Mercurial > repos > iuc > mothur_phylotype

comparison phylotype.xml @ 3:61846dca0ad1 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 09:14:14 -0500
parents 4f5ecd0c94b3
children a9da762b1688
comparison
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2:1cb5e1ab17f5 3:61846dca0ad1
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 "$taxonomy" taxonomy.dat && 13 ln -s '$taxonomy' taxonomy.dat &&
14 ln -s "$name" name.dat && 14 ln -s '$name' name.dat &&
15 15
16 echo 'phylotype( 16 echo 'phylotype(
17 taxonomy=taxonomy.dat 17 taxonomy=taxonomy.dat
18 #if $cutoff: 18 #if $cutoff:
19 ,cutoff=$cutoff 19 ,cutoff=$cutoff
20 #end if 20 #end if
21 #if $name: 21 #if $name:
22 ,name=name.dat 22 ,name=name.dat
23 #end if 23 #end if
24 #if $label: 24 #if $label:
25 ,label=${ str($label).replace(",","-") } 25 ,label=${ str($label).replace(",","-") }
26 #end if 26 #end if
27 )' 27 )'
28 | sed 's/ //g' ## mothur trips over whitespace 28 | sed 's/ //g' ## mothur trips over whitespace
29 | mothur 29 | mothur
30 | tee mothur.out.log 30 | tee mothur.out.log
31 ]]></command> 31 ]]></command>
32 <inputs> 32 <inputs>
33 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy"/> 33 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy"/>
34 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names reference file for the taxonomy"/> 34 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names reference file for the taxonomy"/>
35 <param name="label" type="select" label="label - Taxonomy Levels to report (All when none are selected)" multiple="true"> 35 <param name="label" type="select" label="label - Taxonomy Levels to report (All when none are selected)" multiple="true">
69 <output name="sabund" md5="582825c475bffbf7e450156ff26c844a" ftype="mothur.sabund"/> 69 <output name="sabund" md5="582825c475bffbf7e450156ff26c844a" ftype="mothur.sabund"/>
70 <output name="otulist" md5="424a2c62df2e37b32542731b9631f8ed" ftype="mothur.list"/> 70 <output name="otulist" md5="424a2c62df2e37b32542731b9631f8ed" ftype="mothur.list"/>
71 <expand macro="logfile-test"/> 71 <expand macro="logfile-test"/>
72 </test> 72 </test>
73 </tests> 73 </tests>
74 <help> 74 <help><![CDATA[
75 <![CDATA[
76 75
77 @MOTHUR_OVERVIEW@ 76 @MOTHUR_OVERVIEW@
78 77
79 **Command Documentation** 78 **Command Documentation**
80 79
83 .. _list: https://www.mothur.org/wiki/List_file 82 .. _list: https://www.mothur.org/wiki/List_file
84 .. _rabund: https://www.mothur.org/wiki/Rabund_file 83 .. _rabund: https://www.mothur.org/wiki/Rabund_file
85 .. _sabund: https://www.mothur.org/wiki/Sabund_file 84 .. _sabund: https://www.mothur.org/wiki/Sabund_file
86 .. _phylotype: https://www.mothur.org/wiki/Phylotype 85 .. _phylotype: https://www.mothur.org/wiki/Phylotype
87 86
88 ]]> 87 ]]></help>
89 </help>
90 <expand macro="citations"/> 88 <expand macro="citations"/>
91 </tool> 89 </tool>