Mercurial > repos > bgruening > hicexplorer_hicmergematrixbins

comparison hicMergeMatrixBins.xml @ 0:a1cf508bff84 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
author bgruening
date Thu, 02 Nov 2017 11:08:52 -0400
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children cdff00acac0f
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-1:000000000000 0:a1cf508bff84
1 <tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>Merges bins from a Hi-C matrix</description>
3 <macros>
4 <token name="@BINARY@">hicMergeMatrixBins</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9
10 ln -s '$matrix' input.npz.h5 &&
11
12 hicMergeMatrixBins
13 --matrix input.npz.h5
14 --numBins $numBins
15 $runningWindow
16 --outFileName ./out.npz.h5
17
18 ]]>
19 </command>
20 <inputs>
21 <param argument="--matrix" type="data" format="h5" label="Matrix to reduce" />
22 <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="Merge using a running window of length --numBins" />
24 </inputs>
25 <outputs>
26 <data name="outFileName" from_work_dir="out.npz.h5" format="h5"/>
27 </outputs>
28 <tests>
29 <test>
30 <param name="matrix" value="small_test_matrix.h5" />
31 <param name="numBins" value="5" />
32 <output name="outFileName" file="hicMergeMatrixBins_result1.npz.h5" ftype="h5" compare="sim_size" delta="24000" />
33 </test>
34 </tests>
35 <help><![CDATA[
36
37 **What it does**
38
39 Merges neighboring bins in a Hi-C matrix.
40
41 ]]></help>
42 <expand macro="citations" />
43 </tool>