Mercurial > repos > iuc > mothur_list_seqs
comparison list.seqs.xml @ 0:24044cd8ef87 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 05:39:09 -0400 |
parents | |
children | 1dcdb5e6c780 |
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-1:000000000000 | 0:24044cd8ef87 |
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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> |