Mercurial > repos > iuc > mothur_list_seqs

comparison list.seqs.xml @ 0:1fdda3adf67e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:36:48 -0400
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children 8fc365d239a2
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-1:000000000000 0:1fdda3adf67e
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="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$search.input" search.input.dat &&
11
12 echo 'list.seqs(
13 #if $search.intype == "fasta":
14 fasta=search.input.dat
15 #elif $search.intype == "fastq":
16 fastq=search.input.dat
17 #elif $search.intype == "name":
18 name=search.input.dat
19 #else if $search.intype == "group":
20 group=search.input.dat
21 #elif $search.intype == "alignreport":
22 alignreport=search.input.dat
23 #elif $search.intype == "list":
24 list=search.input.dat
25 #elif $search.intype == "taxonomy":
26 taxonomy=search.input.dat
27 #elif $search.intype == "count":
28 count=search.input.dat
29 #end if
30 )'
31 | sed 's/ //g' ## mothur trips over whitespace
32 | mothur
33 ]]></command>
34 <inputs>
35 <conditional name="search">
36 <param name="intype" type="select" label="Type to list" help="">
37 <option value="fasta">Sequence Fasta</option>
38 <option value="fastq">Sequence Fastq</option>
39 <option value="name">Sequences Name reference</option>
40 <option value="group">Groups</option>
41 <option value="alignreport">Align Report</option>
42 <option value="list">OTU List</option>
43 <option value="taxonomy">Sequence Taxonomy</option>
44 <option value="count">Count Table</option>
45 </param>
46 <when value="fasta">
47 <param name="input" type="data" format="fasta" label="fasta - Fasta"/>
48 </when>
49 <when value="fastq">
50 <param name="input" type="data" format="fastq" label="fasta - Fasta"/>
51 </when>
52 <when value="name">
53 <param name="input" type="data" format="mothur.names" label="name - Names"/>
54 </when>
55 <when value="group">
56 <param name="input" type="data" format="mothur.groups" label="group - Groups"/>
57 </when>
58 <when value="alignreport">
59 <param name="input" type="data" format="mothur.align.report" label="alignreport - Align Report"/>
60 </when>
61 <when value="list">
62 <param name="input" type="data" format="mothur.list" label="list - OTU List"/>
63 </when>
64 <when value="taxonomy">
65 <param name="input" type="data" format="mothur.seq.taxonomy" label="taxonomy - Sequence Taxonomy"/>
66 </when>
67 <when value="count">
68 <param name="input" type="data" format="mothur.count_table" label="count - Count Table"/>
69 </when>
70 </conditional>
71 </inputs>
72 <outputs>
73 <expand macro="logfile-output"/>
74 <data name="out_file" format="mothur.accnos" from_work_dir="search.input*.accnos" label="${tool.name} on ${on_string}: accnos"/>
75 </outputs>
76 <tests>
77 <test><!-- test with fasta -->
78 <param name="intype" value="fasta"/>
79 <param name="input" value="amazon.fasta"/>
80 <output name="out_file" md5="590f62ce757219c2e137a532fcd814d1" ftype="mothur.accnos"/>
81 <expand macro="logfile-test"/>
82 </test>
83 <test><!-- test with count file -->
84 <param name="intype" value="count"/>
85 <param name="input" value="amazon.count_table"/>
86 <output name="out_file" md5="360dfea2de2da4d55e75071b026c83b6" ftype="mothur.accnos"/>
87 <expand macro="logfile-test"/>
88 </test>
89 </tests>
90 <help>
91 <![CDATA[
92
93 @MOTHUR_OVERVIEW@
94
95 **Command Documenation**
96
97 The list.seqs_ command writes out the names of the sequences found within a fasta, name_, group_, list_, align.report_ or taxonomy_ file.
98
99 .. _name: http://www.mothur.org/wiki/Name_file
100 .. _group: http://www.mothur.org/wiki/Group_file
101 .. _list: http://www.mothur.org/wiki/List_file
102 .. _align.report: http://www.mothur.org/wiki/Align.seqs
103 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline
104 .. _list.seqs: http://www.mothur.org/wiki/list.seqs
105
106 v.1.20.0: Updated to mothur 1.33, added count and fastq option
107 ]]>
108 </help>
109 <expand macro="citations"/>
110 </tool>