Mercurial > repos > bgruening > hicexplorer_hicplotdistvscounts

comparison hicPlotDistVsCounts.xml @ 11:4a3ccb7d4fc9 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit fd5d2211338239af6c577d66aeee3bb275c9b15b
author iuc
date Wed, 02 May 2018 16:48:34 -0400
parents b6fbf07de5af
children 1beec69e6111
comparison
equal deleted inserted replaced
10:b6fbf07de5af 11:4a3ccb7d4fc9
1 <tool id="hicexplorer_hicplotdistvscounts" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hicplotdistvscounts" name="@BINARY@" version="@WRAPPER_VERSION@.1">
2 <description>compute distance vs Hi-C counts plot per chromosome</description> 2 <description>compute distance vs Hi-C counts plot per chromosome</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicPlotDistVsCounts</token> 4 <token name="@BINARY@">hicPlotDistVsCounts</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
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
34 #if $outFileData_Boolean:
35 $outFileData_Boolean ./outFileData
36 #end if
33 ]]> 37 ]]>
34 </command> 38 </command>
35 <inputs> 39 <inputs>
36 <param argument="--matrices" type="data" format="h5,cool" multiple="True" label="Hi-C corrected matrices"/> 40 <param argument="--matrices" type="data" format="h5,cool" multiple="True" label="Hi-C corrected matrices"/>
37 41
47 help="This is useful for example to exclude the Y chromosome or to reduce the analysis to only a few chromosomes."> 51 help="This is useful for example to exclude the Y chromosome or to reduce the analysis to only a few chromosomes.">
48 <param argument="--chromosomeExclude" type="text" value="" > 52 <param argument="--chromosomeExclude" type="text" value="" >
49 <validator type="empty_field" /> 53 <validator type="empty_field" />
50 </param> 54 </param>
51 </repeat> 55 </repeat>
56 <param name='outFileData_Boolean' type='boolean' truevalue='--outFileData' falsevalue="" checked="false" label="Save data underlying the plots as BAM"
57 help="A bam file containing all data underlying the plots is saved on this file."/>
52 </inputs> 58 </inputs>
53 <outputs> 59 <outputs>
54 <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on [${on_string}]: Plot"/> 60 <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on [${on_string}]: Plot"/>
61 <data name="outFileData" from_work_dir="outFileData" format="txt" label="${tool.name} data file on ${on_string}">
62 <filter>outFileData_Boolean</filter>
63 </data>
55 </outputs> 64 </outputs>
56 <tests> 65 <tests>
57 <test> 66 <test>
58 <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5"/> 67 <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5"/>
59 <param name="skipDiagonal" value="False"/> 68 <param name="skipDiagonal" value="False"/>
60 <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"/>
70 </test>
71 <test>
72 <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5"/>
73 <param name="skipDiagonal" value="False"/>
74 <param name='outFileData_Boolean' value='True'/>
75 <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
76 <output name="outFileData" file="distVsCounts.txt" ftype="txt" compare="sim_size" delta='600'/>
61 </test> 77 </test>
62 <test> 78 <test>
63 <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5,small_test_matrix_50kb_res.h5"/> 79 <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5,small_test_matrix_50kb_res.h5"/>
64 <param name="skipDiagonal" value="False"/> 80 <param name="skipDiagonal" value="False"/>
65 <param name="perchr" value="True" /> 81 <param name="perchr" value="True" />