Mercurial > repos > iuc > qiime_validate_mapping_file

annotate macros.xml @ 7:d1701fcfd7e5 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"
author iuc
date Thu, 05 Dec 2019 08:03:16 -0500
parents 6b784a33f3b3
children
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51ce498c97f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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1 <?xml version="1.0" ?>
51ce498c97f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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2 <macros>
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d1701fcfd7e5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"
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3 <token name="@PROFILE@">18.01</token>
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51ce498c97f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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4 <token name="@WRAPPER_VERSION@">1.9.1</token>
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d1701fcfd7e5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"
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5 <token name="@MPLBACKEND@"><![CDATA[export MPLBACKEND=Agg && echo "backend:agg" > matplotlibrc &&]]></token>
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51ce498c97f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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6 <xml name="requirements">
51ce498c97f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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7 <requirements>
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8 <requirement type="package" version="@WRAPPER_VERSION@">qiime</requirement>
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9 <yield/>
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10 </requirements>
51ce498c97f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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11 </xml>
51ce498c97f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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12 <xml name="citations">
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13 <citation type="doi">10.1038/nmeth.f.303</citation>
51ce498c97f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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14 </xml>
51ce498c97f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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15 <xml name="pick_otus_reference_source">
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16 <conditional name="references">
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17 <param name="source_selector" type="select" label="Use reference sequences from">
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18 <option value="cached">Local cache</option>
51ce498c97f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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19 <option value="history">History</option>
51ce498c97f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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20 </param>
51ce498c97f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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21 <when value="cached">
51ce498c97f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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22 <param argument="--refseqs_fp" label="Reference sequences" type="select">
51ce498c97f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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23 <options from_data_table="qiime_rep_set"/>
51ce498c97f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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24 </param>
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25 </when>
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26 <when value="history">
51ce498c97f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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27 <param argument="--refseqs_fp" type="data" format="fasta" label="Reference sequences to search against"/>
51ce498c97f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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28 </when>
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29 </conditional>
51ce498c97f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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30 </xml>
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31 <xml name="assign_taxonomy_reference_source">
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32 <conditional name="references">
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33 <param name="source_selector" type="select" label="Select a reference sequence file from">
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34 <option value="cached">The local cache</option>
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35 <option value="history">The active history</option>
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36 </param>
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37 <when value="cached">
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38 <param argument="--reference_seqs_fp" type="select" label="Reference sequences either used to generate a blast database (Blast) or used as training sequences for the selected classifier (RDP, Mothur)">
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39 <options from_data_table="qiime_rep_set"/>
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40 </param>
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41 </when>
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42 <when value="history">
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43 <param argument="--reference_seqs_fp" type="data" format="fasta" label="Reference sequences to search against"/>
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44 </when>
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45 </conditional>
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46 </xml>
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47 <xml name="pick_otus_similarity">
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48 <param argument="--similarity" type="float" value="0.97" label="Sequence similarity threshold"/>
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49 </xml>
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50 <xml name="pick_otus_denovo_otu_id_prefix">
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51 <param argument="--denovo_otu_id_prefix" type="text" value="denovo" label="OTU identifier prefix for the de novo OTU pickers"/>
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52 </xml>
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53 <xml name="pick_otus_enable_rev_strand_match">
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54 <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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55 </xml>
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56 <xml name="pick_otus_suppress_presort_by_abundance_uclust">
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57 <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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58 </xml>
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59 <xml name="pick_otus_max">
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60 <param argument="--max_accepts" type="integer" value="1" label="Max_accepts value"/>
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61 <param argument="--max_rejects" type="integer" value="8" label="Max_rejects value"/>
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62 </xml>
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63 <xml name="pick_otus_stepwords">
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64 <param argument="--stepwords" type="integer" value="8" label="Stepwords value"/>
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65 </xml>
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66 <xml name="pick_otus_word_length">
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67 <param argument="--word_length" type="integer" value="8" label="Word length value"/>
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68 </xml>
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69 <xml name="pick_otus_suppress_prefilter_exact_match">
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70 <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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71 </xml>
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72 </macros>