Mercurial > repos > iuc > schicexplorer_schicplotconsensusmatrices

comparison scHicPlotConsensusMatrices.xml @ 3:b1f0a9b02efd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit c535679b4086f5bd1a75e9765b8708bf1bd2d81b
author iuc
date Thu, 31 Jul 2025 16:45:18 +0000
parents 95b1216e1e70
children
comparison
equal deleted inserted replaced
2:95b1216e1e70 3:b1f0a9b02efd
2 <description>plot single-cell Hi-C interaction matrices cluster consensus matrices</description> 2 <description>plot single-cell Hi-C interaction matrices cluster consensus matrices</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">scHicPlotConsensusMatrices</token> 4 <token name="@BINARY@">scHicPlotConsensusMatrices</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="xrefs"/>
7 <expand macro="requirements" /> 8 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
9 @BINARY@ 10 @BINARY@
10 11
11 --matrix $matrix_scooler 12 --matrix $matrix_scooler
12 #if $chromosomes: 13 #if $chromosomes:
13 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ]) 14 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
14 --chromosomes $chromosome 15 --chromosomes $chromosome
15 #end if 16 #end if
16 17
17 #if $colormap: 18 #if $colormap:
18 --colorMap $colormap 19 --colorMap $colormap
19 #end if 20 #end if
20 #if $dpi: 21 #if $dpi:
21 --dpi $dpi 22 --dpi $dpi
22 #end if 23 #end if
23 --outFileName plot.$image_file_format 24 --outFileName plot.$image_file_format
24 25
25 --threads @THREADS@ 26 --threads @THREADS@
26 27
27 && mv plot.$image_file_format plot 28 && mv plot.$image_file_format plot
30 <inputs> 31 <inputs>
31 <expand macro="matrix_scooler_macro"/> 32 <expand macro="matrix_scooler_macro"/>
32 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/> 33 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
33 <expand macro="colormap" /> 34 <expand macro="colormap" />
34 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/> 35 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
35 36
36 <param name="image_file_format" type="select" label="Image output format"> 37 <param name="image_file_format" type="select" label="Image output format">
37 <option value="png" selected="True">png</option> 38 <option value="png" selected="True">png</option>
38 <option value="svg">svg</option> 39 <option value="svg">svg</option>
39 <option value="pdf">pdf</option> 40 <option value="pdf">pdf</option>
40 </param> 41 </param>
41 42
42 </inputs> 43 </inputs>
43 <outputs> 44 <outputs>
44 <data name='output_plot' from_work_dir='plot' format='png' label='Consensus matrix plot on ${on_string}'> 45 <data name='output_plot' from_work_dir='plot' format='png' label='Consensus matrix plot on ${on_string}'>
45 <change_format> 46 <change_format>
46 <when input="image_file_format" value="svg" format="svg" /> 47 <when input="image_file_format" value="svg" format="svg" />
51 <tests> 52 <tests>
52 <test> 53 <test>
53 <param name='matrix_scooler' value='scHicConsensusMatrices/consensus_matrix.scool' /> 54 <param name='matrix_scooler' value='scHicConsensusMatrices/consensus_matrix.scool' />
54 <param name="image_file_format" value="png" /> 55 <param name="image_file_format" value="png" />
55 <param name="dpi" value="300" /> 56 <param name="dpi" value="300" />
56 <output name="output_plot" file="scHicPlotConsensusMatrices/plot.png" ftype="png" compare="sim_size" delta="35000"/> 57 <output name="output_plot" file="scHicPlotConsensusMatrices/plot.png" ftype="png" compare="sim_size" delta="35000"/>
57 </test> 58 </test>
58 <test> 59 <test>
59 <param name='matrix_scooler' value='scHicConsensusMatrices/consensus_matrix.scool' /> 60 <param name='matrix_scooler' value='scHicConsensusMatrices/consensus_matrix.scool' />
60 <param name="image_file_format" value="png" /> 61 <param name="image_file_format" value="png" />
61 <param name="dpi" value="300" /> 62 <param name="dpi" value="300" />
62 <param name="chromosomes" value="chr1 chr2" /> 63 <param name="chromosomes" value="chr1 chr2" />
63 64
64 <output name="output_plot" file="scHicPlotConsensusMatrices/plot_chr1_chr2.png" ftype="png" compare="sim_size" delta="35000"/> 65 <output name="output_plot" file="scHicPlotConsensusMatrices/plot_chr1_chr2.png" ftype="png" compare="sim_size" delta="35000"/>
65 </test> 66 </test>
66 67
67 </tests> 68 </tests>
68 <help><![CDATA[ 69 <help><![CDATA[
69 70
70 Plot consensus matrices 71 Plot consensus matrices
71 ======================= 72 =======================