Mercurial > repos > timpalpant > java_genomics_toolkit

annotate 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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1 <tool id="FindNMers" name="Find NMers" version="1.0.0">
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2 <description>in a DNA sequence</description>
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3 <command interpreter="sh">galaxyToolRunner.sh dna.FindNMers -i
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4 #if $refGenomeSource.genomeSource == "history":
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5 $refGenomeSource.ownFile
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6 #else
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7 ${refGenomeSource.index.fields.path}
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8 #end if
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9 -m $mismatches -n $nmer $rc -o $output
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10 </command>
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11 <inputs>
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12 <conditional name="refGenomeSource">
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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">
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14 <option value="indexed">Use a built-in index</option>
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15 <option value="history">Use one from the history</option>
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16 </param>
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17 <when value="indexed">
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18 <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
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19 <options from_data_table="sam_fa_indexes">
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20 <filter type="sort_by" column="1" />
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21 <validator type="no_options" message="No indexes are available" />
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22 </options>
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23 </param>
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24 </when>
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25 <when value="history">
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26 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
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27 </when> <!-- history -->
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28 </conditional> <!-- refGenomeSource -->
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29
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30 <param name="nmer" type="text" optional="false" label="NMer to search for" />
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31 <param name="mismatches" type="integer" value="0" label="Number of allowed mismatches (Hamming distance)" />
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32 <param name="rc" type="boolean" checked="true" truevalue="--rc" falsevalue="" label="Search reverse-complement as well" />
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33 </inputs>
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34 <outputs>
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35 <data format="bed" name="output"/>
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="genomeSource" value="history"/>
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40 <param name="ownFile" value="test.fasta"/>
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41 <param name="property" value="Twist"/>
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42 <param name="N" value="false"/>
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43 <output name="output" file="twist.wig"/>
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44 </test>
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45 </tests>
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46
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47 <help>
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48
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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.
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50
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51 </help>
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52 </tool>