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annotate tabular_to_fastq.xml @ 3:68f57cc8fad0 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 31edb920789fbd080260f853bc856be72fa7cfa8"
author devteam
date Fri, 01 Nov 2019 13:27:30 -0400
parents b8cdc0507586
children 2dcfbbf9071a
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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>
3
68f57cc8fad0 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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3 <edam_topics>
68f57cc8fad0 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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4 <edam_topic>topic_0622</edam_topic>
68f57cc8fad0 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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5 </edam_topics>
68f57cc8fad0 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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6 <edam_operations>
68f57cc8fad0 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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7 <edam_operation>operation_3434</edam_operation>
68f57cc8fad0 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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8 </edam_operations>
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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9 <command><![CDATA[
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 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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11 ]]></command>
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 <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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13 <param name="input_file" type="data" format="tabular" label="Tabular file to convert" />
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 <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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15 <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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16 <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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17 </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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18 <outputs>
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19 <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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20 </outputs>
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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21 <tests>
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22 <!-- basic test -->
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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 <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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25 <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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26 <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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27 <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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28 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
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29 </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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30 <!-- color space test -->
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31 <test>
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32 <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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33 <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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34 <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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35 <param name="quality" value="3" />
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36 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
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37 </test>
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38 </tests>
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39 <help><![CDATA[
0
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40 **What it does**
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41
2
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42 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.
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43 ]]></help>
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44 <citations>
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45 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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46 </citations>
0
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47 </tool>