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comparison fastq_to_tabular.xml @ 1:7da7ddea4425 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author devteam
date Wed, 11 Nov 2015 12:42:45 -0500
parents bc9269529e88
children ccf4e1d1fcbe
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0:bc9269529e88 1:7da7ddea4425
4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement> 4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python">fastq_to_tabular.py '$input_file' '$output_file' $descr_columns '${input_file.extension[len( 'fastq' ):]}'</command> 6 <command interpreter="python">fastq_to_tabular.py '$input_file' '$output_file' $descr_columns '${input_file.extension[len( 'fastq' ):]}'</command>
7 <inputs> 7 <inputs>
8 <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqillumina,fastqsolexa" label="FASTQ file to convert" /> 8 <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqillumina,fastqsolexa" label="FASTQ file to convert" />
9 <param name="descr_columns" type="integer" size="2" value="1" label="How many columns to divide title string into?" help="Typically 2 to take the ID (first word) and decription (rest) as two columns, or 1 to give a single column"> 9 <param name="descr_columns" type="integer" value="1" label="How many columns to divide title string into?" help="Typically 2 to take the ID (first word) and decription (rest) as two columns, or 1 to give a single column">
10 <validator type="in_range" min="1" /> 10 <validator type="in_range" min="1" />
11 </param> 11 </param>
12 </inputs> 12 </inputs>
13 <outputs> 13 <outputs>
14 <data name="output_file" format="tabular" /> 14 <data name="output_file" format="tabular" />
93 93
94 Note the sequences and quality strings have been truncated for display purposes in the above tables. 94 Note the sequences and quality strings have been truncated for display purposes in the above tables.
95 95
96 ------ 96 ------
97 97
98 **Citation**
99
100 If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20562416&gt;`_
101
102
103 </help> 98 </help>
99
100 <citations>
101 <citation type="doi">10.1093/bioinformatics/btq281</citation>
102 </citations>
103
104 </tool> 104 </tool>