Mercurial > repos > iuc > schicexplorer_schicplotconsensusmatrices

comparison scHicPlotConsensusMatrices.xml @ 0:1a1e085c352e 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 16:02:12 -0500
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-1:000000000000 0:1a1e085c352e
1 <tool id="schicexplorer_schicplotconsensusmatrices" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>plot single-cell Hi-C interaction matrices cluster consensus matrices</description>
3 <macros>
4 <token name="@BINARY@">scHicPlotConsensusMatrices</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 #if $chromosomes:
13 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
14 --chromosomes $chromosome
15 #end if
16
17 #if $colormap:
18 --colorMap $colormap
19 #end if
20 #if $dpi:
21 --dpi $dpi
22 #end if
23 --outFileName plot.$image_file_format
24
25 --threads @THREADS@
26
27 && mv plot.$image_file_format plot
28
29 ]]></command>
30 <inputs>
31 <expand macro="matrix_mcooler_macro"/>
32 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
33 <expand macro="colormap" />
34 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
35
36 <param name="image_file_format" type="select" label="Image output format">
37 <option value="png" selected="True">png</option>
38 <option value="svg">svg</option>
39 <option value="pdf">pdf</option>
40 </param>
41
42 </inputs>
43 <outputs>
44 <data name='output_plot' from_work_dir='plot' format='png' label='Plot SVL'>
45 <change_format>
46 <when input="image_file_format" value="svg" format="svg" />
47 <when input="image_file_format" value="pdf" format="pdf" />
48 </change_format>
49 </data>
50 </outputs>
51 <tests>
52 <test>
53 <param name='matrix_mcooler' value='scHicConsensusMatrices/consensus_matrix.mcool' />
54 <param name="image_file_format" value="png" />
55 <param name="dpi" value="300" />
56 <output name="output_plot" file="scHicPlotConsensusMatrices/plot.png" ftype="png" compare="sim_size" delta="35000"/>
57 </test>
58 <test>
59 <param name='matrix_mcooler' value='scHicConsensusMatrices/consensus_matrix.mcool' />
60 <param name="image_file_format" value="png" />
61 <param name="dpi" value="300" />
62 <param name="chromosomes" value="chr1 chr2" />
63
64 <output name="output_plot" file="scHicPlotConsensusMatrices/plot_chr1_chr2.png" ftype="png" compare="sim_size" delta="35000"/>
65 </test>
66
67 </tests>
68 <help><![CDATA[
69
70 Plot consensus matrices
71 =======================
72
73 scHicPlotConsensusMatrices plots the consensus (average) matrix of a cluster.
74
75 .. image:: $PATH_TO_IMAGES/consensus_svl_spectral.png
76 :width: 50%
77
78 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
79
80 .. _readthedocs.io: http://schicexplorer.readthedocs.io/
81 ]]></help>
82 <expand macro="citations" />
83
84 </tool>