Mercurial > repos > iuc > mothur_list_seqs

comparison list.seqs.xml @ 2:1dcdb5e6c780 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 22:03:58 -0400
parents 24044cd8ef87
children
comparison
equal deleted inserted replaced
1:37a896516dc3 2:1dcdb5e6c780
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 "$search.input" search.input.dat && 13 ln -s '$search.input' search.input.dat &&
14 14
15 echo 'list.seqs( 15 echo 'list.seqs(
16 #if $search.intype == "fasta": 16 #if $search.intype == "fasta":
17 fasta=search.input.dat 17 fasta=search.input.dat
18 #elif $search.intype == "fastq": 18 #elif $search.intype == "fastq":
19 fastq=search.input.dat 19 fastq=search.input.dat
20 #elif $search.intype == "name": 20 #elif $search.intype == "name":
21 name=search.input.dat 21 name=search.input.dat
22 #else if $search.intype == "group": 22 #else if $search.intype == "group":
23 group=search.input.dat 23 group=search.input.dat
24 #elif $search.intype == "alignreport": 24 #elif $search.intype == "alignreport":
25 alignreport=search.input.dat 25 alignreport=search.input.dat
26 #elif $search.intype == "list": 26 #elif $search.intype == "list":
27 list=search.input.dat 27 list=search.input.dat
28 #elif $search.intype == "taxonomy": 28 #elif $search.intype == "taxonomy":
29 taxonomy=search.input.dat 29 taxonomy=search.input.dat
30 #elif $search.intype == "count": 30 #elif $search.intype == "count":
31 count=search.input.dat 31 count=search.input.dat
32 #end if 32 #end if
33 )' 33 )'
34 | sed 's/ //g' ## mothur trips over whitespace 34 | sed 's/ //g' ## mothur trips over whitespace
35 | mothur 35 | mothur
36 | tee mothur.out.log 36 | tee mothur.out.log
37 ]]></command> 37 ]]></command>
38 <inputs> 38 <inputs>
39 <conditional name="search"> 39 <conditional name="search">
40 <param name="intype" type="select" label="Type to list" help=""> 40 <param name="intype" type="select" label="Type to list" help="">
41 <option value="fasta">Sequence Fasta</option> 41 <option value="fasta">Sequence Fasta</option>
70 </when> 70 </when>
71 <when value="count"> 71 <when value="count">
72 <param name="input" type="data" format="mothur.count_table" label="count - Count Table"/> 72 <param name="input" type="data" format="mothur.count_table" label="count - Count Table"/>
73 </when> 73 </when>
74 </conditional> 74 </conditional>
75 <expand macro="param-savelog"/>
75 </inputs> 76 </inputs>
76 <outputs> 77 <outputs>
77 <expand macro="logfile-output"/> 78 <expand macro="logfile-output"/>
78 <data name="out_file" format="mothur.accnos" from_work_dir="search.input*.accnos" label="${tool.name} on ${on_string}: accnos"/> 79 <data name="accnos" format="mothur.accnos" from_work_dir="search.input*.accnos" label="${tool.name} on ${on_string}: accnos"/>
79 </outputs> 80 </outputs>
80 <tests> 81 <tests>
81 <test><!-- test with fasta --> 82 <test><!-- test with fasta -->
82 <param name="intype" value="fasta"/> 83 <param name="intype" value="fasta"/>
83 <param name="input" value="amazon.fasta"/> 84 <param name="input" value="amazon.fasta"/>
84 <output name="out_file" md5="590f62ce757219c2e137a532fcd814d1" ftype="mothur.accnos"/> 85 <output name="accnos" md5="590f62ce757219c2e137a532fcd814d1" ftype="mothur.accnos"/>
86 <param name="savelog" value="true"/>
85 <expand macro="logfile-test"/> 87 <expand macro="logfile-test"/>
86 </test> 88 </test>
87 <test><!-- test with count file --> 89 <test><!-- test with count file -->
88 <param name="intype" value="count"/> 90 <param name="intype" value="count"/>
89 <param name="input" value="amazon.count_table"/> 91 <param name="input" value="amazon.count_table"/>
90 <output name="out_file" md5="360dfea2de2da4d55e75071b026c83b6" ftype="mothur.accnos"/> 92 <output name="accnos" md5="360dfea2de2da4d55e75071b026c83b6" ftype="mothur.accnos"/>
93 <param name="savelog" value="true"/>
91 <expand macro="logfile-test"/> 94 <expand macro="logfile-test"/>
92 </test> 95 </test>
93 </tests> 96 </tests>
94 <help> 97 <help><![CDATA[
95 <![CDATA[
96 98
97 @MOTHUR_OVERVIEW@ 99 @MOTHUR_OVERVIEW@
98 100
99 **Command Documentation** 101 **Command Documentation**
100 102
106 .. _align.report: https://www.mothur.org/wiki/Align.seqs 108 .. _align.report: https://www.mothur.org/wiki/Align.seqs
107 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline 109 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
108 .. _list.seqs: https://www.mothur.org/wiki/list.seqs 110 .. _list.seqs: https://www.mothur.org/wiki/list.seqs
109 111
110 v.1.20.0: Updated to mothur 1.33, added count and fastq option 112 v.1.20.0: Updated to mothur 1.33, added count and fastq option
111 ]]> 113
112 </help> 114 ]]></help>
113 <expand macro="citations"/> 115 <expand macro="citations"/>
114 </tool> 116 </tool>