Mercurial > repos > iuc > mothur_get_coremicrobiome

comparison get.coremicrobiome.xml @ 2:a1d38f9902d9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:04:46 -0400
parents fb34c63ab676
children
comparison
equal deleted inserted replaced
1:c0b8bcf733cf 2:a1d38f9902d9
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$otu" otu.dat && 13 ln -s '$otu' otu.dat &&
14 14
15 echo 'get.coremicrobiome( 15 echo 'get.coremicrobiome(
16 #if $otu.is_of_type("mothur.relabund"): 16 #if $otu.is_of_type("mothur.relabund"):
17 relabund=otu.dat 17 relabund=otu.dat
18 #elif $otu.is_of_type("mothur.shared"): 18 #elif $otu.is_of_type("mothur.shared"):
19 shared=otu.dat 19 shared=otu.dat
20 #end if 20 #end if
21 #if $label: 21 #if $label:
22 ,label=${ str($label).replace(",","-") } 22 ,label=${ str($label).replace(",","-") }
23 #end if 23 #end if
24 #if $groups: 24 #if $groups:
25 ,groups=${ str($groups).replace(",","-") } 25 ,groups=${ str($groups).replace(",","-") }
26 #end if 26 #end if
27 #if $abundance: 27 #if $abundance:
28 ,abundance=$abundance 28 ,abundance=$abundance
29 #end if 29 #end if
30 #if $samples: 30 #if $samples:
31 ,samples=$samples 31 ,samples=$samples
32 #end if 32 #end if
33 )' 33 )'
34 | sed 's/ //g' ## mothur trips over whitespace 34 | sed 's/ //g' ## mothur trips over whitespace
35 | mothur 35 | mothur
36 | tee mothur.out.log 36 | tee mothur.out.log
37 ]]></command> 37 ]]></command>
38 <inputs> 38 <inputs>
39 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - OTU Shared or Relabund"/> 39 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - OTU Shared or Relabund"/>
40 <param name="label" type="select" optional="true" label="label - OTU Labels" multiple="true"> 40 <param name="label" type="select" optional="true" label="label - OTU Labels" multiple="true">
41 <expand macro="labeloptions"/> 41 <expand macro="labeloptions"/>
49 <param name="samples" type="integer" optional="true" value="" min="1" label="samples - minimum number of samples requied to list OTU names"/> 49 <param name="samples" type="integer" optional="true" value="" min="1" label="samples - minimum number of samples requied to list OTU names"/>
50 <param name="output" type="select" label="output - fraction or count"> 50 <param name="output" type="select" label="output - fraction or count">
51 <option value="fraction" selected="true">fraction</option> 51 <option value="fraction" selected="true">fraction</option>
52 <option value="count">count</option> 52 <option value="count">count</option>
53 </param> 53 </param>
54 <expand macro="param-savelog"/>
54 </inputs> 55 </inputs>
55 <outputs> 56 <outputs>
56 <expand macro="logfile-output"/> 57 <expand macro="logfile-output"/>
57 <collection name="core_microbiome" type="list" label="${tool.name} on ${on_string}: core.microbiome files"> 58 <collection name="core_microbiome" type="list" label="${tool.name} on ${on_string}: core.microbiome files">
58 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.core\.microbiome$" format="tabular"/> 59 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.core\.microbiome$" format="tabular"/>
66 <test><!-- test with default params --> 67 <test><!-- test with default params -->
67 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 68 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
68 <output_collection name="core_microbiome" count="36"> 69 <output_collection name="core_microbiome" count="36">
69 <element name="0.45" md5="bae9cb5f1d311fe0cfb7ecb72a177261" ftype="tabular"/> 70 <element name="0.45" md5="bae9cb5f1d311fe0cfb7ecb72a177261" ftype="tabular"/>
70 </output_collection> 71 </output_collection>
72 <param name="savelog" value="true"/>
71 <expand macro="logfile-test"/> 73 <expand macro="logfile-test"/>
72 </test> 74 </test>
73 <test><!-- test with list output and label and group select--> 75 <test><!-- test with list output and label and group select-->
74 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 76 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
75 <param name="abundance" value="30"/> 77 <param name="abundance" value="30"/>
79 <element name="0.05" md5="72bb437ab5f3a66965029a616fbaf317" ftype="tabular"/> 81 <element name="0.05" md5="72bb437ab5f3a66965029a616fbaf317" ftype="tabular"/>
80 </output_collection> 82 </output_collection>
81 <output_collection name="core_microbiome_list" count="3"> 83 <output_collection name="core_microbiome_list" count="3">
82 <element name="0.05" md5="83722b4c52b7faff7fe56ce026250001" ftype="tabular"/> 84 <element name="0.05" md5="83722b4c52b7faff7fe56ce026250001" ftype="tabular"/>
83 </output_collection> 85 </output_collection>
86 <param name="savelog" value="true"/>
84 <expand macro="logfile-test"/> 87 <expand macro="logfile-test"/>
85 </test> 88 </test>
86 </tests> 89 </tests>
87 <help> 90 <help><![CDATA[
88 <![CDATA[
89 91
90 @MOTHUR_OVERVIEW@ 92 @MOTHUR_OVERVIEW@
91 93
92 **Command Documentation** 94 **Command Documentation**
93 95
95 97
96 .. _get.coremicrobiome: https://www.mothur.org/wiki/Get.coremicrobiome 98 .. _get.coremicrobiome: https://www.mothur.org/wiki/Get.coremicrobiome
97 99
98 v1.27.0: Updated to Mothur 1.33 100 v1.27.0: Updated to Mothur 1.33
99 101
100 ]]> 102 ]]></help>
101 </help>
102 <expand macro="citations"/> 103 <expand macro="citations"/>
103 </tool> 104 </tool>