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annotate fastq_to_fasta.xml @ 3:a64c24430f5e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit 31edb920789fbd080260f853bc856be72fa7cfa8"
author devteam
date Fri, 01 Nov 2019 13:27:10 -0400
parents 4844c1810c16
children 297962e79f39
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4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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1 <tool id="fastq_to_fasta_python" name="FASTQ to FASTA" version="1.1.1">
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2 <description>converter</description>
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3 <requirements>
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4 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement>
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5 </requirements>
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a64c24430f5e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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6 <edam_topics>
a64c24430f5e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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7 <edam_topic>topic_0622</edam_topic>
a64c24430f5e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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8 </edam_topics>
a64c24430f5e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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9 <edam_operations>
a64c24430f5e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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10 <edam_operation>operation_3434</edam_operation>
a64c24430f5e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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11 </edam_operations>
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12 <command><![CDATA[
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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13 gx-fastq-to-fasta '$input_file' '$output_file' '${input_file.extension[len('fastq'):]}'
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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14 ]]></command>
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15 <inputs>
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16 <param name="input_file" type="data" format="fastq,fastq.gz,fastq.bz2" label="FASTQ file to convert" />
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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17 </inputs>
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18 <outputs>
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19 <data name="output_file" format="fasta" />
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20 </outputs>
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21 <tests>
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22 <!-- basic test -->
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23 <test>
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24 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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25 <output name="output_file" file="fastq_to_fasta_python_1.out" />
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26 </test>
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27 <!-- color space test -->
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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28 <test>
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29 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" />
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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30 <output name="output_file" file="fastq_to_fasta_python_2.out" />
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31 </test>
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32 <!-- test of ignoring invalid score values: this input has ascii characters falling outside of illumina range, but they should not matter -->
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33 <test>
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34 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqillumina" />
4844c1810c16 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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35 <output name="output_file" file="fastq_to_fasta_python_1.out" />
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36 </test>
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37 </tests>
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38 <help><![CDATA[
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39 **What it does**
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40
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41 This tool converts FASTQ sequencing reads to FASTA sequences.
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42 ]]></help>
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43 <citations>
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44 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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45 </citations>
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46 </tool>