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comparison bigwigCompare.xml @ 0:35c5d2a2f2fa draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
author bgruening
date Wed, 16 Dec 2015 16:36:25 -0500
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-1:000000000000 0:35c5d2a2f2fa
1 <tool id="deeptools_bigwig_compare" name="bigwigCompare" version="@WRAPPER_VERSION@.0">
2 <description>normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference</description>
3 <macros>
4 <token name="@BINARY@">bigwigCompare</token>
5 <import>deepTools_macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command>
9 <![CDATA[
10 @BINARY@
11 @THREADS@
12 --bigwig1 '$bigwigFile1'
13 --bigwig2 '$bigwigFile2'
14
15 --outFileName '$outFileName'
16 --outFileFormat '$outFileFormat'
17
18 --ratio $comparison.comparison_select
19
20 #if $comparison.comparison_select in ['ratio','log2']:
21 --pseudocount $comparison.pseudocount
22 #end if
23
24 #if str($region).strip() != '':
25 --region '$region'
26 #end if
27
28 #if $advancedOpt.showAdvancedOpt == "yes":
29
30 $advancedOpt.keepNAs
31 --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2'
32 --binSize $advancedOpt.binSize
33
34 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
35 --plotTitle '$advancedOpt.plotTitle'
36 #end if
37
38 #end if
39 ]]>
40 </command>
41 <inputs>
42 <param name="bigwigFile1" format="bigwig" type="data" label="Treatment bigwig file" />
43 <param name="bigwigFile2" format="bigwig" type="data" label="bigWig file" />
44
45 <conditional name="comparison">
46 <param name="comparison_select" type="select"
47 label="How to compare the two files"
48 help="The default is to output the log2ratio between the two samples.
49 The reciprocal ratio returns the negative of the inverse of the ratio if
50 the ratio is less than 0. The resulting values are interpreted as negative fold changes. (--ratio)">
51 <option value="log2" selected="true">compute log2 of the number of reads ratio</option>
52 <option value="ratio">compute the ratio of the number of reads</option>
53 <option value="subtract">compute difference (subtract input from treatment) of the number of reads</option>
54 <option value="add">compute the sum over all reads</option>
55 <option value="reciprocal_ratio">Computes the fold change. If the fold change is less than 1, the negative of the inverse is reported. E.g. A fold change of 10 to 5 would be reported not as 0.5 but as -2</option>
56 </param>
57 <when value="log2">
58 <expand macro="pseudocount" />
59 </when>
60 <when value="ratio">
61 <expand macro="pseudocount" />
62 </when>
63 <when value="subtract" />
64 <when value="add" />
65 <when value="reciprocal_ratio">
66 <expand macro="pseudocount" />
67 </when>
68 </conditional>
69
70 <param name="outFileFormat" type="select" label="Coverage file format">
71 <option value="bigwig" selected="true">bigwig</option>
72 <option value="bedgraph">bedgraph</option>
73 </param>
74
75 <expand macro="region_limit_operation" />
76
77 <conditional name="advancedOpt">
78 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
79 <option value="no" selected="true">no</option>
80 <option value="yes">yes</option>
81 </param>
82 <when value="no" />
83 <when value="yes">
84 <param argument="--binSize" type="integer" value="50" min="1"
85 label="Length, in base pairs, of the non-overlapping bin for averaging the score over the regions length"
86 help="Size of the bins in bp for the output of the bigwig/bedgraph file."/>
87
88 <expand macro="keepNAs" />
89 <expand macro="scaleFactor" />
90 <expand macro="plotTitle" />
91 </when>
92 </conditional>
93 </inputs>
94 <outputs>
95 <data format="bigwig" name="outFileName">
96 <change_format>
97 <when input="outFileFormat" value="bigwig" format="bigwig" />
98 <when input="outFileFormat" value="bedgraph" format="bedgraph" />
99 </change_format>
100 </data>
101 </outputs>
102 <tests>
103 <test>
104 <param name="bigwigFile1" value="test.bw" ftype="bigwig" />
105 <param name="bigwigFile2" value="test.bw" ftype="bigwig" />
106 <param name="showAdvancedOpt" value="no" />
107 <param name="outFileFormat" value="bigwig" />
108 <param name="binSize" value="5" />
109 <param name="comparison_select" value="ratio" />
110 <output name="outFileName" file="bigwigCompare_result1.bw" ftype="bigwig" />
111 </test>
112 <test>
113 <param name="bigwigFile1" value="test.bw" ftype="bigwig" />
114 <param name="bigwigFile2" value="test.bw" ftype="bigwig" />
115 <param name="showAdvancedOpt" value="no" />
116 <param name="outFileFormat" value="bedgraph" />
117 <param name="binSize" value="10" />
118 <param name="comparison_select" value="ratio" />
119 <output name="outFileName" file="bigwigCompare_result2.bg" ftype="bedgraph" />
120 </test>
121 </tests>
122 <help>
123 <![CDATA[
124
125 **What it does**
126
127 This tool compares two bigwig files based on the number of mapped reads. To
128 compare the bigwig files the genome is partitioned into bins of equal size,
129 then the number of reads found in each BAM file are counted for such bins and
130 finally a summarizing value is reported. This value can be the ratio of the
131 number of reads per bin, the log2 of the ratio, the sum or the difference.
132
133 -----
134
135 @REFERENCES@
136 ]]>
137 </help>
138 <expand macro="citations" />
139 </tool>