Mercurial > repos > iuc > schicexplorer_schicplotclusterprofiles

comparison scHicPlotClusterProfiles.xml @ 1:fa08edee5a79 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
author iuc
date Tue, 10 Mar 2020 18:58:05 +0000
parents aafd4ef10b13
children 3e72f7176d0a
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0:aafd4ef10b13 1:fa08edee5a79
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 @BINARY@ 9 @BINARY@
10 10
11 --matrix $matrix_mcooler 11 --matrix $matrix_scooler
12 --clusters $clusters 12 --clusters $clusters
13 #if $chromosomes: 13 #if $chromosomes:
14 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ]) 14 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
15 --chromosomes $chromosome 15 --chromosomes $chromosome
16 #end if 16 #end if
31 31
32 && mv plot.$image_file_format plot 32 && mv plot.$image_file_format plot
33 33
34 ]]></command> 34 ]]></command>
35 <inputs> 35 <inputs>
36 <expand macro="matrix_mcooler_macro"/> 36 <expand macro="matrix_scooler_macro"/>
37 <param name='clusters' type='data' format='txt' label='Cluster file' help='Cluster file created by scHicCluster, scHicClusterCompartments, scHicClusterMinHash or scHicClusterSVL'/> 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' /> 38 <param name="maximalDistance" type="integer" value="2000000" label="Maximal distance" help='Maximal distance to consider for plotting' />
39 <conditional name="order_by_conditional"> 39 <conditional name="order_by_conditional">
40 <param name='order_by_selection' label='Order samples by' type='select'> 40 <param name='order_by_selection' label='Order samples by' type='select'>
41 <option value='svl' selected='true'>Short vs long range ratio</option> 41 <option value='svl' selected='true'>Short vs long range ratio</option>
57 <option value="pdf">pdf</option> 57 <option value="pdf">pdf</option>
58 </param> 58 </param>
59 59
60 </inputs> 60 </inputs>
61 <outputs> 61 <outputs>
62 <data name='output_plot' from_work_dir='plot' format='png' label='Plot SVL'> 62 <data name='output_plot' from_work_dir='plot' format='png' label='Cluster profile plot on ${on_string} '>
63 <change_format> 63 <change_format>
64 <when input="image_file_format" value="svg" format="svg" /> 64 <when input="image_file_format" value="svg" format="svg" />
65 <when input="image_file_format" value="pdf" format="pdf" /> 65 <when input="image_file_format" value="pdf" format="pdf" />
66 </change_format> 66 </change_format>
67 </data> 67 </data>
68 </outputs> 68 </outputs>
69 <tests> 69 <tests>
70 <test> 70 <test>
71 <param name='matrix_mcooler' value='test_matrix.mcool' /> 71 <param name='matrix_scooler' value='test_matrix.scool' />
72 <param name='clusters' value='scHicPlotClusterProfiles/cluster_kmeans.txt' /> 72 <param name='clusters' value='scHicPlotClusterProfiles/cluster_kmeans.txt' />
73 <conditional name="order_by_conditional"> 73 <conditional name="order_by_conditional">
74 <param name="order_by_selection" value="svl"/> 74 <param name="order_by_selection" value="svl"/>
75 <param name="distanceShortRange" value="2000000" /> 75 <param name="distanceShortRange" value="2000000" />
76 <param name="distanceLongRange" value="12000000" /> 76 <param name="distanceLongRange" value="12000000" />
86 <help><![CDATA[ 86 <help><![CDATA[
87 87
88 Plot cluster profiles 88 Plot cluster profiles
89 ===================== 89 =====================
90 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. 91 scHicPlotClusterProfiles plots the profile of each scHi-C interaction matrix associated to a cluster, within the cluster the matrices can be ordered either via their short vs long range ratio or by the order of the file.
92 This tool is useful as a quality control of a cluster to check if all matrices assigned to that cluster are displaying similar contacts distribution.
92 93
93 .. image:: $PATH_TO_IMAGES/clusters_svl_spectral.png 94 .. image:: $PATH_TO_IMAGES/clusters_svl_spectral.png
94 :width: 50% 95 :width: 50%
95 96
96 For more information about scHiCExplorer please consider our documentation on readthedocs.io_ 97 For more information about scHiCExplorer please consider our documentation on readthedocs.io_