Mercurial > repos > iuc > mothur_get_coremicrobiome
comparison get.coremicrobiome.xml @ 0:fb34c63ab676 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 05:55:47 -0400 |
parents | |
children | a1d38f9902d9 |
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-1:000000000000 | 0:fb34c63ab676 |
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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="stdio"/> | |
8 <expand macro="version_command"/> | |
9 <command><![CDATA[ | |
10 @SHELL_OPTIONS@ | |
11 | |
12 ## create symlinks to input datasets | |
13 ln -s "$otu" otu.dat && | |
14 | |
15 echo 'get.coremicrobiome( | |
16 #if $otu.is_of_type("mothur.relabund"): | |
17 relabund=otu.dat | |
18 #elif $otu.is_of_type("mothur.shared"): | |
19 shared=otu.dat | |
20 #end if | |
21 #if $label: | |
22 ,label=${ str($label).replace(",","-") } | |
23 #end if | |
24 #if $groups: | |
25 ,groups=${ str($groups).replace(",","-") } | |
26 #end if | |
27 #if $abundance: | |
28 ,abundance=$abundance | |
29 #end if | |
30 #if $samples: | |
31 ,samples=$samples | |
32 #end if | |
33 )' | |
34 | sed 's/ //g' ## mothur trips over whitespace | |
35 | mothur | |
36 | tee mothur.out.log | |
37 ]]></command> | |
38 <inputs> | |
39 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - OTU Shared or Relabund"/> | |
40 <param name="label" type="select" optional="true" label="label - OTU Labels" multiple="true"> | |
41 <expand macro="labeloptions"/> | |
42 </param> | |
43 <param name="groups" type="select" optional="true" label="groups - Pairwise comparision groups" multiple="true"> | |
44 <options> | |
45 <filter type="data_meta" ref="otu" key="groups"/> | |
46 </options> | |
47 </param> | |
48 <param name="abundance" type="integer" optional="true" value="" min="0" max="100" label="abundance - list OTU names at this abundance"/> | |
49 <param name="samples" type="integer" optional="true" value="" min="1" label="samples - minimum number of samples requied to list OTU names"/> | |
50 <param name="output" type="select" label="output - fraction or count"> | |
51 <option value="fraction" selected="true">fraction</option> | |
52 <option value="count">count</option> | |
53 </param> | |
54 </inputs> | |
55 <outputs> | |
56 <expand macro="logfile-output"/> | |
57 <collection name="core_microbiome" type="list" label="${tool.name} on ${on_string}: core.microbiome files"> | |
58 <discover_datasets pattern=".*?\.(?P<designation>.*)\.core\.microbiome$" format="tabular"/> | |
59 </collection> | |
60 <collection name="core_microbiome_list" type="list" label="${tool.name} on ${on_string}: core.microbiome list files"> | |
61 <filter>abundance or samples </filter> | |
62 <discover_datasets pattern=".*?\.(?P<designation>.*)\.core\.microbiomelist" format="tabular"/> | |
63 </collection> | |
64 </outputs> | |
65 <tests> | |
66 <test><!-- test with default params --> | |
67 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> | |
68 <output_collection name="core_microbiome" count="36"> | |
69 <element name="0.45" md5="bae9cb5f1d311fe0cfb7ecb72a177261" ftype="tabular"/> | |
70 </output_collection> | |
71 <expand macro="logfile-test"/> | |
72 </test> | |
73 <test><!-- test with list output and label and group select--> | |
74 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> | |
75 <param name="abundance" value="30"/> | |
76 <param name="label" value="0.05,0.22,0.45"/> | |
77 <param name="group" value="forest,pasture"/> | |
78 <output_collection name="core_microbiome" count="3"> | |
79 <element name="0.05" md5="72bb437ab5f3a66965029a616fbaf317" ftype="tabular"/> | |
80 </output_collection> | |
81 <output_collection name="core_microbiome_list" count="3"> | |
82 <element name="0.05" md5="83722b4c52b7faff7fe56ce026250001" ftype="tabular"/> | |
83 </output_collection> | |
84 <expand macro="logfile-test"/> | |
85 </test> | |
86 </tests> | |
87 <help> | |
88 <![CDATA[ | |
89 | |
90 @MOTHUR_OVERVIEW@ | |
91 | |
92 **Command Documentation** | |
93 | |
94 The get.coremicrobiome_ command determines the fraction of OTUs that are found in varying numbers of samples for different minimum relative abundances. | |
95 | |
96 .. _get.coremicrobiome: https://www.mothur.org/wiki/Get.coremicrobiome | |
97 | |
98 v1.27.0: Updated to Mothur 1.33 | |
99 | |
100 ]]> | |
101 </help> | |
102 <expand macro="citations"/> | |
103 </tool> |