Mercurial > repos > iuc > mothur_bin_seqs

comparison bin.seqs.xml @ 3:82c917a4ed55 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 22:07:19 -0400
parents 905ff5f3e91d
children
comparison
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2:905ff5f3e91d 3:82c917a4ed55
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 "$name" name.dat && 13 ln -s '$name' name.dat &&
14 ln -s "$group" group.dat && 14 ln -s '$group' group.dat &&
15 ln -s "$fasta" fasta.dat && 15 ln -s '$fasta' fasta.dat &&
16 ln -s "$otu" otu.dat && 16 ln -s '$otu' otu.dat &&
17 ln -s "$count" count.dat && 17 ln -s '$count' count.dat &&
18 18
19 echo 'bin.seqs( 19 echo 'bin.seqs(
20 #if $name: 20 #if $name:
21 name=name.dat, 21 name=name.dat,
22 #end if 22 #end if
23 #if $group: 23 #if $group:
24 group=group.dat, 24 group=group.dat,
25 #end if 25 #end if
26 #if $label: 26 #if $label:
27 label=${ str($label).replace(",","-") }, 27 label=${ str($label).replace(",","-") },
28 #end if 28 #end if
29 #if $count: 29 #if $count:
30 count=count.dat, 30 count=count.dat,
31 #end if 31 #end if
32 fasta=fasta.dat, 32 fasta=fasta.dat,
33 list=otu.dat 33 list=otu.dat
34 )' 34 )'
35 | sed 's/ //g' ## mothur trips over whitespace 35 | sed 's/ //g' ## mothur trips over whitespace
36 | mothur 36 | mothur
37 | tee mothur.out.log 37 | tee mothur.out.log
38 ]]></command> 38 ]]></command>
39 <inputs> 39 <inputs>
40 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/> 40 <param argument="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/>
41 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/> 41 <param argument="list" 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"/> 42 <param argument="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"> 43 <param argument="label" type="select" multiple="true" label="label - OTU Labels">
44 <expand macro="labeloptions"/> 44 <expand macro="labeloptions"/>
45 </param> 45 </param>
46 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/> 46 <param argument="group" type="data" format="mothur.groups" 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"/> 47 <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - Count Table"
48 help="Represents the number of duplicate sequences for a given representitive sequence"/>
49 <expand macro="param-savelog"/>
48 </inputs> 50 </inputs>
49 <outputs> 51 <outputs>
50 <expand macro="logfile-output"/> 52 <expand macro="logfile-output"/>
51 <collection name="fastafiles" type="list" label="${tool.name} on ${on_string}: fastafiles per label"> 53 <collection name="fastafiles" type="list" label="${tool.name} on ${on_string}: fastafiles per label">
52 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.fasta" format="fasta"/> 54 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.fasta" format="fasta"/>
55 <tests> 57 <tests>
56 <test><!-- test with defaults --> 58 <test><!-- test with defaults -->
57 <param name="otu" value="amazon.an.list"/> 59 <param name="otu" value="amazon.an.list"/>
58 <param name="fasta" value="amazon.fasta"/> 60 <param name="fasta" value="amazon.fasta"/>
59 <output_collection name="fastafiles" count="36"> 61 <output_collection name="fastafiles" count="36">
60 <element name="0.22" md5="8fd8dd141561dc3e574e0c3f356e7e84" ftype="fasta"/> 62 <element name="0.22" ftype="fasta">
63 <assert_contents>
64 <expand macro="test-fasta-format"/>
65 <has_text text="U68589"/>
66 </assert_contents>
67 </element>
61 </output_collection> 68 </output_collection>
69 <param name="savelog" value="true"/>
62 <expand macro="logfile-test"/> 70 <expand macro="logfile-test"/>
63 </test> 71 </test>
64 <test><!-- test with group and name file and label select --> 72 <test><!-- test with group and name file and label select -->
65 <param name="otu" value="amazon.an.list"/> 73 <param name="otu" value="amazon.an.list"/>
66 <param name="fasta" value="amazon.fasta"/> 74 <param name="fasta" value="amazon.fasta"/>
67 <param name="name" value="amazon.names"/> 75 <param name="name" value="amazon.names"/>
68 <param name="group" value="amazon.groups" ftype="mothur.groups"/> 76 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
69 <param name="label" value="0.03,0.05,0.22"/> 77 <param name="label" value="0.03,0.05,0.22"/>
70 <output_collection name="fastafiles" count="3"> 78 <output_collection name="fastafiles" count="3">
71 <element name="0.22" md5="02755d06b535fdcdb5a70b6eb767d1f6" ftype="fasta"/> 79 <element name="0.22" ftype="fasta">
80 <assert_contents>
81 <expand macro="test-fasta-format"/>
82 <has_text text="U68589"/>
83 </assert_contents>
84 </element>
72 </output_collection> 85 </output_collection>
86 <param name="savelog" value="true"/>
73 <expand macro="logfile-test"/> 87 <expand macro="logfile-test"/>
74 </test> 88 </test>
75 </tests> 89 </tests>
76 <help> 90 <help><![CDATA[
77 <![CDATA[
78 91
79 @MOTHUR_OVERVIEW@ 92 @MOTHUR_OVERVIEW@
80 93
81 **Command Documentation** 94 **Command Documentation**
82 95
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. 96 The bin.seqs_ command generates fasta-formatted files where sequences are ordered according to the OTU
97 from the list_file_ that they belong to. Such an output may be helpful for generating primers specific
98 to an OTU or for classification of sequences.
84 99
85 .. _list_file: https://www.mothur.org/wiki/List_file 100 .. _list_file: https://www.mothur.org/wiki/List_file
86 .. _bin.seqs: https://www.mothur.org/wiki/Bin.seqs 101 .. _bin.seqs: https://www.mothur.org/wiki/Bin.seqs
87 ]]> 102
88 </help> 103 ]]></help>
89 <expand macro="citations"/> 104 <expand macro="citations"/>
90 </tool> 105 </tool>