Mercurial > repos > iuc > qiime_beta_diversity
annotate beta_diversity.xml @ 7:b666756ba7f6 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"
| author | iuc |
|---|---|
| date | Thu, 05 Dec 2019 12:17:11 +0000 |
| parents | bc1d507d371f |
| children |
| rev | line source |
|---|---|
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7
b666756ba7f6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"
iuc
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1 <tool id="qiime_beta_diversity" name="Calculate beta diversity" version="@WRAPPER_VERSION@.0" profile="@PROFILE@"> |
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bc1d507d371f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents:
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2 <description>(pairwise sample dissimilarity) on one or many otu tables (beta_diversity)</description> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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3 <macros> |
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24d558841cc8
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> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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5 </macros> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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6 <expand macro="requirements"/> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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7 <stdio> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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8 <regex match="VisibleDeprecationWarning" source="both" level="warning" description="VisibleDeprecationWarning on numpy for `rank`"/> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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9 </stdio> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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10 <version_command>beta_diversity.py --version</version_command> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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11 <command detect_errors="aggressive"><![CDATA[ |
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7
b666756ba7f6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"
iuc
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12 @MPLBACKEND@ |
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bc1d507d371f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents:
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13 #set $chosen_metrics = str( $metrics ).split( "," ) |
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bc1d507d371f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents:
0
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14 beta_diversity.py |
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bc1d507d371f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents:
0
diff
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15 --input_path '$input_path' |
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bc1d507d371f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents:
0
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16 #if $rows |
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bc1d507d371f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents:
0
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17 --rows '$rows' |
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bc1d507d371f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents:
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18 #end if |
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bc1d507d371f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents:
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19 -o beta_diversity |
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bc1d507d371f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents:
0
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20 --metrics '$metrics' |
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bc1d507d371f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents:
0
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21 #if ("unifrac_g" in $chosen_metrics or "unifrac_g_full_tree" in $chosen_metrics or "unweighted_unifrac" in $chosen_metrics or "unweighted_unifrac_full_tree" in $chosen_metrics or "weighted_normalized_unifrac" in $chosen_metrics or "weighted_unifrac" in $chosen_metrics) and $tree_path |
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bc1d507d371f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents:
0
diff
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22 --tree_path '$tree_path' |
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bc1d507d371f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents:
0
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23 #end if |
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bc1d507d371f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents:
0
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24 $full_tree |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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25 ]]></command> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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26 <inputs> |
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bc1d507d371f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents:
0
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27 <param argument="--input_path" type="data" format="tabular,txt,tsv" label="OTU table"/> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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28 <param argument="--rows" type="text" value="" optional="true" label="Rows on which distance matrix is computed (optional)" help="A comma-separated list of sample names is expected"/> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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29 <param argument="--metrics" type="select" multiple="True" display="checkboxes" label="Beta-diversity metric(s) to use"> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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30 <option value="abund_jaccard">Abundance weighted Jaccard distance</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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31 <option value="binary_chisq">Binary chi-square distance</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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32 <option value="binary_chord">Binary chord distance</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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33 <option value="binary_euclidean">Binary euclidean distance</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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34 <option value="binary_hamming">Binary Hamming distance (binary Manhattan distance)</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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35 <option value="binary_jaccard">Binary Jaccard distance (binary Soergel distance)</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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36 <option value="binary_lennon">Binary Lennon distance</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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37 <option value="binary_ochiai">Binary Ochiai distance</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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38 <option value="binary_pearson">Binary Pearson distance</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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39 <option value="binary_sorensen_dice">Binary Sörensen-Dice distance (binary Bray-Curtis distance or binary Whittaker distance)</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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40 <option value="bray_curtis">Bray-Curtis distance (normalized Manhattan distance)</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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41 <option value="canberra">Canberra distance</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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42 <option value="chisq">Chi-square distance</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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43 <option value="chord">Chord distance</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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44 <option value="euclidean">Euclidean distance</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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45 <option value="gower">Gower distance</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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46 <option value="hellinger">Hellinger distance</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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47 <option value="kulczynski">Kulczynski distance</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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48 <option value="manhattan">Manhattan distance</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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49 <option value="morisita_horn">Morisita-Horn distance</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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50 <option value="pearson">Pearson distance</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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51 <option value="soergel">Soergel distance</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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52 <option value="spearman_approx">Spearman rank distance</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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53 <option value="specprof">Species profile distance</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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54 <option value="unifrac_g">G UniFrac metric (phylogenetic)</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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55 <option value="unifrac_g_full_tree">G UniFrac full tree metric (phylogenetic)</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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56 <option value="unweighted_unifrac" selected="true">Unweighted UniFrac metric (phylogenetic)</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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57 <option value="unweighted_unifrac_full_tree">Unweighted UniFrac full tree metric (phylogenetic)</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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58 <option value="weighted_normalized_unifrac">Normalized weighted UniFrac metric (phylogenetic)</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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59 <option value="weighted_unifrac" selected="true">Weighted UniFrac metric (phylogenetic)</option> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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60 </param> |
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bc1d507d371f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
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61 <param argument="--tree_path" type="data" format="nhx,txt" optional="true" label="Newick tree (optional, except for PD_whole_tree metric)"/> |
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bc1d507d371f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
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62 <param argument="--full_tree" type="boolean" truevalue="--full_tree" falsevalue="" checked="false" label="Skip the removal of tips not corresponding to OTUs in the OTU table from the tree for diversity calculations?" help="By default, tips not corresponding to OTUs in the OTU table are removed from the tree for diversity calculations. Pass to skip this step if you’re already passing a minimal tree. Beware with 'full_tree' metrics, as extra tips in the tree change the result"/> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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63 </inputs> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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64 <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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65 <collection name="beta_diversity" type="list" label="${tool.name} on ${on_string}: Beta diversity metrics"> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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66 <discover_datasets pattern="(?P<designation>.*)_dataset.*\.txt*" directory="beta_diversity"/> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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67 </collection> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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68 </outputs> |
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24d558841cc8
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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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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70 <test> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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71 <param name="input_path" value="beta_diversity/otu_table.biom"/> |
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24d558841cc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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72 <param name="tree_path" value="beta_diversity/rep_set.tre"/> |
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73 <param name="metrics" value="unweighted_unifrac,weighted_unifrac"/> |
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74 <param name="full_tree" value=""/> |
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75 <output_collection name="beta_diversity" count="2"> |
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76 <element name="unweighted_unifrac" md5="59ab72d4e729c9bcd3194b86ce82c327"/> |
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77 <element name="weighted_unifrac" md5="c9815ca77064e014579797ab0d0023f7"/> |
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78 </output_collection> |
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79 </test> |
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80 <test> |
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81 <param name="input_path" value="beta_diversity/otu_table.biom"/> |
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82 <param name="tree_path" value="beta_diversity/rep_set.tre"/> |
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83 <param name="metrics" value="abund_jaccard,binary_chisq,binary_chord,binary_euclidean,binary_hamming,binary_jaccard,binary_lennon,binary_ochiai,binary_pearson,binary_sorensen_dice,bray_curtis,canberra,chisq,chord,euclidean,gower,hellinger,kulczynski,manhattan,morisita_horn,pearson,soergel,spearman_approx,specprof,unifrac_g,unifrac_g_full_tree,unweighted_unifrac,unweighted_unifrac_full_tree,weighted_normalized_unifrac,weighted_unifrac"/> |
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84 <param name="full_tree" value=""/> |
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85 <output_collection name="beta_diversity" count="30"> |
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86 <element name="canberra" md5="79d919bef870d6e43a49ee3da9c6e2f9"/> |
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87 <element name="pearson" md5="c87ebfdb7b4a2cfbbc9a5c228aaec38d"/> |
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88 </output_collection> |
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89 </test> |
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90 </tests> |
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91 <help><![CDATA[ |
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92 **What it does** |
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93 |
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94 This script generate distance matrices containing a dissimilarity value for each |
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95 pairwise comparison. |
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96 |
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97 A number of metrics are currently supported, including unweighted and weighted UniFrac (pass the -s option to see available metrics). In general, because unifrac uses phylogenetic information, one of the unifrac metrics is recommended, as results can be vastly more useful (Hamady & Knight, 2009). Quantitative measures (e.g. weighted unifrac) are ideally suited to revealing community differences that are due to changes in relative taxon abundance (e.g., when a particular set of taxa flourish because a limiting nutrient source becomes abundant). Qualitative measures (e.g. unweighted unifrac) are most informative when communities differ primarily by what can live in them (e.g., at high temperatures), in part because abundance information can obscure significant patterns of variation in which taxa are present (Lozupone et al., 2007). Most qualitative measures are referred to here e.g. “binary_jaccard”. Typically both weighted and unweighted unifrac are used. |
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98 |
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99 More information about this tool is available on |
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100 `QIIME documentation <http://qiime.org/scripts/beta_diversity.html>`_. |
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101 ]]></help> |
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102 <citations> |
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103 <expand macro="citations"/> |
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104 </citations> |
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105 </tool> |