Mercurial > repos > iuc > obi_tab
comparison obitab.xml @ 0:e606e311396a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
author | iuc |
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date | Wed, 12 Apr 2017 17:39:41 -0400 |
parents | |
children | c92e057db87a |
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-1:000000000000 | 0:e606e311396a |
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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> |