Mercurial > repos > iuc > qiime_beta_diversity
annotate beta_diversity.xml @ 7:b38301bc5335 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 07:49:40 -0500 |
| parents | 206c7eb264db |
| children |
| rev | line source |
|---|---|
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7
b38301bc5335
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"
iuc
parents:
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1 <tool id="qiime_beta_diversity" name="Calculate beta diversity" version="@WRAPPER_VERSION@.0" profile="@PROFILE@"> |
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206c7eb264db
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
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2 <description>(pairwise sample dissimilarity) on one or many otu tables (beta_diversity)</description> |
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0f76694d7591
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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0f76694d7591
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> |
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0f76694d7591
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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0f76694d7591
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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0f76694d7591
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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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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8 <regex match="VisibleDeprecationWarning" source="both" level="warning" description="VisibleDeprecationWarning on numpy for `rank`"/> |
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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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9 </stdio> |
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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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10 <version_command>beta_diversity.py --version</version_command> |
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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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11 <command detect_errors="aggressive"><![CDATA[ |
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7
b38301bc5335
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"
iuc
parents:
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12 @MPLBACKEND@ |
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206c7eb264db
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
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13 #set $chosen_metrics = str( $metrics ).split( "," ) |
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206c7eb264db
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
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14 beta_diversity.py |
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206c7eb264db
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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15 --input_path '$input_path' |
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206c7eb264db
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
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16 #if $rows |
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206c7eb264db
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
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17 --rows '$rows' |
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206c7eb264db
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
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18 #end if |
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206c7eb264db
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
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19 -o beta_diversity |
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206c7eb264db
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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20 --metrics '$metrics' |
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206c7eb264db
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
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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 $tree_path |
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206c7eb264db
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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22 --tree_path '$tree_path' |
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206c7eb264db
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
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23 #end if |
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206c7eb264db
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
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24 $full_tree |
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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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25 ]]></command> |
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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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26 <inputs> |
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5
206c7eb264db
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
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27 <param argument="--input_path" type="data" format="tabular,txt,tsv" label="OTU table"/> |
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0f76694d7591
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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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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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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0f76694d7591
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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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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31 <option value="binary_chisq">Binary chi-square distance</option> |
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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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32 <option value="binary_chord">Binary chord distance</option> |
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0f76694d7591
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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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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34 <option value="binary_hamming">Binary Hamming distance (binary Manhattan distance)</option> |
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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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35 <option value="binary_jaccard">Binary Jaccard distance (binary Soergel distance)</option> |
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0f76694d7591
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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0f76694d7591
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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0f76694d7591
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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0f76694d7591
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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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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40 <option value="bray_curtis">Bray-Curtis distance (normalized Manhattan distance)</option> |
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0f76694d7591
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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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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42 <option value="chisq">Chi-square distance</option> |
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0f76694d7591
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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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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44 <option value="euclidean">Euclidean distance</option> |
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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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45 <option value="gower">Gower distance</option> |
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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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46 <option value="hellinger">Hellinger distance</option> |
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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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47 <option value="kulczynski">Kulczynski distance</option> |
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0f76694d7591
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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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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49 <option value="morisita_horn">Morisita-Horn distance</option> |
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0f76694d7591
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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0f76694d7591
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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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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52 <option value="spearman_approx">Spearman rank distance</option> |
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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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53 <option value="specprof">Species profile distance</option> |
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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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54 <option value="unifrac_g">G UniFrac metric (phylogenetic)</option> |
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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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55 <option value="unifrac_g_full_tree">G UniFrac full tree metric (phylogenetic)</option> |
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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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56 <option value="unweighted_unifrac" selected="true">Unweighted UniFrac metric (phylogenetic)</option> |
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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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57 <option value="unweighted_unifrac_full_tree">Unweighted UniFrac full tree metric (phylogenetic)</option> |
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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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58 <option value="weighted_normalized_unifrac">Normalized weighted UniFrac metric (phylogenetic)</option> |
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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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59 <option value="weighted_unifrac" selected="true">Weighted UniFrac metric (phylogenetic)</option> |
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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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60 </param> |
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206c7eb264db
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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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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206c7eb264db
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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63 </inputs> |
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0f76694d7591
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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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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65 <collection name="beta_diversity" type="list" label="${tool.name} on ${on_string}: Beta diversity metrics"> |
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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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66 <discover_datasets pattern="(?P<designation>.*)_dataset.*\.txt*" directory="beta_diversity"/> |
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0f76694d7591
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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0f76694d7591
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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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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69 <tests> |
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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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70 <test> |
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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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71 <param name="input_path" value="beta_diversity/otu_table.biom"/> |
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0f76694d7591
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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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> |