Mercurial > repos > timpalpant > java_genomics_toolkit

comparison galaxy-conf/IntervalLengthDistribution.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 eb53be9a09f4
children
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14:f58706d4d421 15:3e477c7e0e73
6 <param name="freq" type="boolean" checked="false" truevalue="-f" falsevalue="" label="Output normalized frequencies rather than counts" /> 6 <param name="freq" type="boolean" checked="false" truevalue="-f" falsevalue="" label="Output normalized frequencies rather than counts" />
7 </inputs> 7 </inputs>
8 <outputs> 8 <outputs>
9 <data format="tabular" name="output" /> 9 <data format="tabular" name="output" />
10 </outputs> 10 </outputs>
11 <tests>
12 <test>
13 <param name="input" value="test.bed"/>
14 <param name="freq" value="false"/>
15 <output name="output" file="intervallengthdistribution1.txt"/>
16 </test>
17 <test>
18 <param name="input" value="test.bed"/>
19 <param name="freq" value="true"/>
20 <output name="output" file="intervallengthdistribution2.txt"/>
21 </test>
22 <test>
23 <param name="input" value="test2.bed"/>
24 <param name="freq" value="false"/>
25 <output name="output" file="intervallengthdistribution3.txt"/>
26 </test>
27 </tests>
11 28
12 <help> 29 <help>
13 30
14 This tool calculates the distribution of interval lengths from a list of intervals or reads in SAM, BAM, Bed, BedGraph, or GFF format. 31 This tool calculates the distribution of interval lengths from a list of intervals or reads in SAM, BAM, Bed, BedGraph, or GFF format.
15 32