Mercurial > repos > bgruening > hicexplorer_hicplotdistvscounts

comparison hicPlotDistVsCounts.xml @ 0:6abd5817e0cd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
author bgruening
date Thu, 30 Mar 2017 02:40:49 -0400
parents
children f768ce54ee2a
comparison
equal deleted inserted replaced
-1:000000000000 0:6abd5817e0cd
1 <tool id="hicexplorer_hicplotdistvscounts" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>distance vs HiC counts plot per chromosome</description>
3 <macros>
4 <token name="@BINARY@">hicPlotDistVsCounts</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="aggressive"><![CDATA[
9 ln -s '$matrix' input_matrix.npz.h5 &&
10 @BINARY@
11 --matrix input_matrix.npz.h5
12 $skipDiagonal
13 --plotFile plot.png
14 #if $plotTitle and $plotTitle is not None:
15 --plotTitle '$plotTitle'
16 #end if
17
18 ## special: --chromosomeExclude is optional, but if given needs at least one argument
19 #set chroms = '" "'.join([ str($var.chromosomeExclude) for $var in $chromosomeExclude ])
20 #if $chromosomeExclude:
21 --chromosomeExclude $chroms
22 #end if
23 ]]>
24 </command>
25 <inputs>
26 <param argument="--matrix" type="data" format="h5" label="Hi-C normalized/corrected matrix"/>
27
28 <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" label="Exclude diagonal counts" />
29 <param argument="--plotTitle" type="text" optional="true" label="Plot title"/>
30 <repeat name="chromosomeExclude" min="0" title="Chromosomes to exclude">
31 <param argument="--chromosomeExclude" type="text" value="" />
32 </repeat>
33
34 </inputs>
35 <outputs>
36 <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on ${on_string}"/>
37 </outputs>
38 <tests>
39 <test>
40 <param name="matrix" ftype="h5" value="small_test_matrix_50kb_res.h5"/>
41 <param name="skipDiagonal" value="False"/>
42 <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
43 </test>
44 <test>
45 <param name="matrix" ftype="h5" value="small_test_matrix_50kb_res.h5"/>
46 <param name="skipDiagonal" value="False"/>
47 <param name="plotTitle" value="Excluded chrUextra"/>
48 <repeat name="chromosomeExclude">
49 <param name="chromosomeExclude" value="chrUextra"/>
50 </repeat>
51 <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
52 </test>
53 </tests>
54 <help><![CDATA[
55
56 **What it does**
57
58 This program makes a distance vs. hi-c counts plot per chromosome.
59
60
61 ]]></help>
62 <expand macro="citations" />
63 </tool>
64