Mercurial > repos > iuc > mothur_parse_list

comparison parse.list.xml @ 3:fe05fc98c62a 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 09:48:51 -0500
parents 033b821e30e1
children 1f3a245edf62
comparison
equal deleted inserted replaced
2:f08c4ee023da 3:fe05fc98c62a
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 ln -s "$group" group.dat && 14 ln -s '$group' group.dat &&
15 ln -s "$count" count.dat && 15 ln -s '$count' count.dat &&
16 16
17 echo 'parse.list( 17 echo 'parse.list(
18 list=otu.dat, 18 list=otu.dat,
19 #if $label: 19 #if $label:
20 label=${ str($label).replace(",","-") }, 20 label=${ str($label).replace(",","-") },
21 #end if 21 #end if
22 #if $count: 22 #if $count:
23 count=count.dat, 23 count=count.dat,
24 #end if 24 #end if
25 group=group.dat 25 group=group.dat
26 )' 26 )'
27 | sed 's/ //g' ## mothur trips over whitespace 27 | sed 's/ //g' ## mothur trips over whitespace
28 | mothur 28 | mothur
29 | tee mothur.out.log 29 | tee mothur.out.log
30 ]]></command> 30 ]]></command>
31 <inputs> 31 <inputs>
32 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/> 32 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
33 <param name="group" type="data" format="mothur.groups" label="group - Sequences Name reference"/> 33 <param name="group" type="data" format="mothur.groups" label="group - Sequences Name reference"/>
34 <param name="label" type="select" optional="true" multiple="true" label="label - To filter: Select OTU Labels to include"> 34 <param name="label" type="select" optional="true" multiple="true" label="label - To filter: Select OTU Labels to include">
57 <param name="label" value="0.03,0.05"/> 57 <param name="label" value="0.03,0.05"/>
58 <output_collection name="listfiles" count="4"/> 58 <output_collection name="listfiles" count="4"/>
59 <expand macro="logfile-test"/> 59 <expand macro="logfile-test"/>
60 </test> 60 </test>
61 </tests> 61 </tests>
62 <help> 62 <help><![CDATA[
63 <![CDATA[
64 63
65 @MOTHUR_OVERVIEW@ 64 @MOTHUR_OVERVIEW@
66 65
67 **Command Documentation** 66 **Command Documentation**
68 67
71 .. _list: https://www.mothur.org/wiki/List_file 70 .. _list: https://www.mothur.org/wiki/List_file
72 .. _group: https://www.mothur.org/wiki/Group_file 71 .. _group: https://www.mothur.org/wiki/Group_file
73 .. _parse.list: https://www.mothur.org/wiki/Parse.list 72 .. _parse.list: https://www.mothur.org/wiki/Parse.list
74 73
75 v.1.19.0: Updated to mothur 1.33, added count parameter 74 v.1.19.0: Updated to mothur 1.33, added count parameter
76 ]]> 75
77 </help> 76 ]]></help>
78 <expand macro="citations"/> 77 <expand macro="citations"/>
79 </tool> 78 </tool>