Mercurial > repos > timpalpant > java_genomics_toolkit
comparison galaxy-conf/Summary.xml @ 15:3e477c7e0e73 draft
Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
author | timpalpant |
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date | Sat, 09 Jun 2012 16:03:59 -0400 |
parents | |
children | b43c420a6135 |
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14:f58706d4d421 | 15:3e477c7e0e73 |
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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> |