Mercurial > repos > iuc > mothur_get_coremicrobiome

comparison get.coremicrobiome.xml @ 0:1dd4d752f823 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:31:03 -0400
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children af8e6f1110b3
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-1:000000000000 0:1dd4d752f823
1 <tool profile="16.07" id="mothur_get_coremicrobiome" name="Get.coremicrobiome" version="@WRAPPER_VERSION@.0">
2 <description>fraction of OTUs for samples or abundances</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$otu" otu.dat &&
11
12 echo 'get.coremicrobiome(
13 #if $otu.is_of_type("mothur.relabund"):
14 relabund=otu.dat
15 #elif $otu.is_of_type("mothur.shared"):
16 shared=otu.dat
17 #end if
18 #if $label:
19 ,label=${ str($label).replace(",","-") }
20 #end if
21 #if $groups:
22 ,groups=${ str($groups).replace(",","-") }
23 #end if
24 #if $abundance:
25 ,abundance=$abundance
26 #end if
27 #if $samples:
28 ,samples=$samples
29 #end if
30 )'
31 | sed 's/ //g' ## mothur trips over whitespace
32 | mothur
33 ]]></command>
34 <inputs>
35 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - OTU Shared or Relabund"/>
36 <param name="label" type="select" optional="true" label="label - OTU Labels" multiple="true">
37 <expand macro="labeloptions"/>
38 </param>
39 <param name="groups" type="select" optional="true" label="groups - Pairwise comparision groups" multiple="true">
40 <options>
41 <filter type="data_meta" ref="otu" key="groups"/>
42 </options>
43 </param>
44 <param name="abundance" type="integer" optional="true" value="" min="0" max="100" label="abundance - list OTU names at this abundance"/>
45 <param name="samples" type="integer" optional="true" value="" min="1" label="samples - minimum number of samples requied to list OTU names"/>
46 <param name="output" type="select" label="output - fraction or count">
47 <option value="fraction" selected="true">fraction</option>
48 <option value="count">count</option>
49 </param>
50 </inputs>
51 <outputs>
52 <expand macro="logfile-output"/>
53 <collection name="core_microbiome" type="list" label="${tool.name} on ${on_string}: core.microbiome files">
54 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.core\.microbiome$" format="tabular"/>
55 </collection>
56 <collection name="core_microbiome_list" type="list" label="${tool.name} on ${on_string}: core.microbiome list files">
57 <filter>abundance or samples </filter>
58 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.core\.microbiomelist" format="tabular"/>
59 </collection>
60 </outputs>
61 <tests>
62 <test><!-- test with default params -->
63 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
64 <output_collection name="core_microbiome" count="36">
65 <element name="0.45" md5="bae9cb5f1d311fe0cfb7ecb72a177261" ftype="tabular"/>
66 </output_collection>
67 <expand macro="logfile-test"/>
68 </test>
69 <test><!-- test with list output and label and group select-->
70 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
71 <param name="abundance" value="30"/>
72 <param name="label" value="0.05,0.22,0.45"/>
73 <param name="group" value="forest,pasture"/>
74 <output_collection name="core_microbiome" count="3">
75 <element name="0.05" md5="72bb437ab5f3a66965029a616fbaf317" ftype="tabular"/>
76 </output_collection>
77 <output_collection name="core_microbiome_list" count="3">
78 <element name="0.05" md5="83722b4c52b7faff7fe56ce026250001" ftype="tabular"/>
79 </output_collection>
80 <expand macro="logfile-test"/>
81 </test>
82 </tests>
83 <help>
84 <![CDATA[
85
86 @MOTHUR_OVERVIEW@
87
88 **Command Documenation**
89
90 The get.coremicrobiome_ command determines the fraction of OTUs that are found in varying numbers of samples for different minimum relative abundances.
91
92 .. _get.coremicrobiome: http://www.mothur.org/wiki/Get.coremicrobiome
93
94 v1.27.0: Updated to Mothur 1.33
95
96 ]]>
97 </help>
98 <expand macro="citations"/>
99 </tool>