Mercurial > repos > bgruening > hicexplorer_hicplotdistvscounts

comparison hicPlotDistVsCounts.xml @ 2:9b664f43a90e draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
author bgruening
date Thu, 02 Nov 2017 11:11:34 -0400
parents f768ce54ee2a
children ed96f2fd7e3f
comparison
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1:f768ce54ee2a 2:9b664f43a90e
26 #end if 26 #end if
27 --maxdepth $maxdepth 27 --maxdepth $maxdepth
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 ]]>
34 </command> 34 </command>
35 <inputs> 35 <inputs>
36 <param argument="--matrices" type="data" format="h5" multiple="True" label="HiC normalized (corrected) matrices"/> 36 <param argument="--matrices" type="data" format="h5" multiple="True" label="HiC normalized (corrected) matrices"/>
42 help="Maximum distance from diagonal to use. In other words, distances up to maxDeph are computed." /> 42 help="Maximum distance from diagonal to use. In other words, distances up to maxDeph are computed." />
43 <param argument="--plotsize" type="text" optional="True" label="Plot size" 43 <param argument="--plotsize" type="text" optional="True" label="Plot size"
44 help="Width and height of the plot (in inches). Default is 6*number of cols, 4 * number of rows. The maximum number of rows is 4. Example --plotsize 6 5." /> 44 help="Width and height of the plot (in inches). Default is 6*number of cols, 4 * number of rows. The maximum number of rows is 4. Example --plotsize 6 5." />
45 <repeat name="chromosomeExclude" min="0" title="Chromosomes to exclude" 45 <repeat name="chromosomeExclude" min="0" title="Chromosomes to exclude"
46 help="This is useful for example to exclude the Y chromosome."> 46 help="This is useful for example to exclude the Y chromosome.">
47 <param argument="--chromosomeExclude" type="text" value="" /> 47 <param argument="--chromosomeExclude" type="text" value="" >
48 <validator type="empty_field" />
49 </param>
48 </repeat> 50 </repeat>
49 51
50 </inputs> 52 </inputs>
51 <outputs> 53 <outputs>
52 <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on ${on_string}"/> 54 <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on ${on_string}"/>
68 <param name="chromosomeExclude" value="chrM"/> 70 <param name="chromosomeExclude" value="chrM"/>
69 </repeat> 71 </repeat>
70 <repeat name="chromosomeExclude"> 72 <repeat name="chromosomeExclude">
71 <param name="chromosomeExclude" value="chr3LHet"/> 73 <param name="chromosomeExclude" value="chr3LHet"/>
72 </repeat> 74 </repeat>
73 <output name="plotFile" file="hicPlotDistVsCounts_result2.png" ftype="png" compare="sim_size" delta="15000"/> 75 <output name="plotFile" file="hicPlotDistVsCounts_result2.png" ftype="png" compare="sim_size" delta="40000"/>
74 </test> 76 </test>
75 </tests> 77 </tests>
76 <help><![CDATA[ 78 <help><![CDATA[
77 79
78 **What it does** 80 **What it does**
79 81
80 This program makes a distance vs. hi-c counts plots. It can use several matrix files to compare 82 This program makes a distance vs. Hi-C counts plots. It can use several matrix files to compare
81 them. If the `--perchr` option is given, each chromosome is plotted independently. In the case 83 them. If the `--perchr` option is given, each chromosome is plotted independently. In the case
82 of more than one matrix, multiple plots are created, one per chromosome. When plotting multiple 84 of more than one matrix, multiple plots are created, one per chromosome. When plotting multiple
83 matrices denser matrices are scaled down to match the sum of the smaller matrix. 85 matrices denser matrices are scaled down to match the sum of the smaller matrix.
84 86
85 87