Mercurial > repos > iuc > schicexplorer_schicplotclusterprofiles

comparison scHicPlotClusterProfiles.xml @ 0:aafd4ef10b13 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
author iuc
date Thu, 23 Jan 2020 20:54:33 +0000
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children fa08edee5a79
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-1:000000000000 0:aafd4ef10b13
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>