Mercurial > repos > bgruening > hicexplorer_hicsummatrices

comparison hicSumMatrices.xml @ 7:e0df60f3b0d5 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 13:31:47 -0500
parents b9f41afc3312
children c109622e0cf5
comparison
equal deleted inserted replaced
6:34da5ed2507c 7:e0df60f3b0d5
1 <tool id="hicexplorer_hicsummatrices" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hicsummatrices" name="@BINARY@" version="@WRAPPER_VERSION@.1">
2 <description>combines Hi-C matrices of the same size</description> 2 <description>combines Hi-C matrices of the same size</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicSumMatrices</token> 4 <token name="@BINARY@">hicSumMatrices</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
12 #end for 12 #end for
13 #set $m = '" "'.join([ '%s_matrix' % $counter for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ]) 13 #set $m = '" "'.join([ '%s_matrix' % $counter for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
14 14
15 hicSumMatrices 15 hicSumMatrices
16 --matrices "$m" 16 --matrices "$m"
17 #if $outputFormat == 'h5' 17 --outFileName matrix.$outputFormat
18 --outFileName matrix.h5 18
19 #elif $outputFormat == 'cool' 19 && mv matrix.$outputFormat matrix
20 --outFileName matrix.cool
21 #end if
22 ]]> 20 ]]>
23 </command> 21 </command>
24 <inputs> 22 <inputs>
25 <expand macro='matrix_h5_cooler_multiple_macro'/> 23 <expand macro='matrix_h5_cooler_multiple_macro'/>
26 24
28 <option value='h5'>HiCExplorer format</option> 26 <option value='h5'>HiCExplorer format</option>
29 <option value="cool">cool</option> 27 <option value="cool">cool</option>
30 </param> 28 </param>
31 </inputs> 29 </inputs>
32 <outputs> 30 <outputs>
33 <data name="outFileName_h5" from_work_dir="matrix.h5" format="h5"> 31 <data name="outFileName" from_work_dir="matrix" format="h5">
34 <filter>outputFormat == 'h5'</filter> 32 <change_format>
35 </data> 33 <when input="outputFormat" value="cool" format="cool" />
36 <data name="outFileName_cool" from_work_dir="matrix.cool" format="cool"> 34 </change_format>
37 <filter>outputFormat == 'cool'</filter>
38 </data> 35 </data>
39 </outputs> 36 </outputs>
40 <tests> 37 <tests>
41 <test> 38 <test>
42 <param name="matrix_h5_cooler_multiple" value="hicCorrectMatrix_result1.npz.h5,hicCorrectMatrix_result1.npz.h5"/> 39 <param name="matrix_h5_cooler_multiple" value="hicCorrectMatrix_result1.npz.h5,hicCorrectMatrix_result1.npz.h5"/>
43 <!-- <param name="matrices" value="hicCorrectMatrix_result1.npz.h5,hicCorrectMatrix_result1.npz.h5"/> --> 40 <!-- <param name="matrices" value="hicCorrectMatrix_result1.npz.h5,hicCorrectMatrix_result1.npz.h5"/> -->
44 <param name='outputFormat' value='h5'/> 41 <param name='outputFormat' value='h5'/>
45 <output name="outFileName_h5" file="hicSumMatrices_result1.npz.h5" ftype="h5" compare="sim_size" delta="70000"/> 42 <output name="outFileName" file="hicSumMatrices_result1.npz.h5" ftype="h5" compare="sim_size" delta="70000"/>
46 </test> 43 </test>
47 </tests> 44 </tests>
48 <help><![CDATA[ 45 <help><![CDATA[
49 Summation of matrices 46 Summation of matrices
50 ===================== 47 =====================