Mercurial > repos > devteam > tabular_to_fastq
view tabular_to_fastq.xml @ 5:e8ca9af08774 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
author | iuc |
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date | Wed, 19 Feb 2020 17:08:16 +0000 |
parents | 1f75d46e55f5 |
children | 82c4bc769ba8 |
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<tool id="tabular_to_fastq" name="Tabular to FASTQ" version="@TOOL_VERSION@"> <description>converter</description> <edam_topics> <edam_topic>topic_0622</edam_topic> </edam_topics> <edam_operations> <edam_operation>operation_3434</edam_operation> </edam_operations> <macros> <import>macros.xml</import> </macros> <requirements> <requirement type="package" version="3.7">python</requirement> </requirements> <command><![CDATA[ python '$__tool_directory__/tabular_to_fastq.py' '$input_file' '$output_file' '$identifier' '$sequence' '$quality' ]]></command> <inputs> <param name="input_file" type="data" format="tabular" label="Tabular file to convert" /> <param name="identifier" type="data_column" data_ref="input_file" label="Identifier column" /> <param name="sequence" type="data_column" data_ref="input_file" label="Sequence column" /> <param name="quality" type="data_column" data_ref="input_file" label="Quality column" /> </inputs> <outputs> <data name="output_file" format="fastq" /> </outputs> <tests> <!-- basic test --> <test> <param name="input_file" value="fastq_to_tabular_out_1.tabular" ftype="tabular" /> <param name="identifier" value="1" /> <param name="sequence" value="2" /> <param name="quality" value="3" /> <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> </test> <!-- color space test --> <test> <param name="input_file" value="fastq_to_tabular_out_2.tabular" ftype="tabular" /> <param name="identifier" value="1" /> <param name="sequence" value="2" /> <param name="quality" value="3" /> <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" /> </test> </tests> <help><![CDATA[ **What it does** 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. ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btq281</citation> </citations> </tool>