Mercurial > repos > iuc > schicexplorer_schicplotclusterprofiles

comparison scHicPlotClusterProfiles.xml @ 3:0aca9bf1e402 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 16:50:19 +0000
parents 65f2f5d29947
children
comparison
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2:65f2f5d29947 3:0aca9bf1e402
2 <description>plot single-cell Hi-C interaction matrices cluster profiles</description> 2 <description>plot single-cell Hi-C interaction matrices cluster profiles</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">scHicPlotClusterProfiles</token> 4 <token name="@BINARY@">scHicPlotClusterProfiles</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 --clusters $clusters 13 --clusters $clusters
13 #if $chromosomes: 14 #if $chromosomes:
14 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ]) 15 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
15 --chromosomes $chromosome 16 --chromosomes $chromosome
16 #end if 17 #end if
17 18
18 #if $order_by_conditional.order_by_selection == 'orderByFile': 19 #if $order_by_conditional.order_by_selection == 'orderByFile':
19 --orderBy $order_by_conditional.order_by_selection 20 --orderBy $order_by_conditional.order_by_selection
20 #elif $order_by_conditional.order_by_selection == 'svl': 21 #elif $order_by_conditional.order_by_selection == 'svl':
21 --orderBy $order_by_conditional.order_by_selection 22 --orderBy $order_by_conditional.order_by_selection
22 --distanceShortRange $order_by_conditional.distanceShortRange 23 --distanceShortRange $order_by_conditional.distanceShortRange
23 --distanceLongRange $order_by_conditional.distanceLongRange 24 --distanceLongRange $order_by_conditional.distanceLongRange
24 #end if 25 #end if
25 #if $dpi: 26 #if $dpi:
26 --dpi $dpi 27 --dpi $dpi
27 #end if 28 #end if
28 --outFileName plot.$image_file_format 29 --outFileName plot.$image_file_format
29 30
30 --threads @THREADS@ 31 --threads @THREADS@
31 32
32 && mv plot.$image_file_format plot 33 && mv plot.$image_file_format plot
33 34
34 ]]></command> 35 ]]></command>
35 <inputs> 36 <inputs>
36 <expand macro="matrix_scooler_macro"/> 37 <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'/> 38 <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 <param name="maximalDistance" type="integer" value="2000000" label="Maximal distance" help='Maximal distance to consider for plotting' />
39 <conditional name="order_by_conditional"> 40 <conditional name="order_by_conditional">
40 <param name='order_by_selection' label='Order samples by' type='select'> 41 <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='svl' selected='true'>Short vs long range ratio</option>
42 <option value='orderByFile'>Order by file</option> 43 <option value='orderByFile'>Order by file</option>
43 </param> 44 </param>
44 <when value='svl' > 45 <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="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 <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>
48 <when value='orderByFile'> 49 <when value='orderByFile'>
49 </when> 50 </when>
50 </conditional> 51 </conditional>
51 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/> 52 <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 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
53 54
54 <param name="image_file_format" type="select" label="Image output format"> 55 <param name="image_file_format" type="select" label="Image output format">
55 <option value="png" selected="True">png</option> 56 <option value="png" selected="True">png</option>
56 <option value="svg">svg</option> 57 <option value="svg">svg</option>
57 <option value="pdf">pdf</option> 58 <option value="pdf">pdf</option>
58 </param> 59 </param>
59 60
60 </inputs> 61 </inputs>
61 <outputs> 62 <outputs>
62 <data name='output_plot' from_work_dir='plot' format='png' label='Cluster profile plot on ${on_string} '> 63 <data name='output_plot' from_work_dir='plot' format='png' label='Cluster profile plot on ${on_string} '>
63 <change_format> 64 <change_format>
64 <when input="image_file_format" value="svg" format="svg" /> 65 <when input="image_file_format" value="svg" format="svg" />
77 </conditional> 78 </conditional>
78 <param name="maximalDistance" value="50000000" /> 79 <param name="maximalDistance" value="50000000" />
79 <param name="image_file_format" value="png" /> 80 <param name="image_file_format" value="png" />
80 <param name="dpi" value="300" /> 81 <param name="dpi" value="300" />
81 82
82 <output name="output_plot" file="scHicPlotClusterProfiles/plot.png" ftype="png" compare="sim_size" delta="35000"/> 83 <output name="output_plot" file="scHicPlotClusterProfiles/plot.png" ftype="png" compare="sim_size" delta="35000"/>
83 </test> 84 </test>
84 85
85 </tests> 86 </tests>
86 <help><![CDATA[ 87 <help><![CDATA[
87 88
88 Plot cluster profiles 89 Plot cluster profiles
89 ===================== 90 =====================