Mercurial > repos > bgruening > hicexplorer_hicmergematrixbins

comparison hicMergeMatrixBins.xml @ 11:49c8055f6830 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 15:46:21 -0500
parents c14ba4629233
children 03dd3c16ae4e
comparison
equal deleted inserted replaced
10:6bb9545b7c68 11:49c8055f6830
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>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 hicMergeMatrixBins 9 ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
10 --matrix '$matrix_h5_cooler' 10 @BINARY@
11 --matrix 'matrix.$matrix_h5_cooler.ext'
11 --numBins $numBins 12 --numBins $numBins
12 $runningWindow 13 $runningWindow
13 --outFileName matrix.$outputFormat 14 --outFileName 'matrix.$matrix_h5_cooler.ext'
14 && mv matrix.$outputFormat matrix 15 && mv 'matrix.$matrix_h5_cooler.ext' matrix
15 16
16 ]]> 17 ]]>
17 </command> 18 </command>
18 <inputs> 19 <inputs>
19 <expand macro='matrix_h5_cooler_macro' /> 20 <expand macro='matrix_h5_cooler_macro' />
20 21
21 <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" /> 22 <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" />
22 <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Set to merge for using a running window of length --numBins. Usually not set." /> 23 <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Set to merge for using a running window of length --numBins. Usually not set." />
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>
27 </inputs> 24 </inputs>
28 <outputs> 25 <outputs>
29 <data name="outFileName" from_work_dir="matrix" format="h5"> 26 <data name="outFileName" from_work_dir="matrix" format="cool">
30 <change_format> 27 <change_format>
31 <when input="outputFormat" value="cool" format="cool" /> 28 <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5"/>
32 </change_format> 29 </change_format>
33 </data> 30 </data>
34 </outputs> 31 </outputs>
35 <tests> 32 <tests>
36 <test> 33 <test>
37 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> 34 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
38 <param name="numBins" value="5" /> 35 <param name="numBins" value="5" />
39 <output name="outFileName" file="hicMergeMatrixBins_result1.npz.h5" ftype="h5" compare="sim_size" delta="24000" /> 36 <output name="outFileName" ftype="h5">
37 <assert_contents>
38 <has_h5_keys keys='intervals,matrix,nan_bins'/>
39 </assert_contents>
40 </output>
40 </test> 41 </test>
41 </tests> 42 </tests>
42 <help><![CDATA[ 43 <help><![CDATA[
43 44
44 Change matrix resolution 45 Change matrix resolution