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comparison alpha_rarefaction.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_alpha_rarefaction" name="Perform alpha rarefaction" version="1.9.1">
2
3 <description></description>
4
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8
9 <expand macro="requirements" />
10
11 <version_command><![CDATA[
12 alpha_rarefaction.py --version
13 ]]>
14 </version_command>
15
16 <command>
17 <![CDATA[
18 alpha_rarefaction.py
19 -i $otu_table_fp
20 -m $mapping_fp
21 -o alpha_rarefaction
22
23 #if $parameter_fp
24 -p $parameter_fp
25 #end if
26
27 -n $num_steps
28 $parallel
29 -O "\${GALAXY_SLOTS:-4}"
30
31 #if $tree_fp
32 -t $tree_fp
33 #end if
34
35 --min_rare_depth $min_rare_depth
36
37 #if $max_rare_depth
38 -e $max_rare_depth
39 #end if
40
41 &&
42 mkdir -p $alpha_rarefaction_plots.files_path
43 &&
44 cp -r alpha_rarefaction/alpha_rarefaction_plots/rarefaction_plots.html $alpha_rarefaction_plots.files_path
45 &&
46 cp -r alpha_rarefaction/alpha_rarefaction_plots/average_plots $alpha_rarefaction_plots.files_path
47 &&
48 mv $alpha_rarefaction_plots.files_path/rarefaction_plots.html $alpha_rarefaction_plots
49 ]]>
50 </command>
51
52 <inputs>
53 <param name="otu_table_fp" type="data" format="tabular,txt,tsv,biom"
54 label="OTU table" help="(-i/--otu_table_fp)" />
55
56 <param name="mapping_fp" type="data" format="tabular,txt,tsv"
57 label="Mapping file" help="(-m/--mapping_fp)" />
58
59 <param name="parameter_fp" type="data" format="txt"
60 label="Parameter file" help="It specifies changes to the default
61 behavior (-p/--parameter_fp)" optional="true"/>
62
63 <param name="num_steps" type="integer" value="10" label="Number of steps
64 (or rarefied OTU table sizes) to make between min and max counts"
65 help="(-n/--num_steps)"/>
66
67 <param name="parallel" type="boolean" label="Run in parallel where
68 available?" truevalue="--parallel" falsevalue="" checked="True"
69 help="(-a, --parallel)" />
70
71 <param name="tree_fp" type="data" format="tabular,txt,tsv"
72 label="Tree file (optional)" help="Required for phylogenetic measures
73 (-t/--tree_fp)" optional="True"/>
74
75 <param name="min_rare_depth" type="integer" value="10" label="Lower limit
76 of rarefaction depths" help="(--min_rare_depth)"/>
77
78 <param name="max_rare_depth" type="integer" label="Upper limit
79 of rarefaction depths" help="By default, median sequence/sample count
80 is used (-e/--max_rare_depth)" optional="True"/>
81 </inputs>
82
83 <outputs>
84 <data name="alpha_rarefaction_plots" format="html"
85 label="${tool.name} on ${on_string}: Alpha rarefaction plots"/>
86
87 <data format="txt" name="alpha_diversity">
88 <discover_datasets pattern="__designation__" ext="txt"
89 directory="alpha_rarefaction/alpha_div_collated" visible="true" />
90 </data>
91 </outputs>
92
93 <tests>
94 <test>
95 </test>
96 </tests>
97
98 <help><![CDATA[
99
100 **What it does**
101
102 This script performs alpha rarefaction in several steps:
103
104 - Generation of rarefied OTU tables
105 - Computation of alpha diversity metrics for each rarefied OTU table
106 - Concatenation of alpha diversity results
107 - Generation of alpha rarefaction plots
108
109 More information about this tool is available on
110 `QIIME documentation <http://qiime.org/scripts/alpha_rarefaction.html>`_.
111 ]]>
112 </help>
113
114 <citations>
115 <expand macro="citations" />
116 </citations>
117 </tool>