Mercurial > repos > bgruening > hicexplorer_hicmergematrixbins

comparison hicMergeMatrixBins.xml @ 5:1111999ae668 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 13:19:56 -0500 (2018-01-03)
parents 2a62d67cab68
children 0c6d98e9c6e8
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4:936741507eb1 5:1111999ae668
1 <tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@WRAPPER_VERSION@.1">
2 <description>Merges bins from a Hi-C matrix</description> 2 <description>Merges bins from a Hi-C matrix</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicMergeMatrixBins</token> 4 <token name="@BINARY@">hicMergeMatrixBins</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 hicMergeMatrixBins 9 hicMergeMatrixBins
10 --matrix '$matrix_h5_cooler' 10 --matrix '$matrix_h5_cooler'
11 --numBins $numBins 11 --numBins $numBins
12 $runningWindow 12 $runningWindow
13 --outFileName ./out.npz.h5 13 --outFileName matrix.$outputFormat
14 && mv matrix.$outputFormat matrix
14 15
15 ]]> 16 ]]>
16 </command> 17 </command>
17 <inputs> 18 <inputs>
18 <expand macro='matrix_h5_cooler_macro' /> 19 <expand macro='matrix_h5_cooler_macro' />
19 20
20 <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" /> 21 <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" />
21 <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Merge using a running window of length --numBins" /> 22 <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Merge using a running window of length --numBins" />
23 <param name='outputFormat' type='select' label="Output file format">
24 <option value='h5' selected='true'>HiCExplorer format</option>
25 <option value="cool">cool</option>
26 </param>
22 </inputs> 27 </inputs>
23 <outputs> 28 <outputs>
24 <data name="outFileName" from_work_dir="out.npz.h5" format="h5"/> 29 <data name="outFileName" from_work_dir="matrix" format="h5">
30 <change_format>
31 <when input="outputFormat" value="cool" format="cool" />
32 </change_format>
33 </data>
25 </outputs> 34 </outputs>
26 <tests> 35 <tests>
27 <test> 36 <test>
28 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> 37 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
29 <param name="numBins" value="5" /> 38 <param name="numBins" value="5" />