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comparison obiconvert.xml @ 0:88f705673a3a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
author iuc
date Wed, 12 Apr 2017 17:35:11 -0400
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1 <tool id="obi_convert" name="obiconvert" version="@WRAPPER_VERSION@">
2 <description>converts sequence files to different output formats</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8
9 <command>
10 <![CDATA[
11 obiconvert
12 #if $db
13 -d '$db'
14 #end if
15 #if $tax
16 -t '$tax'
17 #end if
18 ${options_inputtype}
19 ${options_seqtype}
20 --${out_format}-output
21 ${uppercase}
22 ${ecopcrdb}
23 #if str( $ecopcrdb) == "--ecopcrdb"
24 --ecopcrdb-output=${ecopcrdb_output}
25 #end if
26 '${input}' > '${output}'
27 ]]>
28
29 </command>
30
31 <inputs>
32 <param name="input" type="data" format="fastq,fasta,txt,tabular" label="Input sequences file" help="database used for the in silico PCR. The database must be in the ecoPCR format (for example output of obiconvert)" />
33 <param name="db" type="data" optional="true" format="txt,tabular" label="ecoPCR taxonomy database" />
34 <param name="tax" type="data" optional="true" format="txt,tabular" label="NCBI taxonomy dump repository"/>
35 <param name="options_inputtype" type="select" label="Specify the input datatype">
36 <expand macro="inputtype"/>
37 </param>
38 <param name="options_seqtype" type="select" label="Specify the sequence datatype" >
39 <option value="--nuc" selected="true">nucleic</option>
40 <option value="--prot">protein</option>
41 </param>
42 <param name="out_format" type="select" label="Output data type">
43 <option value="fasta" selected="true">fasta</option>
44 <option value="fastq">fastq</option>
45 </param>
46 <param name="ecopcrdb" type="boolean" truevalue="--ecopcrdb" falsevalue="" label="Do you want to create an ecoPCR database from sequence records results?" help="Use this option if you want to generate an ecoPCR database output file" />
47 <param name="uppercase" type="boolean" truevalue="--uppercase" falsevalue="" label="Do you want to print sequences in upper case?" />
48
49 </inputs>
50 <outputs>
51 <data format="txt" name="ecopcrdb_output" label="result.ecopcrdb with ${tool.name} on ${on_string}">
52 <filter>ecopcrdb == True</filter>
53 </data>
54 <data format="fasta" name="output" label="output with ${tool.name} on ${on_string}" >
55 <change_format>
56 <when input="out_format" value="fastq" format="fastq" />
57 </change_format>
58 </data>
59 </outputs>
60 <tests>
61 <test>
62 <param name="input" value="output_obisort.fasta" />
63 <param name="options_inputtype" value="fasta"/>
64 <param name="options_seqtype" value="--nuc"/>
65 <param name="out_format" value="fasta"/>
66 <param name="ecopcrdb" value="False"/>
67 <param name="uppercase" value="True"/>
68 <output name="output" file="output_obiconvert.fasta" ftype="fasta"/>
69 </test>
70 </tests>
71 <help><![CDATA[
72
73 .. class:: infomark
74
75 **What it does**
76
77 obiconvert converts sequence files to different output formats. See the documentation for more details on the different formats.
78
79 Input files can be in :
80
81 fasta format
82
83 extended OBITools fasta format
84
85 Sanger fastq format
86
87 Solexa fastq format
88
89 ecoPCR format
90
91 ecoPCR database format
92
93 GenBank format
94
95 EMBL format
96
97 obiconvert converts those files to the :
98
99 extended OBITools fasta format
100
101 Sanger fastq format
102
103 ecoPCR database format
104
105 If no file name is specified, data is read from standard input.
106
107 @OBITOOLS_LINK@
108
109 ]]>
110
111 </help>
112 <expand macro="citation" />
113 </tool>