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comparison phylo.diversity.xml @ 0:917aa3b39ccd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:54:48 -0400
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children 292c7c4d2789
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-1:000000000000 0:917aa3b39ccd
1 <tool profile="16.07" id="mothur_phylo_diversity" name="Phylo.diversity" version="@WRAPPER_VERSION@.0">
2 <description>Alpha Diversity calculates unique branch length</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$tree" tree.dat &&
14 ln -s "$name" name.dat &&
15 ln -s "$count" count.dat &&
16 #if $grouping.use == "yes":
17 ln -s "$grouping.group" grouping.group.dat &&
18 #end if
19
20 echo 'phylo.diversity(
21 tree=tree.dat,
22 #if $grouping.use == "yes":
23 group=grouping.group.dat,
24 #if $grouping.groups:
25 groups=${ str($grouping.groups).replace(",","-") },
26 #end if
27 #end if
28 #if $name:
29 name=name.dat,
30 #end if
31 iters=$iters,
32 freq=$freq,
33 scale=$scale,
34 collect=$collect,
35 rarefy=$rarefy,
36 summary=$summary,
37 #if $count:
38 count=count.dat,
39 #end if
40 processors='\${GALAXY_SLOTS:-8}'
41 )'
42 | sed 's/ //g' ## mothur trips over whitespace
43 | mothur
44 | tee mothur.out.log
45 ]]></command>
46 <inputs>
47 <param name="tree" type="data" format="mothur.tre" label="tree - Phylogenetic Tree"/>
48 <conditional name="grouping">
49 <param name="use" type="select" label="Analyze by group using a Group file">
50 <option value="no" selected="true">no</option>
51 <option value="yes">yes</option>
52 </param>
53 <when value="yes">
54 <param name="group" type="data" format="mothur.groups" label="group - Group file for the tree"/>
55 <param name="groups" type="select" multiple="true" label="groups - Groups to display">
56 <help>All groups displayed if none are selected.</help>
57 <options>
58 <filter type="data_meta" ref="group" key="groups"/>
59 </options>
60 </param>
61 </when>
62 <when value="no"/>
63 </conditional>
64 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference file for the tree"/>
65 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of iterations to try (default 1000)"/>
66 <param name="freq" type="float" value="100" min="0.0" label="freq - Reporting frequency" help="if between 0 and 100, the percentage of sequences to sample, if greater than one - report every n iterations"/>
67 <param name="scale" type="boolean" truevalue="true" falsevalue="false" checked="false" label="scale - Scale output to the number of sequences sampled"/>
68 <param name="rarefy" type="boolean" truevalue="true" falsevalue="false" checked="false" label="rarefy - Calculate the rarefaction data"/>
69 <param name="summary" type="boolean" truevalue="true" falsevalue="false" checked="true" label="summary - Generate a summary file"/>
70 <param name="collect" type="boolean" truevalue="true" falsevalue="false" checked="false" label="collect - Create a collectors curve"/>
71 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
72 </inputs>
73 <outputs>
74 <expand macro="logfile-output"/>
75 <data name="summary_out" format="tabular" from_work_dir="tree*.phylodiv.summary" label="${tool.name} on ${on_string}: summary">
76 <filter>summary</filter>
77 </data>
78 <data name="rarefaction_out" format="tabular" from_work_dir="tree*.phylodiv.rarefaction" label="${tool.name} on ${on_string}: rarefaction">
79 <filter>rarefy</filter>
80 </data>
81 <data name="collectors_out" format="tabular" from_work_dir="tree*.phylodiv" label="${tool.name} on ${on_string}: collectors">
82 <filter>collect</filter>
83 </data>
84 </outputs>
85 <tests>
86 <test><!-- test with tree file only -->
87 <param name="tree" value="treetest.tre" ftype="mothur.tre"/>
88 <param name="use" value="no"/>
89 <output name="summary_out" md5="a9feb4031094b555baf62e0165dd3637" ftype="tabular"/>
90 <expand macro="logfile-test"/>
91 </test>
92 <test><!-- test with tree file and group file and all outputs -->
93 <param name="tree" value="treetest.tre" ftype="mothur.tre"/>
94 <param name="use" value="yes"/>
95 <param name="group" value="treetest.groups"/>
96 <param name="groups" value="orange,green"/>
97 <param name="rarefy" value="true"/>
98 <param name="collect" value="true"/>
99 <output name="summary_out" md5="27375ea164ad39fb56b9606023cae504" ftype="tabular"/>
100 <output name="rarefaction_out" ftype="tabular">
101 <assert_contents>
102 <has_text text="numSampled"/>
103 <has_text text="orange"/>
104 <has_text text="green"/>
105 </assert_contents>
106 </output>
107 <output name="collectors_out" ftype="tabular">
108 <assert_contents>
109 <has_text text="numSampled"/>
110 <has_text text="orange"/>
111 <has_text text="green"/>
112 </assert_contents>
113 </output>
114 <expand macro="logfile-test"/>
115 </test>
116 </tests>
117 <help>
118 <![CDATA[
119
120 @MOTHUR_OVERVIEW@
121
122
123 **Command Documentation**
124
125 The phylo.diversity_ command calculates alpha diversity as the total of the unique branch length.
126
127 .. _phylo.diversity: https://www.mothur.org/wiki/Phylo.diversity
128
129 v.1.21.0: Updated to Mothur 1.33, added count parameter
130
131 ]]>
132 </help>
133 <expand macro="citations"/>
134 </tool>