Mercurial > repos > bgruening > deeptools_bigwig_average
comparison bigwigAverage.xml @ 0:9987ddd67710 draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit e7e3025eb4fffe5deb34c12a6d402d79241d9ed5
author | bgruening |
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date | Fri, 19 May 2023 08:30:42 +0000 |
parents | |
children | f6f246438eda |
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1 <tool id="deeptools_bigwig_average" name="bigwigAverage" version="@WRAPPER_VERSION@+galaxy0"> | |
2 <description>normalizes and average multiple bigWig files</description> | |
3 <macros> | |
4 <token name="@BINARY@">bigwigAverage</token> | |
5 <import>deepTools_macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements"/> | |
8 <command> | |
9 <![CDATA[ | |
10 @BINARY@ | |
11 @THREADS@ | |
12 --bigwigs | |
13 #for $b in $bigwigs: | |
14 $b | |
15 #end for | |
16 --outFileName '$outFileName' | |
17 --outFileFormat '$outFileFormat' | |
18 | |
19 #if str($region).strip() != '': | |
20 --region '$region' | |
21 #end if | |
22 | |
23 #if $advancedOpt.showAdvancedOpt == "yes": | |
24 | |
25 $advancedOpt.skipNAs | |
26 --scaleFactors '$advancedOpt.scaleFactors' | |
27 --binSize $advancedOpt.binSize | |
28 | |
29 @blacklist@ | |
30 | |
31 #end if | |
32 ]]> | |
33 </command> | |
34 <inputs> | |
35 <param name="bigwigs" format="bigwig" type="data" label="Treatment bigwig file" multiple="true" /> | |
36 | |
37 <param name="outFileFormat" type="select" label="Coverage file format"> | |
38 <option value="bigwig" selected="true">bigwig</option> | |
39 <option value="bedgraph">bedgraph</option> | |
40 </param> | |
41 | |
42 <expand macro="region_limit_operation" /> | |
43 | |
44 <conditional name="advancedOpt"> | |
45 <param name="showAdvancedOpt" type="select" label="Show advanced options" > | |
46 <option value="no" selected="true">no</option> | |
47 <option value="yes">yes</option> | |
48 </param> | |
49 <when value="no" /> | |
50 <when value="yes"> | |
51 <param argument="--binSize" type="integer" value="50" min="1" | |
52 label="Length, in bases, of the non-overlapping bins used for averaging the score over the regions length" | |
53 help="Size of the bins in bases for the output of the bigwig/bedgraph file."/> | |
54 | |
55 <expand macro="skipNAs" /> | |
56 <param name="scaleFactors" type="text" value="1" label="Scale factors (one per bigwig separated by ':')" /> | |
57 <expand macro="blacklist" /> | |
58 </when> | |
59 </conditional> | |
60 </inputs> | |
61 <outputs> | |
62 <data format="bigwig" name="outFileName"> | |
63 <change_format> | |
64 <when input="outFileFormat" value="bigwig" format="bigwig" /> | |
65 <when input="outFileFormat" value="bedgraph" format="bedgraph" /> | |
66 </change_format> | |
67 </data> | |
68 </outputs> | |
69 <tests> | |
70 <test> | |
71 <param name="bigwigs" value="test.bw" ftype="bigwig" /> | |
72 <param name="showAdvancedOpt" value="yes" /> | |
73 <param name="outFileFormat" value="bigwig" /> | |
74 <param name="binSize" value="5" /> | |
75 <output name="outFileName" file="test_compated.bw" ftype="bigwig" | |
76 compare="sim_size" delta="500" /> | |
77 </test> | |
78 <test> | |
79 <param name="bigwigs" value="test.bw" ftype="bigwig" /> | |
80 <param name="showAdvancedOpt" value="yes" /> | |
81 <param name="outFileFormat" value="bigwig" /> | |
82 <param name="binSize" value="5" /> | |
83 <param name="scaleFactors" value="0.5"/> | |
84 <output name="outFileName" file="test_half.bw" ftype="bigwig" | |
85 compare="sim_size" delta="500" /> | |
86 </test> | |
87 <test> | |
88 <param name="bigwigs" value="test.bw,test_half.bw" ftype="bigwig" /> | |
89 <param name="showAdvancedOpt" value="yes" /> | |
90 <param name="outFileFormat" value="bigwig" /> | |
91 <param name="binSize" value="5" /> | |
92 <param name="scaleFactors" value="0.5"/> | |
93 <output name="outFileName" file="bigwigAverage2.bw" ftype="bigwig" | |
94 compare="sim_size" delta="500" /> | |
95 </test> | |
96 <test> | |
97 <param name="bigwigs" value="test.bw,test_half.bw" ftype="bigwig" /> | |
98 <param name="showAdvancedOpt" value="yes" /> | |
99 <param name="outFileFormat" value="bigwig" /> | |
100 <param name="binSize" value="5" /> | |
101 <param name="scaleFactors" value="1:2"/> | |
102 <output name="outFileName" file="test_compated.bw" ftype="bigwig" | |
103 compare="sim_size" delta="500" /> | |
104 </test> | |
105 </tests> | |
106 <help> | |
107 <![CDATA[ | |
108 | |
109 What it does | |
110 -------------- | |
111 | |
112 This tool compute average of multiple bigWig files based on the number of mapped reads. To | |
113 average the bigwig files, the genome is partitioned into bins of equal size, | |
114 then the scores (e.g., number of reads) found in each bigWig file are counted for such bins and, finally, an average value is reported. | |
115 | |
116 Note that you can actually produce a human-readable bedGraph format instead of the compressed bigWig format if you're interested in having a look at the values yourself. | |
117 | |
118 @REFERENCES@ | |
119 ]]> | |
120 </help> | |
121 <expand macro="citations" /> | |
122 </tool> |