Mercurial > repos > bgruening > hicexplorer_hiccorrelate

comparison hicCorrelate.xml @ 2:ae2d7e2dfeef 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 11:12:13 -0400
parents fe0243c46b36
children c153ea23aca8
comparison
equal deleted inserted replaced
1:ef86780a77ff 2:ae2d7e2dfeef
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicCorrelate</token> 4 <token name="@BINARY@">hicCorrelate</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> 8 <command detect_errors="exit_code"><![CDATA[
9 <![CDATA[
10 9
11 @multiple_input_matrices@ 10 @multiple_input_matrices@
12 hicCorrelate 11 hicCorrelate
13 12
14 --matrices $matrices 13 --matrices $matrices
17 #if $method and $method is not None: 16 #if $method and $method is not None:
18 --method $method 17 --method $method
19 #end if 18 #end if
20 $log1p 19 $log1p
21 20
22 #if $use_range.select_use_range == "yes_use_range" 21 #if $use_range.select_use_range == "yes_use_range":
23 --range $range_min:$range_max 22 --range $range_min:$range_max
24 #end if 23 #end if
25 24
26 #if $chromosomes: 25 #if $chromosomes:
27 --chromosomes #echo '" "'.join([ '"%s"' % $chrom for $chrom in $chromosomes ])# 26 --chromosomes #echo "' '".join([ "'%s'" % $chrom.chromosome for $chrom in $chromosomes ])#
28 #end if 27 #end if
29 28
30 --colorMap $colormap 29 --colorMap $colormap
31 30
32 --outFileNameHeatmap ./heatmap.png 31 --outFileNameHeatmap ./heatmap.png
33 --outFileNameScatter ./scatter.png 32 --outFileNameScatter ./scatter.png
34 ]]> 33 ]]>
52 <param name="range_min" type="integer" value="" min="0"/> 51 <param name="range_min" type="integer" value="" min="0"/>
53 <param name="range_max" type="integer" value="" min="0"/> 52 <param name="range_max" type="integer" value="" min="0"/>
54 </when> 53 </when>
55 </conditional> 54 </conditional>
56 <repeat name="chromosomes" title="List of chromosomes to be included in the correlation" min="0"> 55 <repeat name="chromosomes" title="List of chromosomes to be included in the correlation" min="0">
57 <param name="chromosome" type="text"/> 56 <param name="chromosome" type="text">
57 <validator type="empty_field" />
58 </param>
58 </repeat> 59 </repeat>
59 60
60 <expand macro="colormap" /> 61 <expand macro="colormap" />
61 62
62 </inputs> 63 </inputs>
78 <param name="colormap" value="jet"/> 79 <param name="colormap" value="jet"/>
79 <param name="method" value="spearman"/> 80 <param name="method" value="spearman"/>
80 <output name="outFileNameHeatmap" file="hicCorrelate_heatmap_result1.png" ftype="png" compare="sim_size"/> 81 <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 <output name="outFileNameScatter" file="hicCorrelate_scatter_result1.png" ftype="png" compare="sim_size"/>
82 </test> 83 </test>
84 <test>
85 <repeat name="input_files">
86 <param name="matrix" value="hicCorrectMatrix_result1.npz.h5" ftype="h5"/>
87 <param name="mlabel" value="first"/>
88 </repeat>
89 <repeat name="input_files">
90 <param name="matrix" value="hicCorrectMatrix_result1.npz.h5" ftype="h5" />
91 <param name="mlabel" value="second"/>
92 </repeat>
93
94 <param name="log1p" value="True"/>
95 <param name="colormap" value="jet"/>
96 <param name="method" value="spearman"/>
97 <output name="outFileNameHeatmap" file="hicCorrelate_heatmap_result1.png" ftype="png" compare="sim_size"/>
98 <output name="outFileNameScatter" file="hicCorrelate_scatter_result1.png" ftype="png" compare="sim_size"/>
99 </test>
83 </tests> 100 </tests>
84 <help><![CDATA[ 101 <help><![CDATA[
85 102
86 **What it does** 103 **What it does**
87 104
88 Computes pairwise correlations between hic matrices data. 105 Computes pairwise correlations between Hi-C matrices data.
89 The correlation is computed taking the values from each pair of matrices and discarding values that are zero in both matrices. 106 The correlation is computed taking the values from each pair of matrices and discarding values that are zero in both matrices.
90 107
91 108
92 ]]></help> 109 ]]></help>
93 <expand macro="citations" /> 110 <expand macro="citations" />