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comparison bigwigCorrelate.xml @ 30:5231f398d784 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
author bgruening
date Tue, 20 Oct 2015 14:43:12 -0400
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29:3a2aab18a217 30:5231f398d784
1 <tool id="deeptools_bigwigCorrelate" name="bigwigCorrelate" version="@WRAPPER_VERSION@.0">
2 <description>correlates pairs of BigWig files</description>
3 <macros>
4 <token name="@BINARY@">bigwigCorrelate</token>
5 <import>deepTools_macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command>
9 <![CDATA[
10 #set files=[]
11 #set labels=[]
12
13 @multiple_input_bigwigs@
14
15 bigwigCorrelate
16
17 $mode.modeOpt
18
19 @THREADS@
20
21 --bwfiles '#echo "' '".join($files)#'
22 --labels '#echo "' '".join($labels)#'
23 #if $filterPercentile:
24 --filterPercentile $filterPercentile
25 #end if
26 --corMethod $corMethod
27
28 --plotFile $outFileName
29
30 #if $output.showOutputSettings == "yes"
31 --outRawCounts '$outFileRawCounts'
32 --outFileCorMatrix '$outFileCorMatrix'
33 --plotFileFormat '$output.outFileFormat'
34 #else:
35 --plotFileFormat 'png'
36 #end if
37
38 #if $mode.modeOpt == "bins":
39 --binSize '$mode.binSize'
40 #else:
41 --BED $mode.region_file
42 #end if
43
44 #### options available in both modes
45 #if str($region.value) != '':
46 --region '$region'
47 #end if
48
49 #if $advancedOpt.showAdvancedOpt == "yes":
50
51 $advancedOpt.includeZeros
52
53 #if $advancedOpt.zMin:
54 --zMin $advancedOpt.zMin
55 #end if
56 #if $advancedOpt.zMax:
57 --zMax $advancedOpt.zMax
58 #end if
59 --colorMap '$advancedOpt.colorMap'
60
61 #if $plotTitle and str($plotTitle).strip() != "":
62 --plotTitle '$plotTitle'
63 #end if
64 $plotNumbers
65
66 #end if
67 ]]>
68 </command>
69
70 <inputs>
71 <expand macro="multiple_input_bigwigs" />
72
73 <param name="filterPercentile" type="float" optional="True" value="" min="0.0" max="100.0"
74 label="Percentile used to filter out extreme outliers"
75 help ="If not specified, it is automatically set to 99.9 in analyses
76 using Pearson correlation! This means that values
77 above that threshold, which consistently occur in all
78 datasets, will not be taken into account for the
79 correlation analysis. This behavior can be overridden
80 by a user specified value from within the 0.0 to 100.0
81 range. (--filterPercentile)"/>
82
83 <param name="corMethod" type="select" label="Correlation method" help="(--corMethod)">
84 <option value="spearman" selected="True">Spearman</option>
85 <option value="pearson">Pearson</option>
86 </param>
87
88 <conditional name="mode">
89 <param name="modeOpt" type="select" label="Choose computation mode"
90 help="In the bins mode, the correlation is computed based on equal length bins.
91 In the BED file mode, as list of genomic regions in BED format has to be given.
92 For each region in the BED file the number of overlapping reads is counted in
93 each of the BAM files. Then the correlation is computed.">
94 <option value="bins" selected="true">Bins</option>
95 <option value="BED-file">Limit correlation to certain regions (BED file)</option>
96 </param>
97 <when value="bins">
98 <param name="binSize" type="integer" value="10000" min="1"
99 label="Bin size in bp"
100 help="Length in base pairs for a window used to sample the genome. (--binSize)"/>
101 </when>
102 <when value="BED-file">
103 <param name="region_file" type="data" format="bed"
104 label="Region file in BED format"
105 help="Correlation is computed for the number of reads that overlap such regions."/>
106 </when>
107 </conditional>
108
109 <expand macro="bigwigCorrelate_mode_actions" />
110 <conditional name="output">
111 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
112 <option value="no" selected="true">no</option>
113 <option value="yes">yes</option>
114 </param>
115 <when value="no" />
116 <when value="yes">
117 <expand macro="input_image_file_format"/>
118 <param name="saveRawCounts" type="boolean" label="Save the bin counts"/>
119 <param name="saveCorMatrix" type="boolean" label="Save the correlation matrix"/>
120 </when>
121 </conditional>
122
123 </inputs>
124 <outputs>
125 <expand macro="output_image_file_format" />
126 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
127 <filter>
128 ((
129 output['showOutputSettings'] == 'yes' and
130 output['saveRawCounts'] is True
131 ))
132 </filter>
133 </data>
134 <data format="tabular" name="outFileCorMatrix" label="${tool.name} on ${on_string}: correlation matrix">
135 <filter>
136 ((
137 output['showOutputSettings'] == 'yes' and
138 output['saveCorMatrix'] is True
139 ))
140 </filter>
141 </data>
142 </outputs>
143 <tests>
144 <test>
145 <repeat name="input_files">
146 <param name="bigwigfile" value="test.bw" ftype="bigwig" />
147 <param name="label" value="first bigwig file" />
148 </repeat>
149 <repeat name="input_files">
150 <param name="bigwigfile" value="test.bw" ftype="bigwig" />
151 <param name="label" value="second bigwig file" />
152 </repeat>
153 <param name="modeOpt" value="bins" />
154 <param name="binSize" value="10" />
155 <param name="showOutputSettings" value="no" />
156 <param name="corMethod" value="spearman" />
157 <output name="outFileName" file="bigwigCorrelate_result1.png" ftype="png" compare="sim_size" />
158 </test>
159 </tests>
160 <help>
161 <![CDATA[
162 **What it does**
163
164 bigwigCorrelate computes the overall similarity between two or more bigWig
165 files based on coverage means of genomic regions. The correlation analysis
166 is performed for the entire genome by running the program in 'bins' mode,
167 or for certain regions only in 'BED-file' mode. Pearson or Spearman analyses
168 are available to compute correlation coefficients. Results are saved to a
169 heat map file. Further output files are optional.
170
171
172 **Output files**:
173
174 - **diagnostic plot**: clustered heatmap displaying the values for each pair-wise correlation
175 - data matrix (optional): if you want to plot the correlation values using a different program, e.g. R, this matrix can be used
176
177
178 -----
179
180 @REFERENCES@
181 ]]>
182 </help>
183 <expand macro="citations" />
184 </tool>