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annotate 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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b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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1 <tool id="tabular_to_fastq" name="Tabular to FASTQ" version="1.1.1">
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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2 <description>converter</description>
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3 <command><![CDATA[
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4 python '$__tool_directory__/tabular_to_fastq.py' '$input_file' '$output_file' '$identifier' '$sequence' '$quality'
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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5 ]]></command>
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6 <inputs>
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7 <param name="input_file" type="data" format="tabular" label="Tabular file to convert" />
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8 <param name="identifier" type="data_column" data_ref="input_file" label="Identifier column" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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9 <param name="sequence" type="data_column" data_ref="input_file" label="Sequence column" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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10 <param name="quality" type="data_column" data_ref="input_file" label="Quality column" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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11 </inputs>
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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12 <outputs>
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13 <data name="output_file" format="fastq" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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14 </outputs>
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15 <tests>
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16 <!-- basic test -->
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17 <test>
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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18 <param name="input_file" value="fastq_to_tabular_out_1.tabular" ftype="tabular" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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19 <param name="identifier" value="1" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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20 <param name="sequence" value="2" />
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21 <param name="quality" value="3" />
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22 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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23 </test>
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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24 <!-- color space test -->
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25 <test>
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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26 <param name="input_file" value="fastq_to_tabular_out_2.tabular" ftype="tabular" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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27 <param name="identifier" value="1" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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28 <param name="sequence" value="2" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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29 <param name="quality" value="3" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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30 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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31 </test>
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32 </tests>
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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33 <help><![CDATA[
0
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34 **What it does**
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35
2
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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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.
b8cdc0507586 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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37 ]]></help>
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38 <citations>
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39 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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40 </citations>
0
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41 </tool>