Mercurial > repos > bgruening > hicexplorer_hicplotdistvscounts

comparison hicPlotDistVsCounts.xml @ 1:f768ce54ee2a draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
author bgruening
date Mon, 03 Apr 2017 07:07:41 -0400
parents 6abd5817e0cd
children 9b664f43a90e
comparison
equal deleted inserted replaced
0:6abd5817e0cd 1:f768ce54ee2a
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>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 ln -s '$matrix' input_matrix.npz.h5 && 9 #import re
10 #set matrices_path=[]
11 #set matrices_labels=[]
12 #for $counter, $m, in enumerate($matrices):
13 #set identifier = re.sub('[^\s\w\-]', '_', str($m.element_identifier))
14 ln -f -s '${m}' '${identifier}_${counter}.npz.h5' &&
15 #silent $matrices_path.append("'%s_%s.npz.h5'" % ($identifier, $counter))
16 #silent $matrices_labels.append("'%s'" % ($identifier))
17 #end for
18
10 @BINARY@ 19 @BINARY@
11 --matrix input_matrix.npz.h5 20 --matrices #echo " ".join($matrices_path)#
21 --labels #echo " ".join($matrices_labels)#
12 $skipDiagonal 22 $skipDiagonal
13 --plotFile plot.png 23 --plotFile plot.png
14 #if $plotTitle and $plotTitle is not None: 24 #if $plotsize:
15 --plotTitle '$plotTitle' 25 --plotsize $plotsize
16 #end if 26 #end if
17 27 --maxdepth $maxdepth
18 ## special: --chromosomeExclude is optional, but if given needs at least one argument 28 $perchr
19 #set chroms = '" "'.join([ str($var.chromosomeExclude) for $var in $chromosomeExclude ]) 29 #set chroms = " ".join([ "'%s'" % $var.chromosomeExclude for $var in $chromosomeExclude ])
20 #if $chromosomeExclude: 30 #if $chromosomeExclude:
21 --chromosomeExclude $chroms 31 --chromosomeExclude $chroms
22 #end if 32 #end if
23 ]]> 33 ]]>
24 </command> 34 </command>
25 <inputs> 35 <inputs>
26 <param argument="--matrix" type="data" format="h5" label="Hi-C normalized/corrected matrix"/> 36 <param argument="--matrices" type="data" format="h5" multiple="True" label="HiC normalized (corrected) matrices"/>
27 37
28 <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" label="Exclude diagonal counts" /> 38 <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" label="Exclude diagonal counts" />
29 <param argument="--plotTitle" type="text" optional="true" label="Plot title"/> 39 <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" label="Generate plots per chromosome"
30 <repeat name="chromosomeExclude" min="0" title="Chromosomes to exclude"> 40 help="If more than one HiC matrix is given for each chromosome a new plot is made. Otherewise, a single plot with one line per chromosome is created." />
41 <param argument="--maxdepth" type="integer" value="3000000" label="Max Depth"
42 help="Maximum distance from diagonal to use. In other words, distances up to maxDeph are computed." />
43 <param argument="--plotsize" type="text" optional="True" label="Plot size"
44 help="Width and height of the plot (in inches). Default is 6*number of cols, 4 * number of rows. The maximum number of rows is 4. Example --plotsize 6 5." />
45 <repeat name="chromosomeExclude" min="0" title="Chromosomes to exclude"
46 help="This is useful for example to exclude the Y chromosome.">
31 <param argument="--chromosomeExclude" type="text" value="" /> 47 <param argument="--chromosomeExclude" type="text" value="" />
32 </repeat> 48 </repeat>
33 49
34 </inputs> 50 </inputs>
35 <outputs> 51 <outputs>
36 <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on ${on_string}"/> 52 <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on ${on_string}"/>
37 </outputs> 53 </outputs>
38 <tests> 54 <tests>
39 <test> 55 <test>
40 <param name="matrix" ftype="h5" value="small_test_matrix_50kb_res.h5"/> 56 <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5"/>
41 <param name="skipDiagonal" value="False"/> 57 <param name="skipDiagonal" value="False"/>
42 <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/> 58 <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
43 </test> 59 </test>
44 <test> 60 <test>
45 <param name="matrix" ftype="h5" value="small_test_matrix_50kb_res.h5"/> 61 <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5,small_test_matrix_50kb_res.h5"/>
46 <param name="skipDiagonal" value="False"/> 62 <param name="skipDiagonal" value="False"/>
47 <param name="plotTitle" value="Excluded chrUextra"/> 63 <param name="perchr" value="True" />
48 <repeat name="chromosomeExclude"> 64 <repeat name="chromosomeExclude">
49 <param name="chromosomeExclude" value="chrUextra"/> 65 <param name="chromosomeExclude" value="chrUextra"/>
50 </repeat> 66 </repeat>
51 <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/> 67 <repeat name="chromosomeExclude">
68 <param name="chromosomeExclude" value="chrM"/>
69 </repeat>
70 <repeat name="chromosomeExclude">
71 <param name="chromosomeExclude" value="chr3LHet"/>
72 </repeat>
73 <output name="plotFile" file="hicPlotDistVsCounts_result2.png" ftype="png" compare="sim_size" delta="15000"/>
52 </test> 74 </test>
53 </tests> 75 </tests>
54 <help><![CDATA[ 76 <help><![CDATA[
55 77
56 **What it does** 78 **What it does**
57 79
58 This program makes a distance vs. hi-c counts plot per chromosome. 80 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
82 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.
59 84
60 85
61 ]]></help> 86 ]]></help>
62 <expand macro="citations" /> 87 <expand macro="citations" />
63 </tool> 88 </tool>