Mercurial > repos > iuc > qiime_jackknifed_beta_diversity
annotate jackknifed_beta_diversity.xml @ 5:205f4c9739c0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author | iuc |
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date | Sat, 05 Aug 2017 07:23:59 -0400 |
parents | f9df45b8425a |
children | 9d06d3380f1d |
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f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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1 <tool id="qiime_jackknifed_beta_diversity" name="Perform jackknifed UPGMA clustering" version="@WRAPPER_VERSION@.0"> |
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205f4c9739c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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2 <description> and building jackknifed PCoA plots (jackknifed_beta_diversity)</description> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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3 <macros> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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4 <import>macros.xml</import> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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5 </macros> |
f9df45b8425a
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"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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7 <stdio> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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8 <regex match="VisibleDeprecationWarning" source="both" level="warning" description="VisibleDeprecationWarning on numpy for `rank`"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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9 <regex match="RuntimeWarning: The result contains negative eigenvalues" source="both" level="warning" description="Presence of negative eigenvalues"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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10 </stdio> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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11 <version_command>jackknifed_beta_diversity.py --version</version_command> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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12 <command detect_errors="aggressive"><![CDATA[ |
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205f4c9739c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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13 jackknifed_beta_diversity.py |
205f4c9739c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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14 --otu_table_fp '$otu_table_fp' |
205f4c9739c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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15 --mapping_fp '$mapping_fp' |
205f4c9739c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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16 -o jackknifed_beta_diversity |
205f4c9739c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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17 --seqs_per_sample '$seqs_per_sample' |
205f4c9739c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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18 #if $tree_fp |
205f4c9739c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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19 --tree_fp '$tree_fp' |
205f4c9739c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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20 #end if |
205f4c9739c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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21 #if $parameter_fp |
205f4c9739c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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22 --parameter_fp '$parameter_fp' |
205f4c9739c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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23 #end if |
205f4c9739c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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24 --master_tree '$master_tree' |
205f4c9739c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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25 $parallel |
205f4c9739c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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26 -O "\${GALAXY_SLOTS:-4}" |
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f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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27 |
5
205f4c9739c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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28 && python $__tool_directory__/jackknifed_beta_diversity_output_management.py |
205f4c9739c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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29 --data_directory jackknifed_beta_diversity |
205f4c9739c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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30 --html_file '$jackknifed_beta_diversity_report' |
205f4c9739c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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31 --html_dir '$jackknifed_beta_diversity_report.files_path' |
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f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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32 ]]></command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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33 <inputs> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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34 <param argument="--otu_table_fp" type="data" format="tabular,txt,biom" label="OTU table" multiple="True"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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35 <param argument="--mapping_fp" type="data" format="tabular,txt,tsv" label="Mapping file" multiple="True"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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36 <param argument="--seqs_per_sample" type="integer" value="" label="Number of sequences to include in each jackknifed subset"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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37 <param argument="--tree_fp" type="data" format="txt" label="Tree file" help="It is required for phylogenetic measures" optional="True"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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38 <param argument="--parameter_fp" type="data" format="txt" label="Parameter file" help="It specifies changes to the default behavior, e.g. beta diversity metrics" optional="true"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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39 <param argument="--master_tree" type="select" label="Method for computing master trees in jackknife analysis"> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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40 <option value="consensus" selected="True">Consensus of trees from jackknifed otu tables</option> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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41 <option value="full">Tree generated from input (unsubsambled) otu table</option> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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42 </param> |
5
205f4c9739c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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43 <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="true" label="Run in parallel where available?"/> |
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f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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44 </inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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45 <outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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46 <collection name="unrarefied_beta_div_dist_matrix" type="list" label="${tool.name} on ${on_string}: Distance matrix for unrarefied beta diversity"> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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47 <discover_datasets pattern="(?P<designation>.+)\.txt" directory="jackknifed_beta_diversity/unrarefied_bdiv/"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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48 </collection> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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49 <collection name="unrarefied_beta_div_tree" type="list" label="${tool.name} on ${on_string}: UPGMA trees for unrarefied beta diversity"> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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50 <discover_datasets pattern="(?P<designation>.+)\.tre" directory="jackknifed_beta_diversity/unrarefied_bdiv/"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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51 </collection> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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52 <collection name="rarefaction" type="list" label="${tool.name} on ${on_string}: Rarefied OTU tables"> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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53 <discover_datasets pattern="rarefaction_(?P<designation>.+)\.biom" directory="jackknifed_beta_diversity/rarefaction/"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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54 </collection> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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55 <collection name="pcoa" type="list:list" label="${tool.name} on ${on_string}: PCoA"> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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56 <discover_datasets pattern="pcoa_(?P<identifier_0>.+)_rarefaction_(?P<identifier_1>.+)\.txt" ext="txt" directory="jackknifed_beta_diversity/pcoa/"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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57 </collection> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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58 <collection name="rare_dm" type="list:list" label="${tool.name} on ${on_string}: Distance matrix for rarefied beta diversity"> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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59 <discover_datasets pattern="(?P<identifier_0>.+)_rarefaction_(?P<identifier_1>.+)\.txt" ext="txt" directory="jackknifed_beta_diversity/rare_dm/"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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60 </collection> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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61 <collection name="rare_upgma" type="list:list" label="${tool.name} on ${on_string}: UPGMA trees for unrarefied beta diversity"> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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62 <discover_datasets pattern="upgma_(?P<identifier_0>.+)_rarefaction_(?P<identifier_1>.+)\.tre" ext="txt" directory="jackknifed_beta_diversity/rare_upgma/"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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63 </collection> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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64 <collection name="rare_upgma_consensus" type="list" label="${tool.name} on ${on_string}: Consensus UPGMA trees for unrarefied beta diversity"> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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65 <discover_datasets pattern="(?P<designation>.+)\.tre" directory="jackknifed_beta_diversity/rare_upgma_consensus/"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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66 </collection> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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67 <data name="jackknifed_beta_diversity_report" format="html" label="${tool.name} on ${on_string}: Report"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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68 </outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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69 <tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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70 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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71 <param name="otu_table_fp" value="jackknifed_beta_diversity/otu_table.biom"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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72 <param name="mapping_fp" value="jackknifed_beta_diversity/map.txt"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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changeset
|
73 <param name="seqs_per_sample" value="10"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff
changeset
|
74 <param name="tree_fp" value="jackknifed_beta_diversity/rep_set.tre"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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changeset
|
75 <param name="master_tree" value="consensus"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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76 <param name="parallel" value="--parallel"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
77 <output_collection name="unrarefied_beta_div_dist_matrix" type="list" count="2"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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78 <output_collection name="unrarefied_beta_div_tree" type="list" count="2"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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79 <output_collection name="rarefaction" type="list" count="10"/> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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|
80 <output_collection name="pcoa" type="list:list"> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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81 <element name="unweighted_unifrac"> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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82 <element name="10_0"> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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83 <assert_contents> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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changeset
|
84 <has_text text="PC.636" /> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff
changeset
|
85 <has_text text="PC.635" /> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff
changeset
|
86 <has_text text="PC.356" /> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff
changeset
|
87 <has_text text="PC.481" /> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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88 <has_text text="PC.354" /> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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89 <has_text text="PC.593" /> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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90 <has_text text="PC.355" /> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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91 <has_text text="PC.607" /> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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92 <has_text text="PC.634" /> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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93 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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94 </element> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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95 </element> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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96 <element name="weighted_unifrac"> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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97 <element name="10_0"> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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98 <assert_contents> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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99 <has_text text="PC.636" /> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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100 <has_text text="PC.635" /> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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101 <has_text text="PC.356" /> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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102 <has_text text="PC.481" /> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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103 <has_text text="PC.354" /> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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104 <has_text text="PC.593" /> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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105 <has_text text="PC.355" /> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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106 <has_text text="PC.607" /> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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107 <has_text text="PC.634" /> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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108 </assert_contents> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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109 </element> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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110 </element> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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111 </output_collection> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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112 <output_collection name="rare_dm" type="list:list"> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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113 <element name="unweighted_unifrac"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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114 <element name="10_0"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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115 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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116 <has_text text="PC.636" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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117 <has_text text="PC.635" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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118 <has_text text="PC.356" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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119 <has_text text="PC.481" /> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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120 <has_text text="PC.354" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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121 <has_text text="PC.593" /> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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122 <has_text text="PC.355" /> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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123 <has_text text="PC.607" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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124 <has_text text="PC.634" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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125 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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126 </element> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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127 </element> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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128 <element name="weighted_unifrac"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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129 <element name="10_0"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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130 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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131 <has_text text="PC.636" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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132 <has_text text="PC.635" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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133 <has_text text="PC.356" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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134 <has_text text="PC.481" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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135 <has_text text="PC.354" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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136 <has_text text="PC.593" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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137 <has_text text="PC.355" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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138 <has_text text="PC.607" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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139 <has_text text="PC.634" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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140 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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141 </element> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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142 </element> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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143 </output_collection> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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144 <output_collection name="rare_upgma" type="list:list"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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145 <element name="unweighted_unifrac"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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146 <element name="10_0"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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147 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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148 <has_text text="PC.636" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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149 <has_text text="PC.635" /> |
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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 <has_text text="PC.356" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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151 <has_text text="PC.481" /> |
f9df45b8425a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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152 <has_text text="PC.354" /> |
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153 <has_text text="PC.593" /> |
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154 <has_text text="PC.355" /> |
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155 <has_text text="PC.607" /> |
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156 <has_text text="PC.634" /> |
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157 </assert_contents> |
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158 </element> |
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159 </element> |
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160 <element name="weighted_unifrac"> |
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161 <element name="10_0"> |
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162 <assert_contents> |
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163 <has_text text="PC.636" /> |
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164 <has_text text="PC.635" /> |
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165 <has_text text="PC.356" /> |
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166 <has_text text="PC.481" /> |
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167 <has_text text="PC.354" /> |
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168 <has_text text="PC.593" /> |
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169 <has_text text="PC.355" /> |
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170 <has_text text="PC.607" /> |
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171 <has_text text="PC.634" /> |
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172 </assert_contents> |
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173 </element> |
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174 </element> |
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175 </output_collection> |
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176 <output_collection name="rare_upgma_consensus" type="list" count="2"> |
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177 <element name="unweighted_unifrac"> |
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178 <assert_contents> |
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179 <has_text text="PC.636" /> |
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180 <has_text text="PC.635" /> |
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181 <has_text text="PC.356" /> |
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182 <has_text text="PC.481" /> |
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183 <has_text text="PC.354" /> |
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184 <has_text text="PC.593" /> |
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185 <has_text text="PC.355" /> |
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186 <has_text text="PC.607" /> |
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187 <has_text text="PC.634" /> |
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188 </assert_contents> |
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189 </element> |
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190 <element name="weighted_unifrac"> |
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191 <assert_contents> |
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192 <has_text text="PC.636" /> |
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193 <has_text text="PC.635" /> |
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194 <has_text text="PC.356" /> |
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195 <has_text text="PC.481" /> |
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196 <has_text text="PC.354" /> |
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197 <has_text text="PC.593" /> |
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198 <has_text text="PC.355" /> |
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199 <has_text text="PC.607" /> |
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200 <has_text text="PC.634" /> |
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201 </assert_contents> |
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202 </element> |
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203 </output_collection> |
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204 <output name="jackknifed_beta_diversity_report"> |
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205 <assert_contents> |
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206 <has_text text="unweighted_unifrac" /> |
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207 <has_text text="weighted_unifrac" /> |
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208 </assert_contents> |
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209 </output> |
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210 </test> |
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211 </tests> |
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212 <help><![CDATA[ |
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213 **What it does** |
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214 |
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215 This tool performs jackknifing (repeatedly resampling a subset of the available data from each sample) to measure robustness of individual UPGMA clusters and clusters in PCoA plots. |
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216 |
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217 More information about this tool is available on |
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218 `QIIME documentation <http://qiime.org/scripts/jackknifed_beta_diversity.html>`_. |
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219 ]]></help> |
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220 <citations> |
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221 <expand macro="citations"/> |
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222 </citations> |
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223 </tool> |