Mercurial > repos > bgruening > hicexplorer_hiccorrelate

comparison hicCorrelate.xml @ 7:602a0c6f4bb0 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
author bgruening
date Wed, 07 Mar 2018 03:39:03 -0500
parents c1f9dc3b2238
children 2d8543aeeb65
comparison
equal deleted inserted replaced
6:8187f841afea 7:602a0c6f4bb0
16 #if $method and $method is not None: 16 #if $method and $method is not None:
17 --method $method 17 --method $method
18 #end if 18 #end if
19 $log1p 19 $log1p
20 20
21 #if $use_range.select_use_range == "yes_use_range": 21 @USE_RANGE@
22 --range $range_min:$range_max
23 #end if
24 22
25 #if $chromosomes: 23 #if $chromosomes:
26 --chromosomes #echo "' '".join([ "'%s'" % $chrom.chromosome for $chrom in $chromosomes ])# 24 --chromosomes #echo "' '".join([ "'%s'" % $chrom.chromosome for $chrom in $chromosomes ])#
27 #end if 25 #end if
28 26
29 --colorMap $colormap 27 #if $colormap:
28 --colorMap $colormap
29 #end if
30 30
31 --outFileNameHeatmap ./heatmap.png 31 --outFileNameHeatmap ./heatmap.png
32 --outFileNameScatter ./scatter.png 32 --outFileNameScatter ./scatter.png
33 ]]> 33 ]]>
34 </command> 34 </command>
39 <option value="spearman">Spearman</option> 39 <option value="spearman">Spearman</option>
40 <option selected="true" value="pearson">Pearson</option> 40 <option selected="true" value="pearson">Pearson</option>
41 </param> 41 </param>
42 <param name="log1p" type="boolean" argument="--log1p" truevalue="--log1p" falsevalue="" 42 <param name="log1p" type="boolean" argument="--log1p" truevalue="--log1p" falsevalue=""
43 label="Use the log1p of the matrix values" help="(--log1p)" /> 43 label="Use the log1p of the matrix values" help="(--log1p)" />
44 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range --> 44
45 <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range"> 45 <expand macro="use_range" />
46 <option value="no_use_range">No restriction</option> 46
47 <option value="yes_use_range">Only consider counts within a range</option>
48 </param>
49 <when value="no_use_range"/>
50 <when value="yes_use_range">
51 <param name="range_min" type="integer" value="" min="0"/>
52 <param name="range_max" type="integer" value="" min="0"/>
53 </when>
54 </conditional>
55 <repeat name="chromosomes" title="List of chromosomes to be included in the correlation" min="0"> 47 <repeat name="chromosomes" title="List of chromosomes to be included in the correlation" min="0">
56 <param name="chromosome" type="text"> 48 <param name="chromosome" type="text">
57 <validator type="empty_field" /> 49 <validator type="empty_field" />
58 </param> 50 </param>
59 </repeat> 51 </repeat>
60
61 <expand macro="colormap" /> 52 <expand macro="colormap" />
62
63 </inputs> 53 </inputs>
64 <outputs> <!-- not sure if argument is specifiable for output yet, would be cool if so --> 54 <outputs> <!-- not sure if argument is specifiable for output yet, would be cool if so -->
65 <data name="outFileNameHeatmap" from_work_dir="heatmap.png" format="png" /> 55 <data name="outFileNameHeatmap" from_work_dir="heatmap.png" format="png" />
66 <data name="outFileNameScatter" from_work_dir="scatter.png" format="png" /> 56 <data name="outFileNameScatter" from_work_dir="scatter.png" format="png" />
67 </outputs> 57 </outputs>
88 </repeat> 78 </repeat>
89 <repeat name="input_files"> 79 <repeat name="input_files">
90 <param name="matrix" value="hicCorrectMatrix_result1.npz.h5" ftype="h5" /> 80 <param name="matrix" value="hicCorrectMatrix_result1.npz.h5" ftype="h5" />
91 <param name="mlabel" value="second"/> 81 <param name="mlabel" value="second"/>
92 </repeat> 82 </repeat>
93 83
94 <param name="log1p" value="True"/> 84 <param name="log1p" value="True"/>
95 <param name="colormap" value="jet"/> 85 <param name="colormap" value="jet"/>
96 <param name="method" value="spearman"/> 86 <param name="method" value="spearman"/>
97 <output name="outFileNameHeatmap" file="hicCorrelate_heatmap_result1.png" ftype="png" compare="sim_size"/> 87 <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"/> 88 <output name="outFileNameScatter" file="hicCorrelate_scatter_result1.png" ftype="png" compare="sim_size"/>
114 - Two contact matrices which are used for the correlation. 104 - Two contact matrices which are used for the correlation.
115 - Choice if pearson or spearman correlation should be used. 105 - Choice if pearson or spearman correlation should be used.
116 - log scale for the values 106 - log scale for the values
117 - Correlate full matrix or only specific chromosomes 107 - Correlate full matrix or only specific chromosomes
118 - Correlate only within a given range. 108 - Correlate only within a given range.
119 - colormap to use: Colormap_ 109 - colormap to use: Colormap_
120 110
121 Output 111 Output
122 ------ 112 ------
123 113
124 Pearson correlation 114 Pearson correlation