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comparison hicPlotViewpoint.xml @ 0:0b7c51584c07 draft default tip

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
author iuc
date Sat, 30 Dec 2017 08:19:13 -0500
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1 <tool id="hicexplorer_hicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>computes the principal components for A / B compartment analysis</description>
3 <macros>
4 <token name="@BINARY@">hicPlotViewpoint</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9
10 hicPlotViewpoint --matrix '$matrix_h5_cooler'
11 #if $interactionOutFileName:
12 $interactionOutFileName interactions.bedgraph
13 #end if
14 --outFileName plot.$image_file_format
15 --region $region
16 --referencePoint $referencePoint
17 && mv plot.$image_file_format plot
18 ]]>
19 </command>
20 <inputs>
21 <expand macro='matrix_h5_cooler_macro' />
22 <expand macro="region" />
23 <param name="referencePoint" type="text" label="Reference point"
24 help="The format is chr:referencePoint or chr:regionStart-regionEnd."/>
25
26 <param name="interactionOutFileName" type="boolean" truevalue="--interactionOutFileName" falsevalue="" checked="false"
27 label="Create bedgraph file with interactions" />
28 <param name="image_file_format" type="select" label="Image output format">
29 <option value="png">png</option>
30 <option value="svg">svg</option>
31 </param>
32
33 </inputs>
34 <outputs>
35
36 <data format="png" name="outFileName" from_work_dir="plot">
37 <change_format>
38 <when input="image_file_format" value="png" format="png" />
39 <when input="image_file_format" value="svg" format="svg" />
40 </change_format>
41 </data>
42 <data name='interactionFile' from_work_dir='interactions.bedgraph' format='bedgraph'>
43 <filter>interactionOutFileName</filter>
44 </data>
45
46 </outputs>
47 <tests>
48 <test>
49 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
50 <param name="image_file_format" value="png" />
51 <param name='region' value='X:3000000-3500000' />
52 <param name='referencePoint' value='X:3200000' />
53 <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size"/>
54 </test>
55 <test>
56 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
57 <param name="image_file_format" value="png" />
58 <param name='region' value='X:3000000-3500000' />
59 <param name='referencePoint' value='X:3200000-3300000' />
60 <param name='interactionOutFileName' value='True' />
61 <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size"/>
62 <output name="interactionFile" file="li_32-33mb_interactions.bedgraph" ftype="bedgraph" compare="sim_size"/>
63
64 </test>
65 </tests>
66 <help><![CDATA[
67 Principal component analysis
68 ============================
69 `hicPCA` computes two eigenvector files based on the input matrix for an A / B compartment analysis.
70
71 Input
72 -----
73 - the matrix to be analysed
74
75 Parameters
76 __________
77 - Output file format: bigwig or bedgraph
78
79 Output
80 ------
81 Two files with the first and the second eigenvector.
82
83 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
84
85 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
86 ]]></help>
87 <expand macro="citations" />
88 </tool>