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 |
|---|---|
| date | Sat, 09 Jun 2012 16:03:59 -0400 |
| parents | |
| children | b43c420a6135 |
comparison
equal
deleted
inserted
replaced
| 14:f58706d4d421 | 15:3e477c7e0e73 |
|---|---|
| 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> |