Mercurial > repos > iuc > mothur_get_otulist

comparison get.otulist.xml @ 2:7a922d81eca2 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 22:16:35 -0400
parents 2e6fb8f23d5e
children
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1:afc85bfc0542 2:7a922d81eca2
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.otulist( 15 echo 'get.otulist(
16 list=otu.dat, 16 list=otu.dat,
17 #if $label: 17 #if $label:
18 label=${ str($label).replace(",","-") }, 18 label=${ str($label).replace(",","-") },
19 #end if 19 #end if
20 sort=$sort 20 sort=$sort
21 )' 21 )'
22 | sed 's/ //g' ## mothur trips over whitespace 22 | sed 's/ //g' ## mothur trips over whitespace
23 | mothur 23 | mothur
24 | tee mothur.out.log 24 | tee mothur.out.log
25 ]]></command> 25 ]]></command>
26 <inputs> 26 <inputs>
27 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/> 27 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
28 <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="By default, uses all if none are selected."> 28 <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="By default, uses all if none are selected.">
29 <expand macro="labeloptions"/> 29 <expand macro="labeloptions"/>
30 </param> 30 </param>
31 <param name="sort" type="select" label="sort - select the output format" help="If otu is selected the output will be otu number followed by the list of names in that otu. If name is selected the output will be a sequence name followed by its otu number"> 31 <param name="sort" type="select" label="sort - select the output format"
32 help="If otu is selected the output will be otu number followed by the list of names in that otu.
33 If name is selected the output will be a sequence name followed by its otu number">
32 <option value="otu" selected="true">otu</option> 34 <option value="otu" selected="true">otu</option>
33 <option value="name">name</option> 35 <option value="name">name</option>
34 </param> 36 </param>
37 <expand macro="param-savelog"/>
35 </inputs> 38 </inputs>
36 <outputs> 39 <outputs>
37 <expand macro="logfile-output"/> 40 <expand macro="logfile-output"/>
38 <collection name="otufiles" type="list" label="${tool.name} on ${on_string}: OTUs per label"> 41 <collection name="otufiles" type="list" label="${tool.name} on ${on_string}: OTUs per label">
39 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.otu" format="mothur.list"/> 42 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.otu" format="mothur.list"/>
43 <test> 46 <test>
44 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 47 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
45 <output_collection name="otufiles" count="36"> 48 <output_collection name="otufiles" count="36">
46 <element name="0.22" md5="9dfa8c449a45d66e7ae6b30b34a821cb" ftype="mothur.list"/> 49 <element name="0.22" md5="9dfa8c449a45d66e7ae6b30b34a821cb" ftype="mothur.list"/>
47 </output_collection> 50 </output_collection>
51 <param name="savelog" value="true"/>
48 <expand macro="logfile-test"/> 52 <expand macro="logfile-test"/>
49 </test> 53 </test>
50 <test> 54 <test>
51 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 55 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
52 <param name="label" value="0.03,0.38,0.41,0.45"/> 56 <param name="label" value="0.03,0.38,0.41,0.45"/>
53 <output_collection name="otufiles" count="4"> 57 <output_collection name="otufiles" count="4">
54 <element name="0.41" md5="b40486b3739a6d5b86459dc17a23c253" ftype="mothur.list"/> 58 <element name="0.41" md5="b40486b3739a6d5b86459dc17a23c253" ftype="mothur.list"/>
55 </output_collection> 59 </output_collection>
60 <param name="savelog" value="true"/>
56 <expand macro="logfile-test"/> 61 <expand macro="logfile-test"/>
57 </test> 62 </test>
58 </tests> 63 </tests>
59 <help> 64 <help><![CDATA[
60 <![CDATA[
61 65
62 @MOTHUR_OVERVIEW@ 66 @MOTHUR_OVERVIEW@
63 67
64 68
65 **Command Documentation** 69 **Command Documentation**
67 The get.otulist_ command parses a list file and creates an .otu file for each distance containing 2 columns. The first column is the OTU number the second column is a list of sequences in that OTU. 71 The get.otulist_ command parses a list file and creates an .otu file for each distance containing 2 columns. The first column is the OTU number the second column is a list of sequences in that OTU.
68 72
69 .. _get.otulist: https://www.mothur.org/wiki/Get.otulist 73 .. _get.otulist: https://www.mothur.org/wiki/Get.otulist
70 74
71 v.1.20.0: Updated to Mothur 1.33 75 v.1.20.0: Updated to Mothur 1.33
72 ]]> 76
73 </help> 77 ]]></help>
74 <expand macro="citations"/> 78 <expand macro="citations"/>
75 </tool> 79 </tool>