Mercurial > repos > iuc > mothur_get_coremicrobiome

comparison get.coremicrobiome.xml @ 3:5e29cbb2fdef draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 10:09:11 -0500
parents af8e6f1110b3
children a6e3c040eb53
comparison
equal deleted inserted replaced
2:cedb055d7f33 3:5e29cbb2fdef
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"/>
82 <element name="0.05" md5="83722b4c52b7faff7fe56ce026250001" ftype="tabular"/> 82 <element name="0.05" md5="83722b4c52b7faff7fe56ce026250001" ftype="tabular"/>
83 </output_collection> 83 </output_collection>
84 <expand macro="logfile-test"/> 84 <expand macro="logfile-test"/>
85 </test> 85 </test>
86 </tests> 86 </tests>
87 <help> 87 <help><![CDATA[
88 <![CDATA[
89 88
90 @MOTHUR_OVERVIEW@ 89 @MOTHUR_OVERVIEW@
91 90
92 **Command Documentation** 91 **Command Documentation**
93 92
95 94
96 .. _get.coremicrobiome: https://www.mothur.org/wiki/Get.coremicrobiome 95 .. _get.coremicrobiome: https://www.mothur.org/wiki/Get.coremicrobiome
97 96
98 v1.27.0: Updated to Mothur 1.33 97 v1.27.0: Updated to Mothur 1.33
99 98
100 ]]> 99 ]]></help>
101 </help>
102 <expand macro="citations"/> 100 <expand macro="citations"/>
103 </tool> 101 </tool>