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comparison jackknifed_beta_diversity.xml @ 0:c1bd0c560018 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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-1:000000000000 0:c1bd0c560018
1 <tool id="qiime_jackknifed_beta_diversity" name="Perform jackknifed UPGMA
2 clustering" version="1.9.1">
3
4 <description>and building jackknifed PCoA plots</description>
5
6 <macros>
7 <import>macros.xml</import>
8 </macros>
9
10 <expand macro="requirements" />
11
12 <version_command><![CDATA[
13 jackknifed_beta_diversity.py --version
14 ]]>
15 </version_command>
16
17 <stdio>
18 <regex match="VisibleDeprecationWarning"
19 source="both"
20 level="warning"
21 description="VisibleDeprecationWarning on numpy for `rank`" />
22 <regex match="RuntimeWarning: The result contains negative eigenvalues"
23 source="both"
24 level="warning"
25 description="Presence of negative eigenvalues" />
26 <regex match="Error"
27 source="both"
28 level="error"
29 description="Error" />
30 </stdio>
31
32 <command>
33 <![CDATA[
34 jackknifed_beta_diversity.py
35 -i $otu_table_fp
36 -m $mapping_fp
37 -o jackknifed_beta_diversity
38 -e $seqs_per_sample
39
40 #if $tree_fp
41 -t $tree_fp
42 #end if
43
44 #if $parameter_fp
45 -p $parameter_fp
46 #end if
47
48 --master_tree $master_tree
49
50 $parallel
51 -O "\${GALAXY_SLOTS:-4}"
52 &&
53
54 python $__tool_directory__/jackknifed_beta_diversity_through_plots_html_generation.py
55 --data_directory jackknifed_beta_diversity
56 --html_file $jackknifed_beta_diversity_report
57 --html_dir $jackknifed_beta_diversity_report.files_path
58
59 ]]>
60 </command>
61
62 <inputs>
63 <param name="otu_table_fp" type="data" format="tabular,txt,tsv,biom"
64 label="OTU table" help="(-i/--otu_table_fp)"
65 multiple="True"/>
66
67 <param name="mapping_fp" type="data" format="tabular,txt,tsv"
68 label="Mapping file" help="(-m/--mapping_fp)"
69 multiple="True"/>
70
71 <param name="seqs_per_sample" type="integer" value="" label="Number of
72 sequences to include in each jackknifed subset"
73 help="(-e/--seqs_per_sample)"/>
74
75 <param name="tree_fp" type="data" format="txt"
76 label="Tree file (Optional)" help="It is required for phylogenetic
77 measures (-t/--tree_fp)"
78 optional="True"/>
79
80 <param name="parameter_fp" type="data" format="txt"
81 label="Parameter file (Optional)" help="It specifies changes to the
82 default behavior, e.g. beta diversity metrics (-p/--parameter_fp)"
83 optional="true"/>
84
85 <param name="master_tree" type="select"
86 label="Method for computing master trees in jackknife analysis"
87 help="(--master_tree)">
88 <option value="consensus" selected="True">Consensus of trees from jackknifed otu tables</option>
89 <option value="full">Tree generated from input (unsubsambled) otu table</option>
90 </param>
91
92 <param name="parallel" type="boolean" label="Run in parallel where
93 available?" truevalue="--parallel" falsevalue="" checked="true"
94 help="(-a, --parallel)" />
95
96 </inputs>
97
98 <outputs>
99 <data format="html" name="jackknifed_beta_diversity_report"
100 label="${tool.name} on ${on_string}: Report"/>
101 </outputs>
102
103 <tests>
104 <test>
105 </test>
106 </tests>
107
108 <help><![CDATA[
109 **What it does**
110
111 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.
112
113 More information about this tool is available on
114 `QIIME documentation <http://qiime.org/scripts/jackknifed_beta_diversity.html>`_.
115 ]]>
116 </help>
117
118 <citations>
119 <expand macro="citations" />
120 </citations>
121 </tool>