comparison hicCompartmentalization.xml @ 6:ed3dea19c464 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 14:56:24 +0000
parents c6f32406aa3c
children
comparison
equal deleted inserted replaced
5:3afa7d456f61 6:ed3dea19c464
1 <tool id="hicexplorer_hiccompartmentspolarization" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hiccompartmentspolarization" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>compute pairwise correlations between multiple Hi-C contact matrices</description> 2 <description>compute pairwise correlations between multiple Hi-C contact matrices</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicCompartmentalization</token> 4 <token name="@BINARY@">hicCompartmentalization</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
11 ln -s '$m' '${counter}_matrix.$m.ext' && 11 ln -s '$m' '${counter}_matrix.$m.ext' &&
12 #end for 12 #end for
13 #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ]) 13 #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
14 14
15 @BINARY@ 15 @BINARY@
16
17 --obsexp_matrices $m 16 --obsexp_matrices $m
18
19 --pca '$pca' 17 --pca '$pca'
20 --quantile $quantile 18 --quantile $quantile
21 19
22 #if $set_offset_value: 20 #if $set_offset_value:
23 #set $offset_array = $set_offset_value.split(' ') 21 #set $offset_array = $set_offset_value.split(' ')
24 #set $offset = ' '.join([ '%s' % int($value) for $value in $offset_array ]) 22 #set $offset = ' '.join([ '%s' % int($value) for $value in $offset_array ])
25 --offset $offset 23 --offset $offset
26 #end if 24 #end if
27 --outliers $outliers 25 --outliers $outliers
28 --outputFileName plot.$image_file_format 26 --outputFileName plot.$image_file_format
29
30 && mv plot.$image_file_format plot 27 && mv plot.$image_file_format plot
31 ]]> 28 ]]>
32 </command> 29 </command>
33 <inputs> 30 <inputs>
34 <expand macro="matrix_h5_cooler_multiple_macro" /> 31 <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 32 <param name='pca' type="data" format="bedgraph" label="Eigenvector file" help='A PCA vector as a bedgraph file with no header. In case of several matrices with
36 no header. In case of several matrices with 33 different conditions, ie. control treatment, the PCA of control can be
37 different conditions, ie. control 34 used. Note that only one PCA can be provided.' />
38 treatment, the PCA of control can be 35 <param name='quantile' type="integer" value="30" label="Quantile" help='The number of to be used quantiles.' />
39 used. Note that only one PCA can be provided.'/> 36 <param name='outliers' type="float" value="0.0" label="Outliers" help='The number of outliers to be removed.' />
40 <param name='quantile' type="integer" label="Quantile" help='The number of to be used quantiles.' value="30"/> 37 <param name="set_offset_value" type="text" optional='True' value="" label="Offset values">
41 <param name='outliers' type="float" label="Outliers" help='The number of outliers to be removed.' value="0.0"/> 38 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
42 <param name="set_offset_value" type="text" value="" label="Offset values" optional='True'/> 39 </param>
43 40
44 <param name="image_file_format" type="select" label="Image output format"> 41 <param name="image_file_format" type="select" label="Image output format">
45 <option value="png" selected="True">png</option> 42 <option value="png" selected="True">png</option>
46 <option value="svg">svg</option> 43 <option value="svg">svg</option>
47 <option value="pdf">pdf</option> 44 <option value="pdf">pdf</option>
48 </param> 45 </param>
49 </inputs> 46 </inputs>
50 <outputs> 47 <outputs>
51 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot"> 48 <data name="outFileName" format="png" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot">
52 <change_format> 49 <change_format>
53 <when input="image_file_format" value="svg" format="svg" /> 50 <when input="image_file_format" value="svg" format="svg" />
54 <when input="image_file_format" value="pdf" format="pdf" /> 51 <when input="image_file_format" value="pdf" format="pdf" />
55 </change_format> 52 </change_format>
56 </data> 53 </data>
58 <filter>outputMatrix == '--outputMatrix output_matrix.npz'</filter> 55 <filter>outputMatrix == '--outputMatrix output_matrix.npz'</filter>
59 </data> 56 </data>
60 </outputs> 57 </outputs>
61 <tests> 58 <tests>
62 <test> 59 <test>
63 <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5"/> 60 <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5" />
64 <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph"/> 61 <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph" />
65 <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size"/> 62 <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size" />
66 </test> 63 </test>
67 <test> 64 <test>
68 <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5"/> 65 <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5" />
69 <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph"/> 66 <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph" />
70 <param name="quantile" value='30'/> 67 <param name="quantile" value='30' />
71 <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size"/> 68 <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size" />
72 </test> 69 </test>
73 <test> 70 <test>
74 <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5"/> 71 <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5" />
75 <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph"/> 72 <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph" />
76 <param name="outliers" value='1.0'/> 73 <param name="outliers" value='1.0' />
77 <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size"/> 74 <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size" />
78 </test> 75 </test>
79 </tests> 76 </tests>
80 <help><![CDATA[ 77 <help><![CDATA[
81 78
82 Comparmentalization 79 Comparmentalization
88 85
89 For more information about HiCExplorer please consider our documentation on readthedocs.io_. 86 For more information about HiCExplorer please consider our documentation on readthedocs.io_.
90 87
91 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 88 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
92 89
93 ]]></help> 90 ]]> </help>
94 <expand macro="citations" /> 91 <expand macro="citations" />
95 </tool> 92 </tool>