Mercurial > repos > timpalpant > java_genomics_toolkit

comparison galaxy-conf/FindNMers.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
32 <param name="rc" type="boolean" checked="true" truevalue="--rc" falsevalue="" label="Search reverse-complement as well" /> 32 <param name="rc" type="boolean" checked="true" truevalue="--rc" falsevalue="" label="Search reverse-complement as well" />
33 </inputs> 33 </inputs>
34 <outputs> 34 <outputs>
35 <data format="bed" name="output"/> 35 <data format="bed" name="output"/>
36 </outputs> 36 </outputs>
37 <tests>
38 <test>
39 <param name="genomeSource" value="history"/>
40 <param name="ownFile" value="test.fasta"/>
41 <param name="property" value="Twist"/>
42 <param name="N" value="false"/>
43 <output name="output" file="twist.wig"/>
44 </test>
45 </tests>
37 46
38 <help> 47 <help>
39 48
40 This tool will find all matches of a given NMer in a DNA sequence. 49 This tool will find all matches of a given NMer in a DNA sequence. Sequences may be provided in FASTA format or selected from available reference genomes. Mismatches are allowed, but not insertions/deletions. The output is a Bed file with the locations of matches in the reference sequence.
41 50
42 </help> 51 </help>
43 </tool> 52 </tool>