comparison bigwigCompare.xml @ 0:49a569aecb22 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
author bgruening
date Mon, 25 Jan 2016 20:14:59 -0500
parents
children 48f35873bbb1
comparison
equal deleted inserted replaced
-1:000000000000 0:49a569aecb22
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 between them</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 $advancedOpt.skipNAs
31 --scaleFactors '$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 bases, of the non-overlapping bins used for averaging the score over the regions length"
86 help="Size of the bins in bases for the output of the bigwig/bedgraph file."/>
87
88 <expand macro="skipNAs" />
89 <expand macro="scaleFactors" />
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 bigWig file are counted for such bins and
130 finally a summary value 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>