Mercurial > repos > xuebing > sharplabtool
comparison tools/fastq/tabular_to_fastq.xml @ 0:9071e359b9a3
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| author | xuebing |
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| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 <tool id="tabular_to_fastq" name="Tabular to FASTQ" version="1.0.0"> | |
| 2 <description>converter</description> | |
| 3 <command interpreter="python">tabular_to_fastq.py '$input_file' '$output_file' '$identifier' '$sequence' '$quality'</command> | |
| 4 <inputs> | |
| 5 <param name="input_file" type="data" format="tabular" label="Tabular file to convert" /> | |
| 6 <param name="identifier" label="Identifier column" type="data_column" data_ref="input_file" /> | |
| 7 <param name="sequence" label="Sequence column" type="data_column" data_ref="input_file" /> | |
| 8 <param name="quality" label="Quality column" type="data_column" data_ref="input_file" /> | |
| 9 </inputs> | |
| 10 <outputs> | |
| 11 <data name="output_file" format="fastq" /> | |
| 12 </outputs> | |
| 13 <tests> | |
| 14 <!-- basic test --> | |
| 15 <test> | |
| 16 <param name="input_file" value="fastq_to_tabular_out_1.tabular" ftype="tabular" /> | |
| 17 <param name="identifier" value="1" /> | |
| 18 <param name="sequence" value="2" /> | |
| 19 <param name="quality" value="3" /> | |
| 20 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> | |
| 21 </test> | |
| 22 <!-- color space test --> | |
| 23 <test> | |
| 24 <param name="input_file" value="fastq_to_tabular_out_2.tabular" ftype="tabular" /> | |
| 25 <param name="identifier" value="1" /> | |
| 26 <param name="sequence" value="2" /> | |
| 27 <param name="quality" value="3" /> | |
| 28 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" /> | |
| 29 </test> | |
| 30 </tests> | |
| 31 <help> | |
| 32 **What it does** | |
| 33 | |
| 34 This tool attempts to convert a tabular file containing sequencing read data to a FASTQ formatted file. The FASTQ Groomer tool should always be used on the output of this tool. | |
| 35 | |
| 36 ------ | |
| 37 | |
| 38 **Citation** | |
| 39 | |
| 40 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. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ | |
| 41 | |
| 42 | |
| 43 </help> | |
| 44 </tool> |