Mercurial > repos > iuc > qiime_pick_closed_reference_otus

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
author iuc
date Thu, 22 Jun 2017 07:03:06 -0400
parents 2b6d3067087a
children 11314ea5d8ac
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2b6d3067087a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <?xml version="1.0" ?>
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2 <macros>
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3 <token name="@WRAPPER_VERSION@">1.9.1</token>
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4
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5 <xml name="requirements">
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6 <requirements>
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7 <requirement type="package" version="@WRAPPER_VERSION@">qiime</requirement>
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8 <yield/>
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9 </requirements>
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10 </xml>
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11
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12 <xml name="citations">
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13 <citation type="doi">10.1038/nmeth.f.303</citation>
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14 </xml>
2b6d3067087a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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16 <xml name="pick_otus_reference_source">
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17 <conditional name="references">
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18 <param name="source_selector" type="select" label="Use reference sequences from">
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19 <option value="cached">Local cache</option>
2b6d3067087a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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20 <option value="history">History</option>
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21 </param>
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22 <when value="cached">
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23 <param argument="--refseqs_fp" label="Reference sequences" type="select">
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24 <options from_data_table="qiime_rep_set"/>
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25 </param>
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26 </when>
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27 <when value="history">
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28 <param argument="--refseqs_fp" type="data" format="fasta" label="Reference sequences to search against"/>
2b6d3067087a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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29 </when>
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30 </conditional>
2b6d3067087a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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31 </xml>
1
99e653a2ebc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
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32 <xml name="assign_taxonomy_reference_source">
99e653a2ebc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
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33 <conditional name="references">
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34 <param name="source_selector" type="select" label="Select a reference sequence file from">
99e653a2ebc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
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35 <option value="cached">The local cache</option>
99e653a2ebc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
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36 <option value="history">The active history</option>
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37 </param>
99e653a2ebc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
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38 <when value="cached">
99e653a2ebc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
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39 <param argument="--reference_seqs_fp" label="Reference sequences either used to generate a blast database (Blast) or used as training sequences for the selected classifier (RDP, Mothur)" type="select">
99e653a2ebc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
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40 <options from_data_table="qiime_rep_set"/>
99e653a2ebc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
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41 </param>
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42 </when>
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43 <when value="history">
99e653a2ebc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
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44 <param argument="--reference_seqs_fp" type="data" format="fasta" label="Reference sequences to search against"/>
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45 </when>
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46 </conditional>
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47 </xml>
0
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48 <xml name="pick_otus_similarity">
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49 <param argument="--similarity" type="float" value="0.97" label="Sequence similarity threshold"/>
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50 </xml>
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51 <xml name="pick_otus_denovo_otu_id_prefix">
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52 <param argument="--denovo_otu_id_prefix" type="text" value="denovo" label="OTU identifier prefix for the de novo OTU pickers"/>
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53 </xml>
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54 <xml name="pick_otus_enable_rev_strand_match">
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55 <param argument="--enable_rev_strand_match" type="boolean" truevalue="--enable_rev_strand_match" falsevalue="" checked="false" label="Enable reverse strand matching?" help="Will double the amount of memory used"/>
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56 </xml>
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57 <xml name="pick_otus_suppress_presort_by_abundance_uclust">
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58 <param argument="--suppress_presort_by_abundance_uclust" type="boolean" truevalue="--suppress_presort_by_abundance_uclust" falsevalue="" checked="false" label="Suppress presorting of sequences by abundance?"/>
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59 </xml>
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60 <xml name="pick_otus_max">
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61 <param argument="--max_accepts" type="integer" value="1" label="Max_accepts value"/>
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62 <param argument="--max_rejects" type="integer" value="8" label="Max_rejects value"/>
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63 </xml>
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64 <xml name="pick_otus_stepwords">
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65 <param argument="--stepwords" type="integer" value="8" label="Stepwords value"/>
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66 </xml>
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67 <xml name="pick_otus_word_length">
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68 <param argument="--word_length" type="integer" value="8" label="Word length value"/>
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69 </xml>
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70 <xml name="pick_otus_suppress_prefilter_exact_match">
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71 <param argument="--suppress_prefilter_exact_match" type="boolean" truevalue="--suppress_prefilter_exact_match" falsevalue="" checked="false" label="Don't collapse exact matches before calling?"/>
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72 </xml>
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73 </macros>