Mercurial > repos > bgruening > hicexplorer_hiccompartmentspolarization

comparison hicCompartmentalization.xml @ 1:c6f32406aa3c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
author bgruening
date Wed, 05 Feb 2020 19:49:53 -0500
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children ed3dea19c464
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0:8d764e8acdf5 1:c6f32406aa3c
1 <tool id="hicexplorer_hiccompartmentspolarization" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>compute pairwise correlations between multiple Hi-C contact matrices</description>
3 <macros>
4 <token name="@BINARY@">hicCompartmentalization</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9
10 #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
11 ln -s '$m' '${counter}_matrix.$m.ext' &&
12 #end for
13 #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
14
15 @BINARY@
16
17 --obsexp_matrices $m
18
19 --pca '$pca'
20 --quantile $quantile
21
22 #if $set_offset_value:
23 #set $offset_array = $set_offset_value.split(' ')
24 #set $offset = ' '.join([ '%s' % int($value) for $value in $offset_array ])
25 --offset $offset
26 #end if
27 --outliers $outliers
28 --outputFileName plot.$image_file_format
29
30 && mv plot.$image_file_format plot
31 ]]>
32 </command>
33 <inputs>
34 <expand macro="matrix_h5_cooler_multiple_macro" />
35 <param name='pca' type="data" format="bedgraph" label="Eigenvector file" help='A PCA vector as a bedgraph file with
36 no header. In case of several matrices with
37 different conditions, ie. control
38 treatment, the PCA of control can be
39 used. Note that only one PCA can be provided.'/>
40 <param name='quantile' type="integer" label="Quantile" help='The number of to be used quantiles.' value="30"/>
41 <param name='outliers' type="float" label="Outliers" help='The number of outliers to be removed.' value="0.0"/>
42 <param name="set_offset_value" type="text" value="" label="Offset values" optional='True'/>
43
44 <param name="image_file_format" type="select" label="Image output format">
45 <option value="png" selected="True">png</option>
46 <option value="svg">svg</option>
47 <option value="pdf">pdf</option>
48 </param>
49 </inputs>
50 <outputs>
51 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot">
52 <change_format>
53 <when input="image_file_format" value="svg" format="svg" />
54 <when input="image_file_format" value="pdf" format="pdf" />
55 </change_format>
56 </data>
57 <data name='output_matrix' from_work_dir='output_matrix.npz' format='binary' label='Output .npz file includes all the generated matrices'>
58 <filter>outputMatrix == '--outputMatrix output_matrix.npz'</filter>
59 </data>
60 </outputs>
61 <tests>
62 <test>
63 <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5"/>
64 <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph"/>
65 <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size"/>
66 </test>
67 <test>
68 <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5"/>
69 <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph"/>
70 <param name="quantile" value='30'/>
71 <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size"/>
72 </test>
73 <test>
74 <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5"/>
75 <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph"/>
76 <param name="outliers" value='1.0'/>
77 <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size"/>
78 </test>
79 </tests>
80 <help><![CDATA[
81
82 Comparmentalization
83 ===================
84
85 **hicCompartmentalization** rearranges the average interaction frequencies using the first PC values to represent the global compartmentalization signal.
86 To our knowledge this has been first introduced and implemented by Wibke Schwarzer et al. 2017 (Nature. 2017 Nov 2; 551(7678): 51–56)
87
88
89 For more information about HiCExplorer please consider our documentation on readthedocs.io_.
90
91 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
92
93 ]]></help>
94 <expand macro="citations" />
95 </tool>