Mercurial > repos > timpalpant > java_genomics_toolkit

diff galaxy-conf/Summary.xml @ 15:3e477c7e0e73 draft

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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
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/Summary.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -0,0 +1,83 @@
+<tool id="WigSummary" name="Output a summary" version="1.1.0">
+  <description>of a (Big)Wig file</description>
+  <command interpreter="sh">galaxyToolRunner.sh wigmath.Summary -i $input -o $output</command>
+  <inputs>
+      <param format="bigwig,wig" name="input" type="data" label="(Big)Wig file" />
+  </inputs>
+  <outputs>
+      <data format="txt" name="output" />
+  </outputs>
+  <tests>
+      <test>
+      	<param name="input" value="wigmath1.wig"/>
+      	<output name="output" file="wigsummary1.txt"/>
+      </test>
+      <test>
+      	<param name="input" value="test.wig"/>
+      	<output name="output" file="wigsummary2.txt"/>
+      </test>
+      <test>
+      	<param name="input" value="test.bw"/>
+      	<output name="output" file="wigsummary3.txt"/>
+      </test>
+  </tests>
+  
+<help>
+  
+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.
+
+-----
+
+**Example:**
+
+The following is an example of the output of this tool ::
+
+    ASCII Text Wiggle file: track type=wiggle_0
+    Chromosomes:
+      2micron start=1 stop=6318
+      chrVI start=1 stop=270148
+      chrI start=1 stop=230208
+      chrIII start=1 stop=316617
+      chrXII start=1 stop=1078175
+      chrXV start=1 stop=1091289
+      chrXVI start=1 stop=948062
+      chrII start=1 stop=813178
+      chrVIII start=1 stop=562643
+      chrX start=1 stop=745742
+      chrXIII start=1 stop=924429
+      chrV start=1 stop=576869
+      chrXIV start=1 stop=784333
+      chrIV start=1 stop=1531919
+      chrXI start=1 stop=666454
+      chrIX start=1 stop=439885
+      chrM start=1 stop=85779
+      chrVII start=1 stop=1090947
+    Contigs:
+      fixedStep chrom=2micron start=1 span=1 step=1
+      fixedStep chrom=chrVI start=1 span=1 step=1
+      fixedStep chrom=chrI start=1 span=1 step=1
+      fixedStep chrom=chrIII start=1 span=1 step=1
+      fixedStep chrom=chrXII start=1 span=1 step=1
+      fixedStep chrom=chrXVI start=1 span=1 step=1
+      fixedStep chrom=chrXV start=1 span=1 step=1
+      fixedStep chrom=chrII start=1 span=1 step=1
+      fixedStep chrom=chrVIII start=1 span=1 step=1
+      fixedStep chrom=chrXIII start=1 span=1 step=1
+      fixedStep chrom=chrX start=1 span=1 step=1
+      fixedStep chrom=chrV start=1 span=1 step=1
+      fixedStep chrom=chrXIV start=1 span=1 step=1
+      fixedStep chrom=chrIV start=1 span=1 step=1
+      fixedStep chrom=chrXI start=1 span=1 step=1
+      fixedStep chrom=chrIX start=1 span=1 step=1
+      fixedStep chrom=chrM start=1 span=1 step=1
+      fixedStep chrom=chrVII start=1 span=1 step=1
+    Basic Statistics:
+      Mean:               1.000000164913575
+      Standard Deviation: 1.8843731523620193
+      Total:              1.2162997005843896E7
+      Bases Covered:      12162995
+      Min value:          0.0
+      Max value:          277.98996
+  
+</help>
+</tool>