Mercurial > repos > bgruening > hicexplorer_hiccorrelate

comparison hicCorrelate.xml @ 0:fe0243c46b36 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
author bgruening
date Thu, 30 Mar 2017 02:50:08 -0400
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-1:000000000000 0:fe0243c46b36
1 <tool id="hicexplorer_hiccorrelate" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>Computes pairwise correlations between hic matrices data</description>
3 <macros>
4 <token name="@BINARY@">hicCorrelate</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command>
9 <![CDATA[
10
11 @multiple_input_matrices@
12 hicCorrelate
13
14 --matrices $matrices
15 --labels $mlabels
16
17 #if $method and $method is not None:
18 --method $method
19 #end if
20 $log1p
21
22 #if $use_range.select_use_range == "yes_use_range"
23 --range $range_min:$range_max
24 #end if
25
26 #if $chromosomes:
27 --chromosomes #echo '" "'.join([ '"%s"' % $chrom for $chrom in $chromosomes ])#
28 #end if
29
30 --colorMap $colormap
31
32 --outFileNameHeatmap ./heatmap.png
33 --outFileNameScatter ./scatter.png
34 ]]>
35 </command>
36 <inputs>
37 <expand macro="multiple_input_matrices" />
38
39 <param name="method" type="select" label="Correlation method to use" argument="--method" >
40 <option value="spearman">Spearman</option>
41 <option selected="true" value="pearson">Pearson</option>
42 </param>
43 <param name="log1p" type="boolean" argument="--log1p" truevalue="--log1p" falsevalue=""
44 label="Use the log1p of the matrix values" help="(--log1p)" />
45 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
46 <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range">
47 <option value="no_use_range">No restriction</option>
48 <option value="yes_use_range">Only consider counts within a range</option>
49 </param>
50 <when value="no_use_range"/>
51 <when value="yes_use_range">
52 <param name="range_min" type="integer" value="" min="0"/>
53 <param name="range_max" type="integer" value="" min="0"/>
54 </when>
55 </conditional>
56 <repeat name="chromosomes" title="List of chromosomes to be included in the correlation" min="0">
57 <param name="chromosome" type="text"/>
58 </repeat>
59
60 <expand macro="colormap" />
61
62 </inputs>
63 <outputs> <!-- not sure if argument is specifiable for output yet, would be cool if so -->
64 <data name="outFileNameHeatmap" from_work_dir="heatmap.png" format="png" />
65 <data name="outFileNameScatter" from_work_dir="scatter.png" format="png" />
66 </outputs>
67 <tests>
68 <test>
69 <repeat name="input_files">
70 <param name="matrix" value="hicCorrectMatrix_result1.npz.h5" ftype="h5"/>
71 <param name="mlabel" value="first"/>
72 </repeat>
73 <repeat name="input_files">
74 <param name="matrix" value="hicCorrectMatrix_result1.npz.h5" ftype="h5" />
75 <param name="mlabel" value="second"/>
76 </repeat>
77 <param name="log1p" value="True"/>
78 <param name="colormap" value="jet"/>
79 <param name="method" value="spearman"/>
80 <output name="outFileNameHeatmap" file="hicCorrelate_heatmap_result1.png" ftype="png" compare="sim_size"/>
81 <output name="outFileNameScatter" file="hicCorrelate_scatter_result1.png" ftype="png" compare="sim_size"/>
82 </test>
83 </tests>
84 <help><![CDATA[
85
86 **What it does**
87
88 Computes pairwise correlations between hic matrices data.
89 The correlation is computed taking the values from each pair of matrices and discarding values that are zero in both matrices.
90
91
92 ]]></help>
93 <expand macro="citations" />
94 </tool>