Mercurial > repos > devteam > tabular_to_fastq

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
author iuc
date Fri, 04 Oct 2024 10:34:12 +0000
parents e8ca9af08774
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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82c4bc769ba8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
iuc
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1 <tool id="tabular_to_fastq" name="Tabular to FASTQ" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>converter</description>
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82c4bc769ba8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
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3 <macros>
82c4bc769ba8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
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4 <import>macros.xml</import>
82c4bc769ba8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
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5 </macros>
4
1f75d46e55f5 "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_topics>
1f75d46e55f5 "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_topic>topic_0622</edam_topic>
1f75d46e55f5 "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_topics>
1f75d46e55f5 "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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9 <edam_operations>
1f75d46e55f5 "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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10 <edam_operation>operation_3434</edam_operation>
1f75d46e55f5 "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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11 </edam_operations>
5
e8ca9af08774 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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12 <requirements>
e8ca9af08774 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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13 <requirement type="package" version="3.7">python</requirement>
e8ca9af08774 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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14 </requirements>
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15 <command><![CDATA[
643018aa1435 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 python '$__tool_directory__/tabular_to_fastq.py' '$input_file' '$output_file' '$identifier' '$sequence' '$quality'
643018aa1435 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 ]]></command>
643018aa1435 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 <inputs>
643018aa1435 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="input_file" type="data" format="tabular" label="Tabular file to convert" />
643018aa1435 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="identifier" type="data_column" data_ref="input_file" label="Identifier column" />
643018aa1435 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 <param name="sequence" type="data_column" data_ref="input_file" label="Sequence column" />
643018aa1435 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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22 <param name="quality" type="data_column" data_ref="input_file" label="Quality column" />
643018aa1435 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 </inputs>
643018aa1435 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 <outputs>
643018aa1435 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 <data name="output_file" format="fastq" />
643018aa1435 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 </outputs>
643018aa1435 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 <tests>
643018aa1435 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 <!-- basic test -->
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29 <test>
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30 <param name="input_file" value="fastq_to_tabular_out_1.tabular" ftype="tabular" />
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31 <param name="identifier" value="1" />
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32 <param name="sequence" value="2" />
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33 <param name="quality" value="3" />
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34 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
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35 </test>
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36 <!-- color space test -->
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37 <test>
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38 <param name="input_file" value="fastq_to_tabular_out_2.tabular" ftype="tabular" />
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39 <param name="identifier" value="1" />
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40 <param name="sequence" value="2" />
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41 <param name="quality" value="3" />
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42 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
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43 </test>
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44 </tests>
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45 <help><![CDATA[
0
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46 **What it does**
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47
3
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48 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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49 ]]></help>
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50 <citations>
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51 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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52 </citations>
0
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53 </tool>