Mercurial > repos > bgruening > deeptools_plot_enrichment

comparison plotEnrichment.xml @ 0:4b88c90b6f6e draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
author bgruening
date Tue, 20 Sep 2016 03:01:15 -0400
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children 8980933fd546
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-1:000000000000 0:4b88c90b6f6e
1 <tool id="deeptools_plot_enrichment" name="plotEnrichment" version="@WRAPPER_VERSION@.0">
2 <description>plots read/fragment coverage over sets of regions</description>
3 <macros>
4 <token name="@BINARY@">plotEnrichment</token>
5 <import>deepTools_macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command>
9 <![CDATA[
10
11 @multiple_input_bams@
12 @BINARY@
13 @THREADS@
14
15 --plotFile '$outFileName'
16
17 --bamfiles #echo " ".join($files)#
18 --labels #echo " ".join($labels)#
19
20 @multiple_bed@
21
22 #if $outRawCounts:
23 --outRawCounts "$outFileRawCounts"
24 #end if
25
26 --plotFileFormat "$outFileFormat"
27
28 #if str($region).strip() != "":
29 --region '$region'
30 #end if
31
32 #if $advancedOpt.showAdvancedOpt == "yes"
33 #if $advancedOpt.labels and str($advancedOpt.labels).strip() != "":
34 --labels $advancedOpt.labels
35 #end if
36
37 #if $advancedOpt.regionLabels and str($advancedOpt.regionLabels).strip() != "":
38 --regionLabels $advancedOpt.regionLabels
39 #end if
40
41 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
42 --plotTitle '$advancedOpt.plotTitle'
43 #end if
44
45 $advancedOpt.perSample
46
47 $advancedOpt.variableScales
48
49 $advancedOpt.perSample
50
51 $advancedOpt.variableScales
52
53 --plotWidth '$advancedOpt.plotWidth'
54
55 --plotHeight '$advancedOpt.plotHeight'
56
57 #if str($advancedOpt.colors).strip() != "":
58 --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
59 #end if
60
61 --numPlotsPerRow '$advancedOpt.numPlotsPerRow'
62
63 --alpha '$advancedOpt.alpha'
64
65 @ADVANCED_OPTS_READ_PROCESSING@
66
67 @blacklist@
68
69 $advancedOpt.keepExons
70
71 #end if
72 ]]>
73 </command>
74
75 <inputs>
76 <expand macro="multiple_input_bams" />
77 <expand macro="multiple_bed" />
78
79 <expand macro="region_limit_operation" />
80 <expand macro="input_image_file_format" />
81
82 <expand macro="advancedOpt_scaffold">
83 <param argument="--plotHeight" type="integer" value="20" min="3"
84 label="Plot height"
85 help="Height in cm. The default for the plot height is 20 centimeters. The minimum value is 3 cm." />
86
87 <param argument="--plotWidth" type="integer" value="20" min="1"
88 label="Plot width"
89 help="Width in cm. The default value is 20 centimeters. The minimum value is 1 cm." />
90
91 <param argument="--labels" type="text" size="30"
92 label="Labels for the samples (each BAM file) plotted"
93 help="The default is to use the file name of the sample. The sample labels should be separated by
94 spaces and quoted if a label itself contains a space, e.g., label-1 &quot;label 2&quot;">
95 <sanitizer>
96 <valid initial="string.printable" />
97 </sanitizer>
98 </param>
99
100 <param argument="--regionLabels" type="text" size="30"
101 label="Labels for the features"
102 help="For BED files, this sets the label for all entries in each file.
103 For GTF files this is ignored." />
104
105 <expand macro="plotTitle" />
106
107 <param argument="--alpha" type="float" value="0.9" min="0.0" max="1.0"
108 label="Alpha channel"
109 help="The alpha channel value (between 0 and 1). A value of 0 is transparent. Default: 0.9" />
110
111 <param argument="--colors" type="text" value="" size="40"
112 label="List of colors to use for the plotted bars"
113 help="Color names and html hex strings (e.g. #eeff22) are accepted.
114 The color names should be separated by spaces. (--colors red blue green)">
115 <validator type="expression"
116 message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
117 </param>
118
119 <param argument="--perSample" type="boolean" truevalue="--perSample" falsevalue=""
120 label="Create one plot per-sample"
121 help="Plot per-sample, rather than per-feature." />
122
123 <param argument="--variableScales" type="boolean" truevalue="--variableScales" falsevalue=""
124 label="Allow variable scales"
125 help="By default, the y-axis always goes from 0 to 100. If this option is selected, then the maximum value will vary with the dataset." />
126
127 <param argument="--numPlotsPerRow" type="integer" value="4" min="1"
128 label="Number of plots/row"
129 help="" />
130
131 <expand macro="read_processing_options" />
132
133 <param argument="--keepExons" type="boolean" truevalue="--keepExons" falsevalue=""
134 label="Include BED12 exons"
135 help="Only for BED12 files, include columns 10-12 rather than just 2 and 3." />
136
137 <expand macro="blacklist" />
138
139 </expand>
140
141 <param argument="--outRawCounts" type="boolean" label="Save percentages to a file" help=""/>
142
143 </inputs>
144 <outputs>
145 <expand macro="output_image_file_format_not_nested" />
146 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: percentages">
147 <filter>outRawCounts is True</filter>
148 </data>
149 </outputs>
150 <tests>
151 <test>
152 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
153 <param name="BED" value="multiBamSummary_regions.bed,multiBamSummary_regions.bed" ftype="bed" />
154 <param name="outRawCounts" value="true" />
155 <param name="showAdvancedOpt" value="yes" />
156 <param name="minMappingQuality" value="0" />
157 <param name="regionLabels" value="up down" />
158 <output name="outFileName" file="plotEnrichment_output.png" ftype="png" compare="sim_size" delta="1000" />
159 <output name="outFileRawCounts" file="plotEnrichment_output.txt" ftype="tabular" />
160 </test>
161 </tests>
162
163 <help>
164 <![CDATA[
165
166 What it does
167 -------------
168
169 This tool determines read/fragment coverage of regions. The regions (e.g., exons, genes or peaks) can be specified in one or more BED or GTF files. For GTF files, the feature type is taken from column 3. For BED files, the file name is used. For BED files, the feature labels can be changed.
170
171 Output
172 --------
173
174 The output file is a plot in the format specified. A table of the percentages can also be created.
175
176 .. image:: $PATH_TO_IMAGES/plotEnrichment_output.png
177 :width: 600
178 :height: 600
179
180 -----
181
182 @REFERENCES@
183 ]]>
184 </help>
185 <expand macro="citations" />
186 </tool>