Mercurial > repos > iuc > schicexplorer_schicplotclusterprofiles
comparison scHicPlotClusterProfiles.xml @ 0:2427c6d8cdd0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
author | iuc |
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date | Thu, 23 Jan 2020 16:07:58 -0500 |
parents | |
children | 9da580a74230 |
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-1:000000000000 | 0:2427c6d8cdd0 |
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1 <tool id="schicexplorer_schicplotclusterprofiles" name="@BINARY@" version="@WRAPPER_VERSION@.0"> | |
2 <description>plot single-cell Hi-C interaction matrices cluster profiles</description> | |
3 <macros> | |
4 <token name="@BINARY@">scHicPlotClusterProfiles</token> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements" /> | |
8 <command detect_errors="exit_code"><![CDATA[ | |
9 @BINARY@ | |
10 | |
11 --matrix $matrix_mcooler | |
12 --clusters $clusters | |
13 #if $chromosomes: | |
14 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ]) | |
15 --chromosomes $chromosome | |
16 #end if | |
17 | |
18 #if $order_by_conditional.order_by_selection == 'orderByFile': | |
19 --orderBy $order_by_conditional.order_by_selection | |
20 #elif $order_by_conditional.order_by_selection == 'svl': | |
21 --orderBy $order_by_conditional.order_by_selection | |
22 --distanceShortRange $order_by_conditional.distanceShortRange | |
23 --distanceLongRange $order_by_conditional.distanceLongRange | |
24 #end if | |
25 #if $dpi: | |
26 --dpi $dpi | |
27 #end if | |
28 --outFileName plot.$image_file_format | |
29 | |
30 --threads @THREADS@ | |
31 | |
32 && mv plot.$image_file_format plot | |
33 | |
34 ]]></command> | |
35 <inputs> | |
36 <expand macro="matrix_mcooler_macro"/> | |
37 <param name='clusters' type='data' format='txt' label='Cluster file' help='Cluster file created by scHicCluster, scHicClusterCompartments, scHicClusterMinHash or scHicClusterSVL'/> | |
38 <param name="maximalDistance" type="integer" value="2000000" label="Maximal distance" help='Maximal distance to consider for plotting' /> | |
39 <conditional name="order_by_conditional"> | |
40 <param name='order_by_selection' label='Order samples by' type='select'> | |
41 <option value='svl' selected='true'>Short vs long range ratio</option> | |
42 <option value='orderByFile'>Order by file</option> | |
43 </param> | |
44 <when value='svl' > | |
45 <param name="distanceShortRange" type="integer" value="2000000" label="Distance short range" help='Distance for the short range to compute the ratio of sum (short range interactions) / sum (long range interactions)' /> | |
46 <param name="distanceLongRange" type="integer" value="12000000" label="Distance long range" help='Distance for the long range to compute the ratio of sum (short range interactions) / sum (long range interactions)' /> | |
47 </when> | |
48 <when value='orderByFile'> | |
49 </when> | |
50 </conditional> | |
51 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/> | |
52 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/> | |
53 | |
54 <param name="image_file_format" type="select" label="Image output format"> | |
55 <option value="png" selected="True">png</option> | |
56 <option value="svg">svg</option> | |
57 <option value="pdf">pdf</option> | |
58 </param> | |
59 | |
60 </inputs> | |
61 <outputs> | |
62 <data name='output_plot' from_work_dir='plot' format='png' label='Plot SVL'> | |
63 <change_format> | |
64 <when input="image_file_format" value="svg" format="svg" /> | |
65 <when input="image_file_format" value="pdf" format="pdf" /> | |
66 </change_format> | |
67 </data> | |
68 </outputs> | |
69 <tests> | |
70 <test> | |
71 <param name='matrix_mcooler' value='test_matrix.mcool' /> | |
72 <param name='clusters' value='scHicPlotClusterProfiles/cluster_kmeans.txt' /> | |
73 <conditional name="order_by_conditional"> | |
74 <param name="order_by_selection" value="svl"/> | |
75 <param name="distanceShortRange" value="2000000" /> | |
76 <param name="distanceLongRange" value="12000000" /> | |
77 </conditional> | |
78 <param name="maximalDistance" value="50000000" /> | |
79 <param name="image_file_format" value="png" /> | |
80 <param name="dpi" value="300" /> | |
81 | |
82 <output name="output_plot" file="scHicPlotClusterProfiles/plot.png" ftype="png" compare="sim_size" delta="35000"/> | |
83 </test> | |
84 | |
85 </tests> | |
86 <help><![CDATA[ | |
87 | |
88 Plot cluster profiles | |
89 ===================== | |
90 | |
91 scHicPlotClusterProfiles plots the profile of each scHi-C interaction matrix assoziated to a cluster, within the cluster the matrices can be order either via their short vs long range ratio or by the order of the file. | |
92 | |
93 .. image:: $PATH_TO_IMAGES/clusters_svl_spectral.png | |
94 :width: 50% | |
95 | |
96 For more information about scHiCExplorer please consider our documentation on readthedocs.io_ | |
97 | |
98 .. _readthedocs.io: http://schicexplorer.readthedocs.io/ | |
99 ]]></help> | |
100 <expand macro="citations" /> | |
101 | |
102 </tool> |