[2] | 1 | <tool id="fastq_to_tabular" name="FASTQ to Tabular" version="1.0.0"> |
---|
| 2 | <description>converter</description> |
---|
| 3 | <command interpreter="python">fastq_to_tabular.py '$input_file' '$output_file' '${input_file.extension[len( 'fastq' ):]}'</command> |
---|
| 4 | <inputs> |
---|
| 5 | <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqillumina,fastqsolexa" label="FASTQ file to convert" /> |
---|
| 6 | </inputs> |
---|
| 7 | <outputs> |
---|
| 8 | <data name="output_file" format="tabular" /> |
---|
| 9 | </outputs> |
---|
| 10 | <tests> |
---|
| 11 | <!-- basic test --> |
---|
| 12 | <test> |
---|
| 13 | <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
---|
| 14 | <output name="output_file" file="fastq_to_tabular_out_1.tabular" /> |
---|
| 15 | </test> |
---|
| 16 | <!-- color space test --> |
---|
| 17 | <test> |
---|
| 18 | <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" /> |
---|
| 19 | <output name="output_file" file="fastq_to_tabular_out_2.tabular" /> |
---|
| 20 | </test> |
---|
| 21 | </tests> |
---|
| 22 | <help> |
---|
| 23 | **What it does** |
---|
| 24 | |
---|
| 25 | This tool converts FASTQ sequencing reads to a Tabular file. |
---|
| 26 | |
---|
| 27 | Tab characters, if present in the source FASTQ file, will be converted to spaces. |
---|
| 28 | |
---|
| 29 | </help> |
---|
| 30 | </tool> |
---|