Mercurial > repos > bgruening > hicexplorer_hiccomparematrices

comparison hicCompareMatrices.xml @ 11:80abd5e2922a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 15:11:23 +0000
parents 55b4b8bc250d
children 3ee5332bf57c
comparison
equal deleted inserted replaced
10:c48c29d59359 11:80abd5e2922a
1 <tool id="hicexplorer_hiccomparematrices" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hiccomparematrices" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>normalize and compare two Hi-C contact matrices</description> 2 <description>normalize and compare two Hi-C contact matrices</description>
3 <macros> 3 <macros>
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' && 9 ln -s '$matrix1' 'matrix1.$matrix1.ext' &&
10 ln -s '$matrix2' 'matrix2.$matrix2.ext' && 10 ln -s '$matrix2' 'matrix2.$matrix2.ext' &&
11 11
12
13 @BINARY@ 12 @BINARY@
14 --matrices 'matrix1.$matrix1.ext' 'matrix2.$matrix2.ext' 13 --matrices 'matrix1.$matrix1.ext' 'matrix2.$matrix2.ext'
15 --operation $operation 14 --operation $operation
16 --outFileName 'matrix.$matrix1.ext' 15 --outFileName 'matrix.$matrix1.ext'
17 16
18 && mv 'matrix.$matrix1.ext' matrix 17 && mv 'matrix.$matrix1.ext' matrix
19 ]]> 18 ]]>
20 </command> 19 </command>
21 <inputs> 20 <inputs>
22 <param name='matrix1' type="data" format="h5,cool" 21 <param name='matrix1' type="data" format="h5,cool" label="First matrix" />
23 label="First matrix"/> 22 <param name='matrix2' type="data" format="h5,cool" label="Second matrix to compare against the first" />
24 <param name='matrix2' type="data" format="h5,cool"
25 label="Second matrix to compare against the first"/>
26 23
27 <param name='operation' type='select' label="Operation to be used for the comparison"> 24 <param name='operation' type='select' label="Operation to be used for the comparison">
28 <option value='diff'>diff</option> 25 <option value='diff'>diff</option>
29 <option value="ratio">ratio</option> 26 <option value="ratio">ratio</option>
30 <option value="log2ratio">log2ratio</option> 27 <option value="log2ratio">log2ratio</option>
31 </param> 28 </param>
32 </inputs> 29 </inputs>
33 <outputs> 30 <outputs>
34 <data name="outFileName" from_work_dir="matrix" format="cool" label="${tool.name} MATRIX on ${on_string}"> 31 <data name="outFileName" from_work_dir="matrix" format="cool" label="${tool.name} MATRIX on ${on_string}">
35 <change_format> 32 <change_format>
36 <when input_dataset="matrix1" attribute="ext" value="h5" format="h5"/> 33 <when input_dataset="matrix1" attribute="ext" value="h5" format="h5" />
37 </change_format> 34 </change_format>
38 </data> 35 </data>
39 </outputs> 36 </outputs>
40 <tests> 37 <tests>
41 <test> 38 <test>
42 <param name="matrix1" value="small_test_matrix.h5"/> 39 <param name="matrix1" value="small_test_matrix.h5" />
43 <param name="matrix2" value="small_test_matrix.h5"/> 40 <param name="matrix2" value="small_test_matrix.h5" />
44 <param name="operation" value='log2ratio' /> 41 <param name="operation" value='log2ratio' />
45 <output name="outFileName" ftype="h5"> 42 <output name="outFileName" ftype="h5">
46 <assert_contents> 43 <assert_contents>
47 <has_h5_keys keys='intervals,matrix'/> 44 <has_h5_keys keys='intervals,matrix' />
48 </assert_contents> 45 </assert_contents>
49 </output> 46 </output>
50 </test> 47 </test>
51 48
52 </tests> 49 </tests>
53 <help><![CDATA[ 50 <help><![CDATA[
51
54 Comparison of Hi-C matrices 52 Comparison of Hi-C matrices
55 =========================== 53 ===========================
56 54
57 This tool is useful to compare two matrices by applying operations like difference, ratio or log2ratio after normalization. To 55 This tool is useful to compare two matrices by applying operations like difference, ratio or log2ratio after normalization. To
58 normalize the matrices, each element is divided by the sum of the matrix. 56 normalize the matrices, each element is divided by the sum of the matrix.
90 _________________ 88 _________________
91 89
92 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ 90 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
93 91
94 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 92 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
95 ]]></help> 93 ]]> </help>
96 <expand macro="citations" /> 94 <expand macro="citations" />
97 </tool> 95 </tool>