Mercurial > repos > iuc > picrust_format_tree_and_trait_table

annotate format_tree_and_trait_table.xml @ 0:61c60e3c8768 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
author iuc
date Sat, 20 Jan 2018 03:40:36 -0500
parents
children 21999f3aeb04
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
1 <tool id="picrust_format_tree_and_trait_table" name="Format" version="@WRAPPER_VERSION@.0">
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
2 <description>tree and trait tables</description>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
3 <macros>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
4 <import>macros.xml</import>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
5 </macros>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
7 <expand macro="version_command"/>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
8 <command detect_errors="aggressive"><![CDATA[
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
9 format_tree_and_trait_table.py
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
10 -i '$input_trait_table'
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
11 -t '$input_tree'
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
12 -o ./formatted/
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
13 --input_table_delimiter $advanced.input_table_delimiter
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
14 --output_table_delimiter $advanced.output_table_delimiter
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
15
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
16 #if $advanced.input_tree_to_trait
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
17 --tree_to_trait_mapping '$advanced.input_tree_to_trait'
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
18 #end if
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
19
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
20 #if $advanced.input_limit_otus
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
21 --limit_tree_to_otus_fp '$advanced.input_limit_otus'
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
22 #end if
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
23
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
24 $advanced.suppress_bifurcating
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
25 $advanced.convert_to_nexus
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
26 $advanced.convert_values_to_ints
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
27 $advanced.no_minimum_branch_length
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
28 $advanced.supress_tree_filter
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
29 $advanced.supress_table_filter
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
30 $advanced.add_branch_length_to_root
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
31 ]]></command>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
32 <inputs>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
33 <param name="input_trait_table" type="data" format="tabular,txt,csv" label="Input trait table"
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
34 help="Input trait table in QIIME OTU table format"/>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
35 <param name="input_tree" type="data" format="nhx" label="Input tree" help="Input tree in Newick format"/>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
36 <section name="advanced" title="Advanced options" expanded="False">
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
37 <param argument="--input_table_delimiter" type="select" label="Input table delimiter"
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
38 help="The character delimiting fields in the input trait table">
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
39 <option value="tab" selected="true">Tab</option>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
40 <option value="space">Space</option>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
41 <option value="comma">Comma</option>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
42 </param>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
43 <param argument="--output_table_delimiter" type="select" label="Output table delimiter"
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
44 help="The character delimiting fields in the output trait table">
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
45 <option value="tab" selected="true">Tab</option>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
46 <option value="space">Space</option>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
47 <option value="comma">Comma</option>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
48 </param>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
49 <param name="input_tree_to_trait" type="data" format="tabular" optional="true" label="Tree to trait mapping"
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
50 help="An optional two-column, tab-delimited text file mapping identifiers in the tree (column 1) to identifiers in the trait table (column 2). If supplied, the identifiers in the trait table will be converted to match the identifiers in the tree. (This mapping does not need to be supplied if the tree and trait table already use a common set of identifiers.)"/>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
51 <param name="input_limit_otus" type="data" format="tabular,txt,csv" optional="true" label="Limit trees"
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
52 help="Prune the reference tree to contain only those tips that are within the given OTU table"/>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
53 <param argument="--suppress_bifurcating" type="boolean" truevalue="--suppress_bifurcating" falsevalue="" checked="false"
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
54 label="Suppress bifurcating" help="If set, don’t ensure that tree is fully bifurcating"/>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
55 <param argument="--convert_to_nexus" type="boolean" truevalue="--convert_to_nexus" falsevalue="" checked="false"
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
56 label="Convert to NEXUS format" help="Convert tree to NEXUS format, including a translate block mapping tip names to numbers"/>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
57 <param argument="--convert_values_to_ints" type="boolean" truevalue="--convert_values_to_ints" falsevalue="" checked="false"
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
58 label="Convert character state to integers" help="Convert the values for each character state to integers"/>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
59 <param argument="--no_minimum_branch_length" type="boolean" truevalue="--no_minimum_branch_length" falsevalue="" checked="false"
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
60 label="No minimum branch length" help="If set, don’t ensure all branches have at least a small but non-zero branch length"/>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
61 <param argument="--supress_tree_filter" type="boolean" truevalue="--supress_tree_filter" falsevalue="" checked="false"
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
62 label="Supress tree filter" help="If set, don’t filter out tree tips that aren’t listed in the trait table"/>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
63 <param argument="--supress_table_filter" type="boolean" truevalue="--supress_table_filter" falsevalue="" checked="false"
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
64 label="Supress table filter" help="If set, don’t filter out trait table entries that aren’t listed in the tree"/>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
65 <param argument="--add_branch_length_to_root" type="boolean" truevalue="--add_branch_length_to_root" falsevalue="" checked="false"
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
66 label="Add branch to root" help="Add a short branch to the root node (this is required by some phylogeny programs). The length of the branch is determined by the min_branch_length option"/>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
67 </section>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
68 </inputs>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
69 <outputs>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
70 <data name="reference_tree" label="${tool.name} on ${on_string}: Reference tree" format="nhx"
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
71 from_work_dir="formatted/reference_tree.newick"/>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
72 <data name="pruned_tree" label="${tool.name} on ${on_string}: Pruned tree" format="nhx"
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
73 from_work_dir="formatted/pruned_tree.newick">
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
74 <change_format>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
75 <when input="advanced.convert_to_nexus" value="--convert_to_nexus" format="nex"/>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
76 </change_format>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
77 </data>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
78 <data name="trait_table" label="${tool.name} on ${on_string}: Trait table" format="tabular"
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
79 from_work_dir="formatted/trait_table.tab">
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
80 <change_format>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
81 <when input="advanced.output_table_delimiter" value="space" format="txt"/>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
82 <when input="advanced.output_table_delimiter" value="comma" format="csv"/>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
83 </change_format>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
84 </data>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
85 </outputs>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
86 <tests>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
87 <test>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
88 <param name="input_trait_table" value="format_tree_and_trait_table/input_traits.tab"/>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
89 <param name="input_tree" value="format_tree_and_trait_table/input_tree.nwk"/>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
90 <output name="reference_tree" ftype="nhx" file="format_tree_and_trait_table/reference_tree.newick"/>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
91 <output name="pruned_tree" ftype="nhx" file="format_tree_and_trait_table/pruned_tree.newick"/>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
92 <output name="trait_table" ftype="tabular" file="format_tree_and_trait_table/trait_table.tab"/>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
93 </test>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
94 </tests>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
95 <help>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
96 <![CDATA[
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
97 @PICRUST_OVERVIEW@
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
98
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
99 **Command Documenation**
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
100
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
101 This module does numerous formatting and checks to the reference tree and the trait tables. The following steps are done for both the marker gene copy number table and functional trait copy number table:
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
102
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
103 1. All internal nodes in the reference tree are checked for problematic characters and unlabelled internal nodes are given labels.
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
104 2. A pruned tree is created that contains only tips that have copy number predictions from sequenced genomes.
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
105 3. Any traits in the trait table that are not in the reference tree are removed.
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
106
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
107 Optional fixes include:
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
108
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
109 - Add short (epsilon) branch lengths in place of 0 length branches
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
110 - Filter out taxa that don't match between tree and trait table
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
111 - Output tree in NEXUS format
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
112 - Ensure tree is bifurcating (remove polytomies using very short branches)
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
113 - Convert floating point trait values to integers
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
114 - Add a short branch length to the root branch (required by BayesTraits)
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
115 - Remove internal node names (required by BayesTraits)
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
116
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
117 Three output files are produced:
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
118
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
119 - a reference tree Newick file
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
120 - a pruned tree Newick file
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
121 - a trait table file
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
122
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
123 ]]>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
124 </help>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
125 <expand macro="citations"/>
61c60e3c8768 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d4a07fbb603c57131af9cd2223579148a3887baf
iuc
parents:
diff changeset
126 </tool>