Mercurial > repos > bgruening > hicexplorer_hiccompartmentspolarization
comparison hicCompartmentalization.xml @ 6:ed3dea19c464 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author | iuc |
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date | Tue, 16 Mar 2021 14:56:24 +0000 |
parents | c6f32406aa3c |
children | bd6e26c47853 |
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5:3afa7d456f61 | 6:ed3dea19c464 |
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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> |