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comparison tabular_to_fastq.xml @ 2:b8cdc0507586 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
author devteam
date Sat, 30 Sep 2017 13:56:23 -0400
parents 92034dcbb40a
children 68f57cc8fad0
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1:92034dcbb40a 2:b8cdc0507586
1 <tool id="tabular_to_fastq" name="Tabular to FASTQ" version="1.0.0"> 1 <tool id="tabular_to_fastq" name="Tabular to FASTQ" version="1.1.1">
2 <description>converter</description> 2 <description>converter</description>
3 <requirements> 3 <command><![CDATA[
4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement> 4 python '$__tool_directory__/tabular_to_fastq.py' '$input_file' '$output_file' '$identifier' '$sequence' '$quality'
5 </requirements> 5 ]]></command>
6 <command interpreter="python">tabular_to_fastq.py '$input_file' '$output_file' '$identifier' '$sequence' '$quality'</command> 6 <inputs>
7 <inputs> 7 <param name="input_file" type="data" format="tabular" label="Tabular file to convert" />
8 <param name="input_file" type="data" format="tabular" label="Tabular file to convert" /> 8 <param name="identifier" type="data_column" data_ref="input_file" label="Identifier column" />
9 <param name="identifier" label="Identifier column" type="data_column" data_ref="input_file" /> 9 <param name="sequence" type="data_column" data_ref="input_file" label="Sequence column" />
10 <param name="sequence" label="Sequence column" type="data_column" data_ref="input_file" /> 10 <param name="quality" type="data_column" data_ref="input_file" label="Quality column" />
11 <param name="quality" label="Quality column" type="data_column" data_ref="input_file" /> 11 </inputs>
12 </inputs> 12 <outputs>
13 <outputs> 13 <data name="output_file" format="fastq" />
14 <data name="output_file" format="fastq" /> 14 </outputs>
15 </outputs> 15 <tests>
16 <tests> 16 <!-- basic test -->
17 <!-- basic test --> 17 <test>
18 <test> 18 <param name="input_file" value="fastq_to_tabular_out_1.tabular" ftype="tabular" />
19 <param name="input_file" value="fastq_to_tabular_out_1.tabular" ftype="tabular" /> 19 <param name="identifier" value="1" />
20 <param name="identifier" value="1" /> 20 <param name="sequence" value="2" />
21 <param name="sequence" value="2" /> 21 <param name="quality" value="3" />
22 <param name="quality" value="3" /> 22 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
23 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> 23 </test>
24 </test> 24 <!-- color space test -->
25 <!-- color space test --> 25 <test>
26 <test> 26 <param name="input_file" value="fastq_to_tabular_out_2.tabular" ftype="tabular" />
27 <param name="input_file" value="fastq_to_tabular_out_2.tabular" ftype="tabular" /> 27 <param name="identifier" value="1" />
28 <param name="identifier" value="1" /> 28 <param name="sequence" value="2" />
29 <param name="sequence" value="2" /> 29 <param name="quality" value="3" />
30 <param name="quality" value="3" /> 30 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
31 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" /> 31 </test>
32 </test> 32 </tests>
33 </tests> 33 <help><![CDATA[
34 <help>
35 **What it does** 34 **What it does**
36 35
37 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. 36 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.
38 37 ]]></help>
39 </help> 38 <citations>
40 39 <citation type="doi">10.1093/bioinformatics/btq281</citation>
41 <citations> 40 </citations>
42 <citation type="doi">10.1093/bioinformatics/btq281</citation>
43 </citations>
44
45 </tool> 41 </tool>