Mercurial > repos > iuc > mothur_bin_seqs

comparison bin.seqs.xml @ 0:06a0aef8a5f7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:43:37 -0400
parents
children 905ff5f3e91d
comparison
equal deleted inserted replaced
-1:000000000000 0:06a0aef8a5f7
1 <tool profile="16.07" id="mothur_bin_seqs" name="Bin.seqs" version="@WRAPPER_VERSION@.0">
2 <description>Order Sequences by OTU</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$name" name.dat &&
14 ln -s "$group" group.dat &&
15 ln -s "$fasta" fasta.dat &&
16 ln -s "$otu" otu.dat &&
17 ln -s "$count" count.dat &&
18
19 echo 'bin.seqs(
20 #if $name:
21 name=name.dat,
22 #end if
23 #if $group:
24 group=group.dat,
25 #end if
26 #if $label:
27 label=${ str($label).replace(",","-") },
28 #end if
29 #if $count:
30 count=count.dat,
31 #end if
32 fasta=fasta.dat,
33 list=otu.dat
34 )'
35 | sed 's/ //g' ## mothur trips over whitespace
36 | mothur
37 | tee mothur.out.log
38 ]]></command>
39 <inputs>
40 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/>
41 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
42 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
43 <param name="label" type="select" label="label - OTU Labels" multiple="true">
44 <expand macro="labeloptions"/>
45 </param>
46 <param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/>
47 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - Represents the number of duplicate sequences for a given representitive sequence"/>
48 </inputs>
49 <outputs>
50 <expand macro="logfile-output"/>
51 <collection name="fastafiles" type="list" label="${tool.name} on ${on_string}: fastafiles per label">
52 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.fasta" format="fasta"/>
53 </collection>
54 </outputs>
55 <tests>
56 <test><!-- test with defaults -->
57 <param name="otu" value="amazon.an.list"/>
58 <param name="fasta" value="amazon.fasta"/>
59 <output_collection name="fastafiles" count="36">
60 <element name="0.22" md5="8fd8dd141561dc3e574e0c3f356e7e84" ftype="fasta"/>
61 </output_collection>
62 <expand macro="logfile-test"/>
63 </test>
64 <test><!-- test with group and name file and label select -->
65 <param name="otu" value="amazon.an.list"/>
66 <param name="fasta" value="amazon.fasta"/>
67 <param name="name" value="amazon.names"/>
68 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
69 <param name="label" value="0.03,0.05,0.22"/>
70 <output_collection name="fastafiles" count="3">
71 <element name="0.22" md5="02755d06b535fdcdb5a70b6eb767d1f6" ftype="fasta"/>
72 </output_collection>
73 <expand macro="logfile-test"/>
74 </test>
75 </tests>
76 <help>
77 <![CDATA[
78
79 @MOTHUR_OVERVIEW@
80
81 **Command Documentation**
82
83 The bin.seqs_ command generates fasta-formatted files where sequences are ordered according to the OTU from the list_file_ that they belong to. Such an output may be helpful for generating primers specific to an OTU or for classification of sequences.
84
85 .. _list_file: https://www.mothur.org/wiki/List_file
86 .. _bin.seqs: https://www.mothur.org/wiki/Bin.seqs
87 ]]>
88 </help>
89 <expand macro="citations"/>
90 </tool>