Mercurial > repos > iuc > schicexplorer_schicplotconsensusmatrices

comparison scHicPlotConsensusMatrices.xml @ 1:259899fbb6ae 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 15:09:29 -0400
parents 1a1e085c352e
children 95b1216e1e70
comparison
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0:1a1e085c352e 1:259899fbb6ae
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 #if $chromosomes: 12 #if $chromosomes:
13 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ]) 13 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
14 --chromosomes $chromosome 14 --chromosomes $chromosome
15 #end if 15 #end if
16 16
26 26
27 && mv plot.$image_file_format plot 27 && mv plot.$image_file_format plot
28 28
29 ]]></command> 29 ]]></command>
30 <inputs> 30 <inputs>
31 <expand macro="matrix_mcooler_macro"/> 31 <expand macro="matrix_scooler_macro"/>
32 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/> 32 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
33 <expand macro="colormap" /> 33 <expand macro="colormap" />
34 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/> 34 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
35 35
36 <param name="image_file_format" type="select" label="Image output format"> 36 <param name="image_file_format" type="select" label="Image output format">
39 <option value="pdf">pdf</option> 39 <option value="pdf">pdf</option>
40 </param> 40 </param>
41 41
42 </inputs> 42 </inputs>
43 <outputs> 43 <outputs>
44 <data name='output_plot' from_work_dir='plot' format='png' label='Plot SVL'> 44 <data name='output_plot' from_work_dir='plot' format='png' label='Consensus matrix plot on ${on_string}'>
45 <change_format> 45 <change_format>
46 <when input="image_file_format" value="svg" format="svg" /> 46 <when input="image_file_format" value="svg" format="svg" />
47 <when input="image_file_format" value="pdf" format="pdf" /> 47 <when input="image_file_format" value="pdf" format="pdf" />
48 </change_format> 48 </change_format>
49 </data> 49 </data>
50 </outputs> 50 </outputs>
51 <tests> 51 <tests>
52 <test> 52 <test>
53 <param name='matrix_mcooler' value='scHicConsensusMatrices/consensus_matrix.mcool' /> 53 <param name='matrix_scooler' value='scHicConsensusMatrices/consensus_matrix.scool' />
54 <param name="image_file_format" value="png" /> 54 <param name="image_file_format" value="png" />
55 <param name="dpi" value="300" /> 55 <param name="dpi" value="300" />
56 <output name="output_plot" file="scHicPlotConsensusMatrices/plot.png" ftype="png" compare="sim_size" delta="35000"/> 56 <output name="output_plot" file="scHicPlotConsensusMatrices/plot.png" ftype="png" compare="sim_size" delta="35000"/>
57 </test> 57 </test>
58 <test> 58 <test>
59 <param name='matrix_mcooler' value='scHicConsensusMatrices/consensus_matrix.mcool' /> 59 <param name='matrix_scooler' value='scHicConsensusMatrices/consensus_matrix.scool' />
60 <param name="image_file_format" value="png" /> 60 <param name="image_file_format" value="png" />
61 <param name="dpi" value="300" /> 61 <param name="dpi" value="300" />
62 <param name="chromosomes" value="chr1 chr2" /> 62 <param name="chromosomes" value="chr1 chr2" />
63 63
64 <output name="output_plot" file="scHicPlotConsensusMatrices/plot_chr1_chr2.png" ftype="png" compare="sim_size" delta="35000"/> 64 <output name="output_plot" file="scHicPlotConsensusMatrices/plot_chr1_chr2.png" ftype="png" compare="sim_size" delta="35000"/>
68 <help><![CDATA[ 68 <help><![CDATA[
69 69
70 Plot consensus matrices 70 Plot consensus matrices
71 ======================= 71 =======================
72 72
73 scHicPlotConsensusMatrices plots the consensus (average) matrix of a cluster. 73 scHicPlotConsensusMatrices plots the consensus (average) matrix of a cluster. This tool is useful to compare the single cell clusters.
74 74
75 .. image:: $PATH_TO_IMAGES/consensus_svl_spectral.png 75 .. image:: $PATH_TO_IMAGES/consensus_svl_spectral.png
76 :width: 50% 76 :width: 50%
77 77
78 For more information about scHiCExplorer please consider our documentation on readthedocs.io_ 78 For more information about scHiCExplorer please consider our documentation on readthedocs.io_