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comparison galaxy-conf/FindNMers.xml @ 20:9d56b5b85740 draft

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Reuploaded to see if tools get loaded correctly this time.
author timpalpant
date Fri, 15 Jun 2012 15:10:26 -0400
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19:8ad390e82b92 20:9d56b5b85740
1 <tool id="FindNMers" name="Find NMers" version="1.0.0">
2 <description>in a DNA sequence</description>
3 <command interpreter="sh">galaxyToolRunner.sh dna.FindNMers -i
4 #if $refGenomeSource.genomeSource == "history":
5 $refGenomeSource.ownFile
6 #else
7 ${refGenomeSource.index.fields.path}
8 #end if
9 -m $mismatches -n $nmer $rc -o $output
10 </command>
11 <inputs>
12 <conditional name="refGenomeSource">
13 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
14 <option value="indexed">Use a built-in index</option>
15 <option value="history">Use one from the history</option>
16 </param>
17 <when value="indexed">
18 <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
19 <options from_data_table="sam_fa_indexes">
20 <filter type="sort_by" column="1" />
21 <validator type="no_options" message="No indexes are available" />
22 </options>
23 </param>
24 </when>
25 <when value="history">
26 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
27 </when> <!-- history -->
28 </conditional> <!-- refGenomeSource -->
29
30 <param name="nmer" type="text" optional="false" label="NMer to search for" />
31 <param name="mismatches" type="integer" value="0" label="Number of allowed mismatches (Hamming distance)" />
32 <param name="rc" type="boolean" checked="true" truevalue="--rc" falsevalue="" label="Search reverse-complement as well" />
33 </inputs>
34 <outputs>
35 <data format="bed" name="output"/>
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>
46
47 <help>
48
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.
50
51 </help>
52 </tool>