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comparison wiggle_correlation_in_bed.xml @ 0:3d1097835b2f draft default tip

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Imported from capsule None
author jjohnson
date Mon, 22 Sep 2014 11:54:41 -0400
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1 <tool name="Multiple wiggle files correlation in given regions" id="correlation_dataset_bed" version="0.1.0">
2 <description>Calculate the correlation coefficient on the genome scale using one bed file and multiple wiggle / bigwig files</description>
3 <macros>
4 <import>corr_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>
8 #if $maxscore and $minscore and ( $minscore > $maxscore ):
9 echo "maxscore has to be greater than minscore!"
10 exit 1;
11 #end if
12 #if $wfile1.extension == "wig"
13 wig_correlation_in_bed_file.py -d $wfile1.metadata.dbkey -m $method
14 #elif $wfile1.extension == "bigwig"
15 bigwig_correlation_in_bed_file.py
16 #end if
17 #if $maxscore.value
18 --max-score $maxscore
19 #end if
20 #if $minscore.value
21 --min-score $minscore
22 #end if
23 $heatmap -z $size -f PDF -r tmp.r
24 -b $bfile
25 -w $wfile1 -l '$wlabel1' -w $wfile2 -l '$wlabel2'
26 #for $m in $more
27 -w $m.wig -l "$m.label"
28 #end for
29 &amp;> $log &amp;&amp;
30 cp tmp.r $rscript &amp;&amp;
31 #if $imagetype.__str__ == "PNG":
32 convert tmp.r.pdf tmp.r.png &amp;&amp;
33 cp tmp.r.png $output
34 #else
35 cp tmp.r.pdf $output
36 #end if
37 </command>
38 <inputs>
39 <param name="bfile" type="data" format="bed" label="BED file(100,000 lines max)" >
40 <validator type="unspecified_build" />
41 </param>
42 <param format="wig,bigwig" name="wfile1" type="data" label="Wiggle / bigwig file 1">
43 <validator type="unspecified_build" />
44 </param>
45 <param name="wlabel1" type="text" label="Wiggle / bigwig label 1" optional="false">
46 <validator type="length" message="must be between 1 and 255 characters" min="1" max="255"/>
47 </param>
48 <param format="wig,bigwig" name="wfile2" type="data" label="Wiggle / bigwig file 2">
49 <validator type="unspecified_build" />
50 </param>
51 <param name="wlabel2" type="text" label="Wiggle / bigwig label 2" optional="false">
52 <validator type="length" message="must be between 1 and 255 characters" min="1" max="255"/>
53 </param>
54 <repeat name="more" title="wiggle / bigwig file">
55 <param format="wig,bigwig" name="wig" type="data" label="Select another wiggle / bigwig file"/>
56 <param name="label" type="text" label="Wiggle / bigwig label" optional="false">
57 <validator type="length" message="must be between 1 and 255 characters" min="1" max="255"/>
58 </param>
59 </repeat>
60 <param name="method" type="select" label="method:" help="method to process the paired two sets of data in the sampling step." >
61 <option value="mean" selected="true">mean</option>
62 <option value="median">median</option>
63 <option value="sample">sample</option>
64 </param>
65 <param name="maxscore" type="float" label="Max Score" help="Maximum score in the calculation (optional)" value="10000" optional="true"/>
66 <param name="minscore" type="float" label="Min Score" help="Minimum score in the calculation (optional)" value="-10000" optional="true"/>
67 <param name="heatmap" type="boolean" label="Draw Heatmap instead?" checked="no"
68 truevalue="-H" falsevalue=" " />
69 <param name="size" type="integer" label="image Size" value="10" help="Image size in inch. It must be ge 5 and le 20. Default: 10">
70 <validator type="in_range" max="20" min="5" message="image Size is out of range, image Size has to be between 5 to 20" />
71 </param>
72 <param type="select" name="imagetype" display="radio" label="Image Type">
73 <option value="PDF">PDF format</option>
74 <option value="PNG">PNG format</option>
75 </param>
76 </inputs>
77 <outputs>
78 <data format="png" name="output">
79 <change_format>
80 <when input="imagetype" value="PDF" format="pdf" />
81 </change_format>
82 </data>
83 <data format="txt" name="log" label="correlation job log" />
84 <data format="txt" name="rscript" label="correlation job rscript" />
85 </outputs>
86 <expand macro="stdio"/>
87 <tests>
88 <test>
89 <param name="bfile" value="peaks.bed" />
90 <param name="wfile1" value="control.wig" />
91 <param name="wlabel1" value="control" />
92 <param name="wfile2" value="treatment.wig" />
93 <param name="wlabel2" value="treatment" />
94 <param name="step" value="100" />
95 <param name="method" value="mean" />
96 <param name="maxscore" value="10000" />
97 <param name="minscore" value="-10000" />
98 <param name="size" value="10" />
99 <param name="imagetype" value="PDF" />
100 <output name="log">
101 <assert_contents>
102 <has_text_matching expression="Please check tmp.r" />
103 </assert_contents>
104 </output>
105 </test>
106 </tests>
107 <help>
108 This tool calculates the correlation coefficient values on the genome
109 scale using many scores datasets (many wiggle files) within the
110 regions given by a BED file. The tool is written by Tao Liu. It calls
111 R for plotting.
112
113 .. class:: infomark
114
115 **TIP:** This can be used to evaluate the correlation between
116 biological replicates at union peak regions.
117
118 .. class:: warningmark
119
120 **NEED IMPROVEMENT**
121
122 -----
123
124 **Parameters**
125
126 - **BED file** contains the regions to extract scores.
127 - **Wiggle file 1 and 2** are the first two wiggle files to be
128 included. These two are required.
129 - **Wiggle label 1 and 2** are the first two wiggle labels to be
130 plotted in the correlation plot.
131 - **wiggle files** click *Add new wiggle file* to add more wiggle
132 files and labels.
133 - **Genome/Assembly** Genome assembly to be used. The tool will
134 download the chromosome information from UCSC database.
135 - **Method** When scores are extracted for a region in BED file, a
136 method will be applied to calculate a value to represent this
137 region. Options are *median* to use the median value or *mean* to
138 use the average value.
139 - **Max Score** is the maximum score in the calculation. It's
140 optional.
141 - **Min Score** is the minimum score in the calculation. It's
142 optional.
143
144 -----
145
146 **Outputs**
147
148 - **PNG file** is the correlation plot
149 - **LOG file** for job log. If you see errors, please attached this in
150 the bug report
151
152 </help>
153
154 </tool>