Mercurial > repos > bgruening > hicexplorer_hicplotdistvscounts

comparison hicPlotDistVsCounts.xml @ 20:6326cd29c1c3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author iuc
date Wed, 18 Oct 2023 10:16:53 +0000
parents e2971589184b
children 11f39d7f6c64
comparison
equal deleted inserted replaced
19:a4a413dcc59d 20:6326cd29c1c3
28 $perchr 28 $perchr
29 #set chroms = " ".join([ "'%s'" % $var.chromosomeExclude for $var in $chromosomeExclude ]) 29 #set chroms = " ".join([ "'%s'" % $var.chromosomeExclude for $var in $chromosomeExclude ])
30 #if $chromosomeExclude: 30 #if $chromosomeExclude:
31 --chromosomeExclude '$chroms' 31 --chromosomeExclude '$chroms'
32 #end if 32 #end if
33 33 #if $domains:
34 --domains '$domains'
35 #end if
34 #if $outFileData_Boolean: 36 #if $outFileData_Boolean:
35 $outFileData_Boolean ./outFileData 37 $outFileData_Boolean ./outFileData
36 #end if 38 #end if
37 ]]> 39 ]]>
38 </command> 40 </command>
48 <repeat name="chromosomeExclude" min="0" title="Chromosomes to exclude" help="This is useful for example to exclude the Y chromosome or to reduce the analysis to only a few chromosomes."> 50 <repeat name="chromosomeExclude" min="0" title="Chromosomes to exclude" help="This is useful for example to exclude the Y chromosome or to reduce the analysis to only a few chromosomes.">
49 <param argument="--chromosomeExclude" type="text" value=""> 51 <param argument="--chromosomeExclude" type="text" value="">
50 <validator type="empty_field" /> 52 <validator type="empty_field" />
51 </param> 53 </param>
52 </repeat> 54 </repeat>
53 <param name='outFileData_Boolean' type='boolean' truevalue='--outFileData' falsevalue="" checked="false" label="Save data underlying the plots as BAM" help="A bam file containing all data underlying the plots is saved on this file." /> 55 <param argument="--domains" type="data" format="bed" optional="True" label="Bed file with domains coordinates" help="Bed file with domains coordinates: instead of evaluating the distance vs. Hi-C counts for intra chromosomal counts, compute it for intra-domains." />
56
57 <param name="outFileData_Boolean" type="boolean" truevalue="--outFileData" falsevalue="" checked="false" label="Save data underlying the plots as BAM" help="A bam file containing all data underlying the plots is saved on this file." />
54 </inputs> 58 </inputs>
55 <outputs> 59 <outputs>
56 <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on [${on_string}]: Plot" /> 60 <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on [${on_string}]: Plot" />
57 <data name="outFileData" from_work_dir="outFileData" format="txt" label="${tool.name} data file on ${on_string}"> 61 <data name="outFileData" from_work_dir="outFileData" format="txt" label="${tool.name} data file on ${on_string}">
58 <filter>outFileData_Boolean</filter> 62 <filter>outFileData_Boolean</filter>
59 </data> 63 </data>
60 </outputs> 64 </outputs>
61 <tests> 65 <tests>
62 <test> 66 <test expect_num_outputs="1">
63 <param name="matrices" ftype="h5" value="small_test_matrix.h5" /> 67 <param name="matrices" ftype="h5" value="small_test_matrix.h5" />
64 <param name="skipDiagonal" value="False" /> 68 <param name="skipDiagonal" value="False" />
65 <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size" /> 69 <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size" />
66 </test> 70 </test>
67 <test> 71 <test expect_num_outputs="2">
68 <param name="matrices" ftype="h5" value="small_test_matrix.h5" /> 72 <param name="matrices" ftype="h5" value="small_test_matrix.h5" />
69 <param name="skipDiagonal" value="False" /> 73 <param name="skipDiagonal" value="False" />
70 <param name='outFileData_Boolean' value='True' /> 74 <param name="outFileData_Boolean" value="True" />
71 <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size" /> 75 <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size" />
72 <output name="outFileData" file="distVsCounts.txt" ftype="txt" /> 76 <output name="outFileData" file="distVsCounts.txt" ftype="txt" />
73 </test> 77 </test>
74 <test> 78 <test expect_num_outputs="1">
75 <param name="matrices" ftype="h5" value="small_test_matrix.h5,small_test_matrix.h5" /> 79 <param name="matrices" ftype="h5" value="small_test_matrix.h5,small_test_matrix.h5" />
76 <param name="skipDiagonal" value="False" /> 80 <param name="skipDiagonal" value="False" />
77 <param name="perchr" value="True" /> 81 <param name="perchr" value="True" />
78 <repeat name="chromosomeExclude"> 82 <repeat name="chromosomeExclude">
79 <param name="chromosomeExclude" value="chrUextra" /> 83 <param name="chromosomeExclude" value="chrUextra" />