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comparison obitab.xml @ 0:bf1762a2a475 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 17:35:28 -0400
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children b13c85d63711
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-1:000000000000 0:bf1762a2a475
1 <tool id="obi_tab" name="obitab" version="@WRAPPER_VERSION@">
2 <description>converts sequence file to a tabular file that can be open by a spreadsheet program or R</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8
9 <command>
10
11 <![CDATA[
12 obitab
13 #if $additional_file
14 --omit-attribute='$additional_file'
15 #end if
16 ${output_seq_option}
17 ${no_definition_option}
18 ${options_inputtype}
19 ${options_seqtype}
20
21 '$input' > '$output'
22 ]]>
23
24 </command>
25
26 <inputs>
27 <param name="input" type="data" format="fastq,fasta,txt,tabular" label="Input sequences file" />
28 <param name="output_seq_option" type="boolean" checked="false" truevalue="-o" falsevalue="" label="Do you want to add an extra column?" help="Use this option if you want to add an extra column at the end of the table for the sequence itself"/>
29 <param name="no_definition_option" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Do you want to remove column containing the sequence definition?" help="Use this option if you want to remove column containing the sequence definition in the output tab file"/>
30 <param name="additional_file" type="data" optional="true" format="tabular" label="filter attributes from tabular file" />
31 <param name="options_inputtype" type="select" label="Specify the input datatype">
32 <expand macro="inputtype"/>
33 </param>
34 <param name="options_seqtype" type="select" label="Specify the sequence datatype" >
35 <option value="--nuc" selected="true">nucleic</option>
36 <option value="--prot">protein</option>
37 </param>
38 </inputs>
39 <outputs>
40 <data format="tabular" name="output" label="output.tabular with ${tool.name} on ${on_string}" />
41 </outputs>
42 <tests>
43 <test>
44 <param name="input" value="output_obisort.fastq" />
45 <param name="output_seq_option" value="False"/>
46 <param name="no_definition_option" value="True"/>
47 <param name="options_inputtype" value="fasta"/>
48 <param name="options_seqtype" value="--prot"/>
49 <output name="output" file="output_obitab.txt" ftype="tabular"/>
50 </test>
51 </tests>
52 <help><![CDATA[
53
54
55 .. class:: infomark
56
57 **What it does**
58
59 obitab command converts sequence file to a tabular file that can be open by a spreadsheet program or R
60
61 @OBITOOLS_LINK@
62
63 ]]>
64 </help>
65 <expand macro="citation" />
66 </tool>