Mercurial > repos > bgruening > hicexplorer_hiccomparematrices

comparison hicCompareMatrices.xml @ 5:55b4b8bc250d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
author bgruening
date Mon, 16 Dec 2019 15:34:06 -0500
parents 6d2c4187805b
children 80abd5e2922a
comparison
equal deleted inserted replaced
4:6d2c4187805b 5:55b4b8bc250d
4 <token name="@BINARY@">hicCompareMatrices</token> 4 <token name="@BINARY@">hicCompareMatrices</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 ln -s '$matrix1' 'matrix1.$matrix1.ext' &&
10 ln -s '$matrix2' 'matrix2.$matrix2.ext' &&
11
9 12
10 @BINARY@ 13 @BINARY@
11 --matrices '$matrix1' '$matrix2' 14 --matrices 'matrix1.$matrix1.ext' 'matrix2.$matrix2.ext'
12 --operation $operation 15 --operation $operation
13 --outFileName matrix.$outputFormat 16 --outFileName 'matrix.$matrix1.ext'
14 17
15 && mv matrix.$outputFormat matrix 18 && mv 'matrix.$matrix1.ext' matrix
16 ]]> 19 ]]>
17 </command> 20 </command>
18 <inputs> 21 <inputs>
19 <param name='matrix1' type="data" format="h5,cool" 22 <param name='matrix1' type="data" format="h5,cool"
20 label="First matrix"/> 23 label="First matrix"/>
24 <param name='operation' type='select' label="Operation to be used for the comparison"> 27 <param name='operation' type='select' label="Operation to be used for the comparison">
25 <option value='diff'>diff</option> 28 <option value='diff'>diff</option>
26 <option value="ratio">ratio</option> 29 <option value="ratio">ratio</option>
27 <option value="log2ratio">log2ratio</option> 30 <option value="log2ratio">log2ratio</option>
28 </param> 31 </param>
29 <param name='outputFormat' type='select' label="Output file format">
30 <option value='h5'>HiCExplorer format</option>
31 <option value="cool">cool</option>
32 </param>
33 </inputs> 32 </inputs>
34 <outputs> 33 <outputs>
35 <data name="outFileName" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}"> 34 <data name="outFileName" from_work_dir="matrix" format="cool" label="${tool.name} MATRIX on ${on_string}">
36 <change_format> 35 <change_format>
37 <when input="outputFormat" value="cool" format="cool" /> 36 <when input_dataset="matrix1" attribute="ext" value="h5" format="h5"/>
38 </change_format> 37 </change_format>
39 </data> 38 </data>
40 </outputs> 39 </outputs>
41 <tests> 40 <tests>
42 <test> 41 <test>
43 <param name="matrix1" value="small_test_matrix.h5"/> 42 <param name="matrix1" value="small_test_matrix.h5"/>
44 <param name="matrix2" value="small_test_matrix.h5"/> 43 <param name="matrix2" value="small_test_matrix.h5"/>
45 <param name="operation" value='log2ratio' /> 44 <param name="operation" value='log2ratio' />
46 <param name="outputFormat" value="h5" /> 45 <output name="outFileName" ftype="h5">
47 <output name="outFileName" file="compare_matrices_log2ratio.h5" ftype="h5" compare="sim_size" delta='10000'/> 46 <assert_contents>
48 </test> 47 <has_h5_keys keys='intervals,matrix'/>
49 <test> 48 </assert_contents>
50 <param name="matrix1" value="pearson_small_50kb.cool"/> 49 </output>
51 <param name="matrix2" value="pearson_small_50kb.cool"/>
52 <param name="operation" value='ratio' />
53 <param name="outputFormat" value="cool" />
54 <output name="outFileName" file="compare_matrices_pearson_ratio.cool" ftype="cool" compare="sim_size" delta='2000'/>
55 </test> 50 </test>
56 51
57 </tests> 52 </tests>
58 <help><![CDATA[ 53 <help><![CDATA[
59 Comparison of Hi-C matrices 54 Comparison of Hi-C matrices