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"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
author nml
date Tue, 23 Jun 2020 10:26:42 -0400
parents 7f27672ff880
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7e6be57de1a0 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
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1 <tool id="findrepeat" name="Find Repeats" version ="@VERSION@+galaxy1">
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2 <description>Identify repeat elements using Mummer</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="3.23">mummer</requirement>
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8 </expand>
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9 <command detect_errors="exit_code">
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10 find-repeats.pl -l $length -p $pid $fasta > $out
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11 </command>
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12 <inputs>
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13 <param name="fasta" type="data" label="Fasta file" format="fasta"/>
7f27672ff880 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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14 <param name="length" label="Minimum length of repeat region" type="integer" value="150"/>
7f27672ff880 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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15 <param name="pid" label="Minimum PID of repeat region" type="integer" value="90"/>
7f27672ff880 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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16 </inputs>
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17 <outputs>
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18 <data format="tabular" name="out" />
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="length" value="150"/>
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23 <param name="pid" value="90"/>
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24 <param name="fasta" value="find-repeats-input-1.fasta"/>
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25 <output name="out" file="find-repeats-output-1.tabular"/>
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26 </test>
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27 </tests>
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7f27672ff880 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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29 <help>
7f27672ff880 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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30 What it does
7f27672ff880 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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31 ============
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7f27672ff880 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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33 Searches a fasta reference file for repeats.
7f27672ff880 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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7f27672ff880 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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7f27672ff880 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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36 Usage
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37 =====
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7f27672ff880 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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39 **Parameters**
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40 - Fasta file: A fasta reference file to search for repeats.
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7f27672ff880 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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42 **Options**
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43 - Minimum length of repeat region (150).
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44 - Minimum PID of repeat region (90).
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45 </help>
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46 <expand macro="citations">
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47 <citation type="doi">10.1186/gb-2004-5-2-r12</citation>
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48 </expand>
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49 </tool>