 </change_format>
33 </data> 32 </data>
34 <data name="pearson_h5" from_work_dir="pearson_matrix.h5" format="h5"> 33 <data name="pearson" from_work_dir="pearson_matrix" format="h5">
35 <filter>outputFormat == 'h5'</filter> 34 <change_format>
35 <when input="outputFormat" value="cool" format="cool" />
36 </change_format>
36 </data> 37 </data>
37 <data name="covariance_h5" from_work_dir="covariance_matrix.h5" format="h5"> 38 <data name="covariance" from_work_dir="covariance_matrix" format="h5">
38 <filter>outputFormat == 'h5'</filter> 39 <change_format>
39 </data> 40 <when input="outputFormat" value="cool" format="cool" />
40 <data name="obs_exp_cool" from_work_dir="obs_exp_matrix.cool" format="cool"> 41 </change_format>
41 <filter>outputFormat == 'cool'</filter>
42 </data>
43 <data name="pearson_cool" from_work_dir="pearson_matrix.cool" format="cool">
44 <filter>outputFormat == 'cool'</filter>
45 </data>
46 <data name="covariance_cool" from_work_dir="covariance_matrix.cool" format="cool">
47 <filter>outputFormat == 'cool'</filter>
48 </data> 42 </data>
49 43
50 </outputs> 44 </outputs>
51 <tests> 45 <tests>
52 <test> 46 <test>
53 <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/> 47 <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/>
54 <param name="outputFormat" value="h5" /> 48 <param name="outputFormat" value="h5" />
55 <output name="obs_exp_h5" file="obs_exp_small_50kb.h5" ftype="h5" compare="sim_size"/> 49 <output name="obs_exp" file="obs_exp_small_50kb.h5" ftype="h5" compare="sim_size"/>
56 <output name="pearson_h5" file="pearson_small_50kb.h5" ftype="h5" compare="sim_size"/> 50 <output name="pearson" file="pearson_small_50kb.h5" ftype="h5" compare="sim_size"/>
57 <output name="covariance_h5" file="covariance_small_50kb.h5" ftype="h5" compare="sim_size"/> 51 <output name="covariance" file="covariance_small_50kb.h5" ftype="h5" compare="sim_size"/>
58 </test> 52 </test>
59 <test> 53 <test>
60 <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/> 54 <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/>
61 <param name="outputFormat" value="cool" /> 55 <param name="outputFormat" value="cool" />
62 <output name="obs_exp_cool" file="obs_exp_small_50kb.cool" ftype="cool" compare="sim_size"/> 56 <output name="obs_exp" file="obs_exp_small_50kb.cool" ftype="cool" compare="sim_size"/>
63 <output name="pearson_cool" file="pearson_small_50kb.cool" ftype="cool" compare="sim_size"/> 57 <output name="pearson" file="pearson_small_50kb.cool" ftype="cool" compare="sim_size"/>
64 <output name="covariance_cool" file="covariance_small_50kb.cool" ftype="cool" compare="sim_size"/> 58 <output name="covariance" file="covariance_small_50kb.cool" ftype="cool" compare="sim_size"/>
65 </test> 59 </test>
66 </tests> 60 </tests>
67 <help><![CDATA[ 61 <help><![CDATA[
68 Transformation of matrix for plotting 62 Transformation of matrix for plotting
69 ===================================== 63 =====================================