[2] | 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 | </help> |
---|
| 37 | </tool> |
---|