Mercurial > repos > bgruening > hicexplorer_hicmergematrixbins

comparison hicMergeMatrixBins.xml @ 17:03dd3c16ae4e 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 15:09:57 +0000
parents 49c8055f6830
children 977dc15add20
comparison
equal deleted inserted replaced
16:9e357a8b2ec3 17:03dd3c16ae4e
1 <tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>merge adjacent bins from a Hi-C contact matrix to reduce its resolution</description> 2 <description>merge adjacent bins from a Hi-C contact matrix to reduce its resolution</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>
11 --matrix 'matrix.$matrix_h5_cooler.ext' 11 --matrix 'matrix.$matrix_h5_cooler.ext'
12 --numBins $numBins 12 --numBins $numBins
13 $runningWindow 13 $runningWindow
14 --outFileName 'matrix.$matrix_h5_cooler.ext' 14 --outFileName 'matrix.$matrix_h5_cooler.ext'
15 && mv 'matrix.$matrix_h5_cooler.ext' matrix 15 && mv 'matrix.$matrix_h5_cooler.ext' matrix
16
17 ]]> 16 ]]>
18 </command> 17 </command>
19 <inputs> 18 <inputs>
20 <expand macro='matrix_h5_cooler_macro' /> 19 <expand macro='matrix_h5_cooler_macro' />
21
22 <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" /> 20 <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" />
23 <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Set to merge for using a running window of length --numBins. Usually not set." /> 21 <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Set to merge for using a running window of length --numBins. Usually not set." />
24 </inputs> 22 </inputs>
25 <outputs> 23 <outputs>
26 <data name="outFileName" from_work_dir="matrix" format="cool"> 24 <data name="outFileName" from_work_dir="matrix" format="cool">
27 <change_format> 25 <change_format>
28 <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5"/> 26 <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5" />
29 </change_format> 27 </change_format>
30 </data> 28 </data>
31 </outputs> 29 </outputs>
32 <tests> 30 <tests>
33 <test> 31 <test>
34 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> 32 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
35 <param name="numBins" value="5" /> 33 <param name="numBins" value="5" />
36 <output name="outFileName" ftype="h5"> 34 <output name="outFileName" ftype="h5">
37 <assert_contents> 35 <assert_contents>
38 <has_h5_keys keys='intervals,matrix,nan_bins'/> 36 <has_h5_keys keys='intervals,matrix,nan_bins' />
39 </assert_contents> 37 </assert_contents>
40 </output> 38 </output>
41 </test> 39 </test>
42 </tests> 40 </tests>
43 <help><![CDATA[ 41 <help><![CDATA[
92 _________________ 90 _________________
93 91
94 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ 92 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
95 93
96 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 94 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
97 ]]></help> 95 ]]> </help>
98 <expand macro="citations" /> 96 <expand macro="citations" />
99 </tool> 97 </tool>