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annotate readreduce.xml @ 0:08f2130e39b3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit f009487e8fec49f10396185ffd2fc4fe65bf4f29-dirty
author dave
date Tue, 19 Mar 2019 13:25:46 -0400
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1 <tool id="readreduce" name="Merge matching reads" version="1.0.4">
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2 <description>into clusters with TN-93</description>
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3 <requirements>
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4 <requirement type="package" version="1.0.4">tn93</requirement>
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5 </requirements>
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6 <version_command><![CDATA[tn93 --version]]></version_command>
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7 <command detect_errors="exit_code"><![CDATA[
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8 readreduce
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9 -q
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10 -o '$output'
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11 #if str($options.advanced) == 'advanced':
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12 -a $options.ambigs
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13 -l $options.overlap
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14 #if $options.counts_in_name:
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15 -d '$options.counts_in_name'
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16 #end if
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17 -s '$size'
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18 #end if
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19 '$input'
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20 ]]></command>
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21 <inputs>
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22 <param name="input" type="data" format="fasta" label="Input in FASTA format" />
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23 <conditional name="options">
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24 <param label="Additional options" name="advanced" type="select">
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25 <option value="defaults">Use defaults</option>
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26 <option value="advanced">Specify additional parameters</option>
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27 </param>
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28 <when value="defaults" />
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29 <when value="advanced">
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30 <param name="size" argument="-s" type="integer" min="0" value="18" label="Mimimum cluster size to report in output" />
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31 <param name="ambigs" argument="-a" type="select" label="Strategy for ambiguous nucleotides">
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32 <option value="handle">handle</option>
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33 <option value="resolve">resolve</option>
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34 <option value="average">average</option>
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35 <option value="skip">skip</option>
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36 <option value="gapmm">gapmm</option>
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37 </param>
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38 <param name="overlap" argument="-l" type="integer" value="100"
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39 label="Only count pairs that overlap by at least N bases" />
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40 <param name="counts_in_name" argument="-d" type="text"
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41 optional="true" label="Sequence name component immediately preceding a copy number" />
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42 </when>
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43 </conditional>
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44 </inputs>
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45 <outputs>
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46 <data format="fasta" name="output" />
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47 </outputs>
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48 <tests>
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49 <test>
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50 <param name="input" value="readreduce-in1.fa" />
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51 <output file="readreduce-out1.fa" ftype="fasta" name="output" sort="True" />
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52 </test>
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53 <test>
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54 <param name="input" value="readreduce-in2.fa" />
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55 <output file="readreduce-out2.fa" ftype="fasta" name="output" sort="True" />
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56 </test>
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57 </tests>
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58 <help><![CDATA[
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59 readreduce
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60 ----------
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61
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62 Merge matching reads into clusters using the
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63 [Tamura Nei 93 distance](http://www.ncbi.nlm.nih.gov/pubmed/8336541) algorithm.
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64 ]]></help>
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65 <citations>
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66 <citation type="bibtex">
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67 @UNPUBLISHED{spond,
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68 author = "Sergei Kosakovsky Pond",
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69 title = "HyPhy: Hypothesis Testing using Phylogenies",
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70 year = "2000",
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71 note = "http://hyphy.org/",
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72 url = "http://hyphy.org/"}
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73 </citation>
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74 </citations>
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75 </tool>