Mercurial > repos > iuc > mothur_list_seqs

comparison list.seqs.xml @ 0:24044cd8ef87 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:39:09 -0400
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children 1dcdb5e6c780
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-1:000000000000 0:24044cd8ef87
1 <tool profile="16.07" id="mothur_list_seqs" name="List.seqs" version="@WRAPPER_VERSION@.0">
2 <description>Lists the names (accnos) of the sequences</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 "$search.input" search.input.dat &&
14
15 echo 'list.seqs(
16 #if $search.intype == "fasta":
17 fasta=search.input.dat
18 #elif $search.intype == "fastq":
19 fastq=search.input.dat
20 #elif $search.intype == "name":
21 name=search.input.dat
22 #else if $search.intype == "group":
23 group=search.input.dat
24 #elif $search.intype == "alignreport":
25 alignreport=search.input.dat
26 #elif $search.intype == "list":
27 list=search.input.dat
28 #elif $search.intype == "taxonomy":
29 taxonomy=search.input.dat
30 #elif $search.intype == "count":
31 count=search.input.dat
32 #end if
33 )'
34 | sed 's/ //g' ## mothur trips over whitespace
35 | mothur
36 | tee mothur.out.log
37 ]]></command>
38 <inputs>
39 <conditional name="search">
40 <param name="intype" type="select" label="Type to list" help="">
41 <option value="fasta">Sequence Fasta</option>
42 <option value="fastq">Sequence Fastq</option>
43 <option value="name">Sequences Name reference</option>
44 <option value="group">Groups</option>
45 <option value="alignreport">Align Report</option>
46 <option value="list">OTU List</option>
47 <option value="taxonomy">Sequence Taxonomy</option>
48 <option value="count">Count Table</option>
49 </param>
50 <when value="fasta">
51 <param name="input" type="data" format="fasta" label="fasta - Fasta"/>
52 </when>
53 <when value="fastq">
54 <param name="input" type="data" format="fastq" label="fasta - Fasta"/>
55 </when>
56 <when value="name">
57 <param name="input" type="data" format="mothur.names" label="name - Names"/>
58 </when>
59 <when value="group">
60 <param name="input" type="data" format="mothur.groups" label="group - Groups"/>
61 </when>
62 <when value="alignreport">
63 <param name="input" type="data" format="mothur.align.report" label="alignreport - Align Report"/>
64 </when>
65 <when value="list">
66 <param name="input" type="data" format="mothur.list" label="list - OTU List"/>
67 </when>
68 <when value="taxonomy">
69 <param name="input" type="data" format="mothur.seq.taxonomy" label="taxonomy - Sequence Taxonomy"/>
70 </when>
71 <when value="count">
72 <param name="input" type="data" format="mothur.count_table" label="count - Count Table"/>
73 </when>
74 </conditional>
75 </inputs>
76 <outputs>
77 <expand macro="logfile-output"/>
78 <data name="out_file" format="mothur.accnos" from_work_dir="search.input*.accnos" label="${tool.name} on ${on_string}: accnos"/>
79 </outputs>
80 <tests>
81 <test><!-- test with fasta -->
82 <param name="intype" value="fasta"/>
83 <param name="input" value="amazon.fasta"/>
84 <output name="out_file" md5="590f62ce757219c2e137a532fcd814d1" ftype="mothur.accnos"/>
85 <expand macro="logfile-test"/>
86 </test>
87 <test><!-- test with count file -->
88 <param name="intype" value="count"/>
89 <param name="input" value="amazon.count_table"/>
90 <output name="out_file" md5="360dfea2de2da4d55e75071b026c83b6" ftype="mothur.accnos"/>
91 <expand macro="logfile-test"/>
92 </test>
93 </tests>
94 <help>
95 <![CDATA[
96
97 @MOTHUR_OVERVIEW@
98
99 **Command Documentation**
100
101 The list.seqs_ command writes out the names of the sequences found within a fasta, name_, group_, list_, align.report_ or taxonomy_ file.
102
103 .. _name: https://www.mothur.org/wiki/Name_file
104 .. _group: https://www.mothur.org/wiki/Group_file
105 .. _list: https://www.mothur.org/wiki/List_file
106 .. _align.report: https://www.mothur.org/wiki/Align.seqs
107 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
108 .. _list.seqs: https://www.mothur.org/wiki/list.seqs
109
110 v.1.20.0: Updated to mothur 1.33, added count and fastq option
111 ]]>
112 </help>
113 <expand macro="citations"/>
114 </tool>