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comparison galaxy-conf/Summary.xml @ 24:a77e126ae856 draft

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Reupload since last upload did not load correctly
author timpalpant
date Tue, 19 Jun 2012 22:15:09 -0400
parents 3e477c7e0e73
children b43c420a6135
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23:01d5d20eaadd 24:a77e126ae856
1 <tool id="WigSummary" name="Output a summary" version="1.1.0">
2 <description>of a (Big)Wig file</description>
3 <command interpreter="sh">galaxyToolRunner.sh wigmath.Summary -i $input -o $output</command>
4 <inputs>
5 <param format="bigwig,wig" name="input" type="data" label="(Big)Wig file" />
6 </inputs>
7 <outputs>
8 <data format="txt" name="output" />
9 </outputs>
10 <tests>
11 <test>
12 <param name="input" value="wigmath1.wig"/>
13 <output name="output" file="wigsummary1.txt"/>
14 </test>
15 <test>
16 <param name="input" value="test.wig"/>
17 <output name="output" file="wigsummary2.txt"/>
18 </test>
19 <test>
20 <param name="input" value="test.bw"/>
21 <output name="output" file="wigsummary3.txt"/>
22 </test>
23 </tests>
24
25 <help>
26
27 This tool will output a summary of a Wig or BigWig file, including information about the chromosomes and types of contigs in the Wig file, as well as basic descriptive statistics.
28
29 -----
30
31 **Example:**
32
33 The following is an example of the output of this tool ::
34
35 ASCII Text Wiggle file: track type=wiggle_0
36 Chromosomes:
37 2micron start=1 stop=6318
38 chrVI start=1 stop=270148
39 chrI start=1 stop=230208
40 chrIII start=1 stop=316617
41 chrXII start=1 stop=1078175
42 chrXV start=1 stop=1091289
43 chrXVI start=1 stop=948062
44 chrII start=1 stop=813178
45 chrVIII start=1 stop=562643
46 chrX start=1 stop=745742
47 chrXIII start=1 stop=924429
48 chrV start=1 stop=576869
49 chrXIV start=1 stop=784333
50 chrIV start=1 stop=1531919
51 chrXI start=1 stop=666454
52 chrIX start=1 stop=439885
53 chrM start=1 stop=85779
54 chrVII start=1 stop=1090947
55 Contigs:
56 fixedStep chrom=2micron start=1 span=1 step=1
57 fixedStep chrom=chrVI start=1 span=1 step=1
58 fixedStep chrom=chrI start=1 span=1 step=1
59 fixedStep chrom=chrIII start=1 span=1 step=1
60 fixedStep chrom=chrXII start=1 span=1 step=1
61 fixedStep chrom=chrXVI start=1 span=1 step=1
62 fixedStep chrom=chrXV start=1 span=1 step=1
63 fixedStep chrom=chrII start=1 span=1 step=1
64 fixedStep chrom=chrVIII start=1 span=1 step=1
65 fixedStep chrom=chrXIII start=1 span=1 step=1
66 fixedStep chrom=chrX start=1 span=1 step=1
67 fixedStep chrom=chrV start=1 span=1 step=1
68 fixedStep chrom=chrXIV start=1 span=1 step=1
69 fixedStep chrom=chrIV start=1 span=1 step=1
70 fixedStep chrom=chrXI start=1 span=1 step=1
71 fixedStep chrom=chrIX start=1 span=1 step=1
72 fixedStep chrom=chrM start=1 span=1 step=1
73 fixedStep chrom=chrVII start=1 span=1 step=1
74 Basic Statistics:
75 Mean: 1.000000164913575
76 Standard Deviation: 1.8843731523620193
77 Total: 1.2162997005843896E7
78 Bases Covered: 12162995
79 Min value: 0.0
80 Max value: 277.98996
81
82 </help>
83 </tool>