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
date Sat, 05 Aug 2017 07:23:59 -0400
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1 <tool id="qiime_jackknifed_beta_diversity" name="Perform jackknifed UPGMA clustering" version="@WRAPPER_VERSION@.0">
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2 <description> and building jackknifed PCoA plots (jackknifed_beta_diversity)</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <stdio>
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8 <regex match="VisibleDeprecationWarning" source="both" level="warning" description="VisibleDeprecationWarning on numpy for `rank`"/>
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9 <regex match="RuntimeWarning: The result contains negative eigenvalues" source="both" level="warning" description="Presence of negative eigenvalues"/>
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10 </stdio>
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11 <version_command>jackknifed_beta_diversity.py --version</version_command>
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12 <command detect_errors="aggressive"><![CDATA[
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13 jackknifed_beta_diversity.py
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14 --otu_table_fp '$otu_table_fp'
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15 --mapping_fp '$mapping_fp'
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16 -o jackknifed_beta_diversity
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17 --seqs_per_sample '$seqs_per_sample'
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18 #if $tree_fp
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19 --tree_fp '$tree_fp'
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20 #end if
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21 #if $parameter_fp
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22 --parameter_fp '$parameter_fp'
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23 #end if
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24 --master_tree '$master_tree'
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25 $parallel
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26 -O "\${GALAXY_SLOTS:-4}"
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27
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28 && python $__tool_directory__/jackknifed_beta_diversity_output_management.py
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29 --data_directory jackknifed_beta_diversity
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30 --html_file '$jackknifed_beta_diversity_report'
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31 --html_dir '$jackknifed_beta_diversity_report.files_path'
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32 ]]></command>
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33 <inputs>
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34 <param argument="--otu_table_fp" type="data" format="tabular,txt,biom" label="OTU table" multiple="True"/>
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35 <param argument="--mapping_fp" type="data" format="tabular,txt,tsv" label="Mapping file" multiple="True"/>
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36 <param argument="--seqs_per_sample" type="integer" value="" label="Number of sequences to include in each jackknifed subset"/>
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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"/>
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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"/>
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39 <param argument="--master_tree" type="select" label="Method for computing master trees in jackknife analysis">
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40 <option value="consensus" selected="True">Consensus of trees from jackknifed otu tables</option>
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41 <option value="full">Tree generated from input (unsubsambled) otu table</option>
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42 </param>
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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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44 </inputs>
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45 <outputs>
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46 <collection name="unrarefied_beta_div_dist_matrix" type="list" label="${tool.name} on ${on_string}: Distance matrix for unrarefied beta diversity">
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47 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" directory="jackknifed_beta_diversity/unrarefied_bdiv/"/>
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48 </collection>
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49 <collection name="unrarefied_beta_div_tree" type="list" label="${tool.name} on ${on_string}: UPGMA trees for unrarefied beta diversity">
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50 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tre" directory="jackknifed_beta_diversity/unrarefied_bdiv/"/>
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51 </collection>
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52 <collection name="rarefaction" type="list" label="${tool.name} on ${on_string}: Rarefied OTU tables">
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53 <discover_datasets pattern="rarefaction_(?P&lt;designation&gt;.+)\.biom" directory="jackknifed_beta_diversity/rarefaction/"/>
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54 </collection>
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55 <collection name="pcoa" type="list:list" label="${tool.name} on ${on_string}: PCoA">
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56 <discover_datasets pattern="pcoa_(?P&lt;identifier_0&gt;.+)_rarefaction_(?P&lt;identifier_1&gt;.+)\.txt" ext="txt" directory="jackknifed_beta_diversity/pcoa/"/>
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57 </collection>
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58 <collection name="rare_dm" type="list:list" label="${tool.name} on ${on_string}: Distance matrix for rarefied beta diversity">
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59 <discover_datasets pattern="(?P&lt;identifier_0&gt;.+)_rarefaction_(?P&lt;identifier_1&gt;.+)\.txt" ext="txt" directory="jackknifed_beta_diversity/rare_dm/"/>
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60 </collection>
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61 <collection name="rare_upgma" type="list:list" label="${tool.name} on ${on_string}: UPGMA trees for unrarefied beta diversity">
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62 <discover_datasets pattern="upgma_(?P&lt;identifier_0&gt;.+)_rarefaction_(?P&lt;identifier_1&gt;.+)\.tre" ext="txt" directory="jackknifed_beta_diversity/rare_upgma/"/>
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63 </collection>
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64 <collection name="rare_upgma_consensus" type="list" label="${tool.name} on ${on_string}: Consensus UPGMA trees for unrarefied beta diversity">
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65 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tre" directory="jackknifed_beta_diversity/rare_upgma_consensus/"/>
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66 </collection>
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67 <data name="jackknifed_beta_diversity_report" format="html" label="${tool.name} on ${on_string}: Report"/>
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68 </outputs>
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69 <tests>
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70 <test>
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71 <param name="otu_table_fp" value="jackknifed_beta_diversity/otu_table.biom"/>
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72 <param name="mapping_fp" value="jackknifed_beta_diversity/map.txt"/>
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73 <param name="seqs_per_sample" value="10"/>
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74 <param name="tree_fp" value="jackknifed_beta_diversity/rep_set.tre"/>
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75 <param name="master_tree" value="consensus"/>
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76 <param name="parallel" value="--parallel"/>
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77 <output_collection name="unrarefied_beta_div_dist_matrix" type="list" count="2"/>
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78 <output_collection name="unrarefied_beta_div_tree" type="list" count="2"/>
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iuc
parents:
diff changeset
79 <output_collection name="rarefaction" type="list" count="10"/>
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iuc
parents:
diff changeset
80 <output_collection name="pcoa" type="list:list">
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iuc
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diff changeset
81 <element name="unweighted_unifrac">
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iuc
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diff changeset
82 <element name="10_0">
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iuc
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diff changeset
83 <assert_contents>
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
parents:
diff changeset
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iuc
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
parents:
diff changeset
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iuc
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diff changeset
91 <has_text text="PC.607" />
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iuc
parents:
diff changeset
92 <has_text text="PC.634" />
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iuc
parents:
diff changeset
93 </assert_contents>
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iuc
parents:
diff changeset
94 </element>
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iuc
parents:
diff changeset
95 </element>
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iuc
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diff changeset
96 <element name="weighted_unifrac">
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iuc
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diff changeset
97 <element name="10_0">
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iuc
parents:
diff changeset
98 <assert_contents>
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iuc
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diff changeset
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iuc
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diff changeset
100 <has_text text="PC.635" />
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iuc
parents:
diff changeset
101 <has_text text="PC.356" />
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iuc
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diff changeset
102 <has_text text="PC.481" />
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iuc
parents:
diff changeset
103 <has_text text="PC.354" />
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iuc
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diff changeset
104 <has_text text="PC.593" />
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iuc
parents:
diff changeset
105 <has_text text="PC.355" />
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iuc
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diff changeset
106 <has_text text="PC.607" />
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iuc
parents:
diff changeset
107 <has_text text="PC.634" />
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iuc
parents:
diff changeset
108 </assert_contents>
f9df45b8425a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
109 </element>
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iuc
parents:
diff changeset
110 </element>
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iuc
parents:
diff changeset
111 </output_collection>
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iuc
parents:
diff changeset
112 <output_collection name="rare_dm" type="list:list">
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iuc
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diff changeset
113 <element name="unweighted_unifrac">
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iuc
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diff changeset
114 <element name="10_0">
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iuc
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115 <assert_contents>
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
118 <has_text text="PC.356" />
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iuc
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iuc
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diff changeset
120 <has_text text="PC.354" />
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iuc
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iuc
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diff changeset
122 <has_text text="PC.355" />
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iuc
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diff changeset
123 <has_text text="PC.607" />
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iuc
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diff changeset
124 <has_text text="PC.634" />
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iuc
parents:
diff changeset
125 </assert_contents>
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iuc
parents:
diff changeset
126 </element>
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iuc
parents:
diff changeset
127 </element>
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iuc
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diff changeset
128 <element name="weighted_unifrac">
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iuc
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diff changeset
129 <element name="10_0">
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iuc
parents:
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130 <assert_contents>
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iuc
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diff changeset
131 <has_text text="PC.636" />
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iuc
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diff changeset
132 <has_text text="PC.635" />
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iuc
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diff changeset
133 <has_text text="PC.356" />
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iuc
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diff changeset
134 <has_text text="PC.481" />
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iuc
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diff changeset
135 <has_text text="PC.354" />
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iuc
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diff changeset
136 <has_text text="PC.593" />
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iuc
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diff changeset
137 <has_text text="PC.355" />
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iuc
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diff changeset
138 <has_text text="PC.607" />
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iuc
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diff changeset
139 <has_text text="PC.634" />
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iuc
parents:
diff changeset
140 </assert_contents>
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iuc
parents:
diff changeset
141 </element>
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iuc
parents:
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142 </element>
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iuc
parents:
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143 </output_collection>
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iuc
parents:
diff changeset
144 <output_collection name="rare_upgma" type="list:list">
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iuc
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diff changeset
145 <element name="unweighted_unifrac">
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iuc
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diff changeset
146 <element name="10_0">
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iuc
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147 <assert_contents>
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iuc
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148 <has_text text="PC.636" />
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iuc
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diff changeset
149 <has_text text="PC.635" />
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iuc
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diff changeset
150 <has_text text="PC.356" />
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iuc
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diff changeset
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iuc
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diff changeset
152 <has_text text="PC.354" />
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iuc
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diff changeset
153 <has_text text="PC.593" />
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iuc
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diff changeset
154 <has_text text="PC.355" />
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iuc
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diff changeset
155 <has_text text="PC.607" />
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iuc
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diff changeset
156 <has_text text="PC.634" />
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iuc
parents:
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157 </assert_contents>
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iuc
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158 </element>
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iuc
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159 </element>
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iuc
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diff changeset
160 <element name="weighted_unifrac">
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iuc
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diff changeset
161 <element name="10_0">
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iuc
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162 <assert_contents>
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iuc
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163 <has_text text="PC.636" />
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iuc
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164 <has_text text="PC.635" />
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iuc
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165 <has_text text="PC.356" />
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iuc
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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>