Mercurial > repos > iuc > qiime_assign_taxonomy
annotate assign_taxonomy.xml @ 2:70206002b220 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit e5d24fc90f811c8994ec8b72371ab4100d2c294c
author | iuc |
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date | Fri, 19 May 2017 04:09:30 -0400 |
parents | fa330c61c0a5 |
children | ec3c4654eacc |
rev | line source |
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fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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1 <tool id="qiime_assign_taxonomy" name="Assign taxonomy" version="@WRAPPER_VERSION@.0"> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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2 <description>to each sequence</description> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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3 <macros> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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4 <import>macros.xml</import> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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5 </macros> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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6 <expand macro="requirements"> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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7 <requirement type="package" version="2.0.2">rdptools</requirement> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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8 <requirement type="package" version="2.2.22">blast-legacy</requirement> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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9 <requirement type="package" version="2.3.4">vsearch</requirement> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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10 <requirement type="package" version="1.36.1">mothur</requirement> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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11 </expand> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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12 <version_command>assign_taxonomy.py --version</version_command> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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13 <command detect_errors="aggressive"><![CDATA[ |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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14 assign_taxonomy.py |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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15 --input_fasta_fp '$input_fasta_fp' |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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16 #if $id_to_taxonomy_fp |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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17 --id_to_taxonomy_fp '$id_to_taxonomy_fp' |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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18 #end if |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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19 --assignment_method '$methodcond.assignment_method' |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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20 #if $methodcond.assignment_method == "uclust" |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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21 --min_consensus_fraction '$methodcond.min_consensus_fraction' |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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22 --similarity '$methodcond.similarity' |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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23 --uclust_max_accepts '$methodcond.uclust_max_accepts' |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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24 #else if $methodcond.assignment_method == "rdp" |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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25 #if $methodcond.reference_seqs_fp |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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26 --reference_seqs_fp '$methodcond.reference_seqs_fp' |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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27 #end if |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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28 --confidence '$methodcond.confidence' |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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29 #else if $methodcond.assignment_method == "blast" |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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30 --reference_seqs_fp '$methodcond.reference_seqs_fp' |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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31 --blast_e_value '$methodcond.blast_e_value' |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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32 #else if $methodcond.assignment_method == "rtax" |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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33 --read_1_seqs_fp '$methodcond.read_1_seqs_fp' |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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34 --read_2_seqs_fp '$methodcond.read_2_seqs_fp' |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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35 $methodcond.single_ok |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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36 $methodcond.no_single_ok_generic |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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37 --read_id_regex '$methodcond.read_id_regex' |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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38 --amplicon_id_regex '$methodcond.amplicon_id_regex' |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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39 --header_id_rege '$methodcond.header_id_regex' |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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40 #else if $methodcond.assignment_method == "mothur" |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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41 --confidence '$methodcond.confidence' |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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42 #else if $methodcond.assignment_method == "sortmerna" |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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43 --sortmerna_threads \${GALAXY_SLOTS:-1} |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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44 #if $methodcond.sortmerna_db |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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45 --sortmerna_db '$methodcond.sortmerna_db' |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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46 #end if |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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47 --min_consensus_fraction '$methodcond.min_consensus_fraction' |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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48 --similarity '$methodcond.similarity' |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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49 --sortmerna_e_value '$methodcond.sortmerna_e_value' |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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50 --sortmerna_coverage '$methodcond.sortmerna_coverage' |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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51 --sortmerna_best_N_alignments '$methodcond.sortmerna_best_N_alignments' |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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52 #end if |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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53 -o assign_taxonomy |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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54 ]]></command> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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55 <inputs> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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56 <param argument="--input_fasta_fp" type="data" format="fasta" label="Input fasta file" /> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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57 <param argument="--id_to_taxonomy_fp" label="Tab-delimited file mapping sequences to assigned taxonomy" type="data" format="tabular" help="Each assigned taxonomy is provided as a semicolon-separated list. For assignment with rdp, each assigned taxonomy must be exactly 6 levels deep" optional="True"/> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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58 <conditional name="methodcond"> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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59 <param argument="--assignment_method" label="Taxon assignment method" type="select"> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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60 <option selected="True" value="uclust">uclust</option> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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61 <!--<option value="rdp">rdp</option> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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62 <option value="blast">blast</option> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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63 <option value="rtax">rtax</option> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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64 <option value="mothur">mothur</option> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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65 <option value="sortmerna">sortmerna</option>--> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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66 </param> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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67 <when value="uclust"> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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68 <param argument="--min_consensus_fraction" type="float" value="0.51" label="Minimum fraction of database hits that must have a specific taxonomic assignment to assign that taxonomy to a query"/> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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69 <param argument="--similarity" type="float" value="0.9" label="Minimum percent similarity (expressed as a fraction between 0 and 1) to consider a database match a hit"/> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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70 <param argument="uclust_max_accepts" type="integer" value="3" label="Number of database hits to consider when making an assignment"/> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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71 </when> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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72 <when value="rdp"> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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73 <param argument="--reference_seqs_fp" label="Reference sequences used as training sequences for the classifier" type="data" format="fasta" optional="True"/> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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74 <param argument="--confidence" type="float" value="0.5" label="Minimum confidence to record an assignment"/> |
fa330c61c0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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75 </when> |
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76 <when value="blast"> |
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77 <param argument="--reference_seqs_fp" label="Reference sequences used to generate a blast database" type="data" format="fasta" optional="True"/> |
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78 <param argument="--blast_e_value" type="float" value="0.001" label="Maximum e-value to record an assignment"/> |
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79 </when> |
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80 <when value="rtax"> |
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81 <param argument="--read_1_seqs_fp" type="data" format="fasta" label="First reads from paired-end sequencing, prior to OTU clustering" help="This file is the result of split_illumina_fastq"/> |
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82 <param argument="--read_2_seqs_fp" type="data" format="fasta" label="Second reads from paired-end sequencing, prior to OTU clustering" help="This file is the result of split_illumina_fastq"/> |
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83 <param argument="--single_ok" type="boolean" truevalue="--single_ok" falsevalue="" checked="false" label="Allow fallback to single-ended classification when the mate pair is lacking?"/> |
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84 <param argument="--no_single_ok_generic" type="boolean" truevalue="--no_single_ok_generic" falsevalue="" checked="false" label="Allow fallback to single-ended classification when the mate pair is overly generic?"/> |
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85 <param argument="--read_id_regex" type="text" value="\S+\s+(\S+)" label="Regex used to parse the result of OTU clustering, to get the read_1_id for each clusterID" help="The clusterID itself is assumed to be the first field, and is not captured by the regex"/> |
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86 <param argument="--amplicon_id_regex" type="text" value="(\S+)\s+(\S+?)\/" label="Regex used to parse the result of split_libraries, to get the ampliconID for each read_1_id" help="Two groups capture read_1_id and ampliconID, respectively."/> |
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87 <param argument="--header_id_regex" type="text" value="\S+\s+(\S+?)\/" label="Regex used to parse the result of split_libraries, to get the portion of the header that RTAX uses to match mate pairs" help="The default uses the amplicon ID, not including /1 or /3, as the primary key for the query sequences. Typically this regex will be the same as amplicon_id_regex, except that only the second group is captured" /> |
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88 </when> |
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89 <when value="mothur"> |
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90 <param argument="--confidence" type="float" value="0.5" label="Minimum confidence to record an assignment"/> |
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91 </when> |
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92 <when value="sortmerna"> |
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93 <param argument="--sortmerna_db" type="data" format="fasta" label="Pre-existing database to search against" optional="True"/> |
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94 <param argument="--min_consensus_fraction" type="float" value="0.51" label="Minimum fraction of database hits that must have a specific taxonomic assignment to assign that taxonomy to a query"/> |
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95 <param argument="--similarity" type="float" value="0.9" label="Minimum percent similarity (expressed as a fraction between 0 and 1) to consider a database match a hit"/> |
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96 <param argument="--sortmerna_e_value" type="float" value="1.0" label="Maximum E-value when clustering"/> |
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97 <param argument="--sortmerna_coverage" type="float" value="0.9" label="Mininum percent query coverage (of an alignment) to consider a hit, expressed as a fraction between 0 and 1"/> |
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98 <param argument="--sortmerna_best_N_alignments" type="integer" value="5" label="Number best alignments per read to be written"/> |
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99 </when> |
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100 </conditional> |
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101 </inputs> |
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102 <outputs> |
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103 <data name="log" format="txt" from_work_dir="assign_taxonomy/*_assignments.log" label="${tool.name} on ${on_string}: Log"/> |
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104 <data name="tax_assignments" format="txt" from_work_dir="assign_taxonomy/*.txt" label="${tool.name} on ${on_string}: Taxonomic assignment"/> |
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105 <data name="sortmerna_map" format="tabular" from_work_dir="assign_taxonomy/sortmerna_map.blast" label="${tool.name} on ${on_string}: SortMeRNA Blast"> |
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106 <filter>methodcond['assignment_method']=="sortmerna"</filter> |
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107 </data> |
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108 </outputs> |
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109 <tests> |
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110 <test> |
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111 <param name="input_fasta_fp" value="assign_taxonomy/uclust_input_seqs.fasta"/> |
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112 <param name="assignment_method" value="uclust"/> |
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113 <param name="min_consensus_fraction" value="0.51"/> |
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114 <param name="similarity" value="0.9"/> |
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115 <param name="uclust_max_accepts" value="3" /> |
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116 <output name="tax_assignments" value="assign_taxonomy/uclust_taxonomic_assignation.txt"/> |
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117 <output name="log"> |
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118 <assert_contents> |
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119 <has_text text="UclustConsensusTaxonAssigner" /> |
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120 <has_text text="2751331" /> |
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121 </assert_contents> |
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122 </output> |
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123 </test> |
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124 <!--<test> |
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125 <param name="input_fasta_fp" value="assign_taxonomy/mothur_ref_seq_set.fna"/> |
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126 <param name="assignment_method" value="sortmerna"/> |
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127 <param name="min_consensus_fraction" value="0.51" /> |
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128 <param name="similarity" value="0.9" /> |
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129 <param name="sortmerna_e_value" value="1.0" /> |
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130 <param name="sortmerna_coverage" value="0.9" /> |
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131 <param name="sortmerna_best_N_alignments" value="5" /> |
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132 <output name="log"> |
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133 <assert_contents> |
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134 <has_text text="Application:SortMeRNA" /> |
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135 <has_text text="min_consensus_fraction" /> |
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136 </assert_contents> |
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137 </output> |
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138 <output name="tax_assignments" value="assign_taxonomy/sortmerna_taxonomic_assignation.txt"/> |
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139 <output name="sortmerna_map" value="assign_taxonomy/sortmerna_map.blast"/> |
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140 </test>--> |
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141 </tests> |
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142 <help><![CDATA[ |
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143 **What it does** |
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144 |
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145 Contains code for assigning taxonomy, using several techniques. |
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146 |
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147 Given a set of sequences, the program attempts to assign the taxonomy of each sequence. |
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148 |
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149 Currently the methods implemented are assignment with BLAST, the RDP classifier, RTAX, mothur, and uclust. The output of this step is an observation metadata mapping file of input sequence identifiers (1st column of output file) to taxonomy (2nd column) and quality score (3rd column). There may be method-specific information in subsequent columns. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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150 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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151 Reference data sets and id-to-taxonomy maps for 16S rRNA sequences can be found in the Greengenes reference OTU builds. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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152 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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153 The consensus taxonomy assignment implemented here is the most detailed lineage description shared by 90% or more of the sequences within the OTU (this level of agreement can be adjusted by the user). The full lineage information for each sequence is one of the output files of the analysis. In addition, a conflict file |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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154 records cases in which a phylum-level taxonomy assignment disagreement exists within an OTU (such instances are rare and can reflect sequence misclassification within the greengenes database). |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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155 ]]></help> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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156 <citations> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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157 <expand macro="citations"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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158 </citations> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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159 </tool> |