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comparison bigwigCompare.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
parents 3a2aab18a217
children
comparison
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29:3a2aab18a217 30:5231f398d784
1 <tool id="deeptools_bigwigCompare" name="bigwigCompare" version="@WRAPPER_VERSION@.0"> 1 <tool id="deeptools_bigwigCompare" name="bigwigCompare" version="@WRAPPER_VERSION@.0">
2 <description>normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference</description> 2 <description>normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference</description>
3 <expand macro="requirements"/>
4 <expand macro="stdio" />
5 <macros> 3 <macros>
6 <token name="@BINARY@">bigwigCompare</token> 4 <token name="@BINARY@">bigwigCompare</token>
7 <import>deepTools_macros.xml</import> 5 <import>deepTools_macros.xml</import>
8 </macros> 6 </macros>
7 <expand macro="requirements"/>
9 <command> 8 <command>
9 <![CDATA[
10 bigwigCompare 10 bigwigCompare
11 11
12 @THREADS@ 12 @THREADS@
13 13
14 --bigwig1 '$bigwigFile1' 14 --bigwig1 '$bigwigFile1'
15 --bigwig2 '$bigwigFile2' 15 --bigwig2 '$bigwigFile2'
16 16
17 --outFileName '$outFileName' 17 --outFileName '$outFileName'
18 --outFileFormat '$outFileFormat' 18 --outFileFormat '$outFileFormat'
19 19
20 --ratio $comparison.type 20 --ratio $comparison.comparison_select
21 21
22 #if $comparison.type in ['ratio','log2']: 22 #if $comparison.comparison_select in ['ratio','log2']:
23 --pseudocount $comparison.pseudocount 23 --pseudocount $comparison.pseudocount
24 #end if 24 #end if
25 25
26 #if str($region).strip() != '': 26 #if str($region).strip() != '':
27 --region '$region' 27 --region '$region'
31 31
32 --missingDataAsZero $advancedOpt.missingDataAsZero 32 --missingDataAsZero $advancedOpt.missingDataAsZero
33 --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2' 33 --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2'
34 --binSize $advancedOpt.binSize 34 --binSize $advancedOpt.binSize
35 35
36 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
37 --plotTitle '$advancedOpt.plotTitle'
38 #end if
39
36 #end if 40 #end if
41 ]]>
37 </command> 42 </command>
38 <inputs> 43 <inputs>
39 <param name="bigwigFile1" format="bigwig" type="data" label="Treatment bigwig file" /> 44 <param name="bigwigFile1" format="bigwig" type="data" label="Treatment bigwig file" />
40 <param name="bigwigFile2" format="bigwig" type="data" label="bigWig file" /> 45 <param name="bigwigFile2" format="bigwig" type="data" label="bigWig file" />
41 46
42
43 <conditional name="comparison"> 47 <conditional name="comparison">
44 <param name="type" type="select" 48 <param name="comparison_select" type="select"
45 label="How to compare the two files"> 49 label="How to compare the two files"
50 help="The default is to output the log2ratio between the two samples.
51 The reciprocal ratio returns the negative of the inverse of the ratio if
52 the ratio is less than 0. The resulting values are interpreted as negative fold changes. (--ratio)">
46 <option value="log2" selected="true">compute log2 of the number of reads ratio</option> 53 <option value="log2" selected="true">compute log2 of the number of reads ratio</option>
47 <option value="ratio">compute the ratio of the number of reads</option> 54 <option value="ratio">compute the ratio of the number of reads</option>
48 <option value="subtract">compute difference (subtract input from treatment) of the number of reads</option> 55 <option value="subtract">compute difference (subtract input from treatment) of the number of reads</option>
49 <option value="add">compute the sum over all reads</option> 56 <option value="add">compute the sum over all reads</option>
50 <option value="reciprocal_ratio">compute the reciprocal ratio of the number of reads</option> 57 <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>
51 </param> 58 </param>
52 <when value="log2"> 59 <when value="log2">
53 <expand macro="pseudocount" /> 60 <expand macro="pseudocount" />
54 </when> 61 </when>
55 <when value="ratio"> 62 <when value="ratio">
56 <expand macro="pseudocount" /> 63 <expand macro="pseudocount" />
57 </when> 64 </when>
58 <when value="subtract" /> 65 <when value="subtract" />
59 <when value="add" /> 66 <when value="add" />
60 <when value="reciprocal_ratio" /> 67 <when value="reciprocal_ratio">
68 <expand macro="pseudocount" />
69 </when>
61 </conditional> 70 </conditional>
62 71
63 <param name="outFileFormat" type="select" label="Coverage file format"> 72 <param name="outFileFormat" type="select" label="Coverage file format">
64 <option value="bigwig" selected="true">bigwig</option> 73 <option value="bigwig" selected="true">bigwig</option>
65 <option value="bedgraph">bedgraph</option> 74 <option value="bedgraph">bedgraph</option>
73 <option value="yes">yes</option> 82 <option value="yes">yes</option>
74 </param> 83 </param>
75 <when value="no" /> 84 <when value="no" />
76 <when value="yes"> 85 <when value="yes">
77 <param name="binSize" type="integer" value="50" min="1" 86 <param name="binSize" type="integer" value="50" min="1"
78 label="Bin size in bp" 87 label="Length, in base pairs, of the non-overlapping bin for averaging the score over the regions length"
79 help="Size of the bins in bp for the output of the bigwig/bedgraph file "/> 88 help="Size of the bins in bp for the output of the bigwig/bedgraph file. (--binSize)"/>
80
81 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True" 89 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
82 label ="Treat missing data as zero" 90 label ="Treat missing data as zero"
83 help ="This parameter determines if missing data should be replaced with a zero. If set to &quot;no&quot;, missing data will be ignored and will not be included in the output file at all. Missing data is defined as those regions for which no value exists in *any* of the bigwig files. The decision to include or exclude missing data depends on the interpretation of the data. Missing data in a bigwig file may mean that there is no information available for certain regions, for example a repetitive region that is not being considered. In the same file regions with low coverage may get zero read counts. If missing data is replaced by zero, this would convert the excluded repetitive regions into regions of low coverage." /> 91 help ="This parameter determines if missing data should be replaced with a zero.
84 92 If set to &quot;no&quot;, missing data will be ignored and will not be included in the
85 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment"/> 93 output file at all. Missing data is defined as those regions for which no value exists in
86 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input"/> 94 *any* of the bigwig files. The decision to include or exclude missing data depends on
95 the interpretation of the data. Missing data in a bigwig file may mean that there is no
96 information available for certain regions, for example a repetitive region that is not
97 being considered. In the same file regions with low coverage may get zero read counts.
98 If missing data is replaced by zero, this would convert the excluded repetitive regions
99 into regions of low coverage. (--missingDataAsZero)" />
100 <expand macro="scaleFactor" />
101 <expand macro="plotTitle" />
87 </when> 102 </when>
88 </conditional> 103 </conditional>
89 </inputs> 104 </inputs>
90 <outputs> 105 <outputs>
91 <data format="bigwig" name="outFileName"> 106 <data format="bigwig" name="outFileName">
92 <change_format> 107 <change_format>
93 <when input="outFileFormat" value="bigwig" format="bigwig" /> 108 <when input="outFileFormat" value="bigwig" format="bigwig" />
94 <when input="outFileFormat" value="bedgraph" format="bedgraph" /> 109 <when input="outFileFormat" value="bedgraph" format="bedgraph" />
95 </change_format> 110 </change_format>
96 </data> 111 </data>
97 </outputs> 112 </outputs>
98 113 <tests>
99 <help> 114 <test>
100 115 <param name="bigwigFile1" value="test.bw" ftype="bigwig" />
116 <param name="bigwigFile2" value="test.bw" ftype="bigwig" />
117 <param name="showAdvancedOpt" value="no" />
118 <param name="outFileFormat" value="bigwig" />
119 <param name="binSize" value="5" />
120 <param name="comparison_select" value="ratio" />
121 <output name="outFileName" file="bigwigCompare_result1.bw" ftype="bigwig" />
122 </test>
123 <test>
124 <param name="bigwigFile1" value="test.bw" ftype="bigwig" />
125 <param name="bigwigFile2" value="test.bw" ftype="bigwig" />
126 <param name="showAdvancedOpt" value="no" />
127 <param name="outFileFormat" value="bedgraph" />
128 <param name="binSize" value="10" />
129 <param name="comparison_select" value="ratio" />
130 <output name="outFileName" file="bigwigCompare_result2.bg" ftype="bedgraph" />
131 </test>
132 </tests>
133 <help>
134 <![CDATA[
101 **What it does** 135 **What it does**
102 136
103 This tool compares two bigwig files based on the number of mapped reads. To 137 This tool compares two bigwig files based on the number of mapped reads. To
104 compare the bigwig files the genome is partitioned into bins of equal size, 138 compare the bigwig files the genome is partitioned into bins of equal size,
105 then the number of reads found in each BAM file are counted for such bins and 139 then the number of reads found in each BAM file are counted for such bins and
108 142
109 143
110 ----- 144 -----
111 145
112 @REFERENCES@ 146 @REFERENCES@
113 147 ]]>
114 </help> 148 </help>
115 <expand macro="citations" /> 149 <expand macro="citations" />
116 </tool> 150 </tool>