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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
author iuc
date Fri, 04 Oct 2024 10:34:07 +0000
parents 25ef82e04b49
children
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6156c02cd993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
iuc
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1 <tool id="fastq_to_fasta_python" name="FASTQ to FASTA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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74831e85c49b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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2 <description>converter</description>
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25ef82e04b49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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3 <macros>
25ef82e04b49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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4 <import>macros.xml</import>
25ef82e04b49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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5 </macros>
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b81234d203a1 "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>
b81234d203a1 "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>
b81234d203a1 "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>
b81234d203a1 "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>
b81234d203a1 "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>
b81234d203a1 "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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6156c02cd993 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
iuc
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12 <expand macro="requirements"/>
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74831e85c49b 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 <command><![CDATA[
74831e85c49b 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 gx-fastq-to-fasta '$input_file' '$output_file' '${input_file.extension[len('fastq'):]}'
74831e85c49b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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15 ]]></command>
74831e85c49b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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16 <inputs>
74831e85c49b 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 <param name="input_file" type="data" format="fastq,fastq.gz,fastq.bz2" label="FASTQ file to convert" />
74831e85c49b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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18 </inputs>
74831e85c49b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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19 <outputs>
74831e85c49b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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20 <data name="output_file" format="fasta" />
74831e85c49b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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21 </outputs>
74831e85c49b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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22 <tests>
74831e85c49b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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23 <!-- basic test -->
74831e85c49b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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24 <test>
74831e85c49b 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 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
74831e85c49b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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26 <output name="output_file" file="fastq_to_fasta_python_1.out" />
74831e85c49b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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27 </test>
74831e85c49b 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 <!-- color space test -->
74831e85c49b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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29 <test>
74831e85c49b 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 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" />
74831e85c49b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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31 <output name="output_file" file="fastq_to_fasta_python_2.out" />
74831e85c49b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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32 </test>
74831e85c49b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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33 <!-- test of ignoring invalid score values: this input has ascii characters falling outside of illumina range, but they should not matter -->
74831e85c49b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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34 <test>
74831e85c49b 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 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqillumina" />
74831e85c49b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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36 <output name="output_file" file="fastq_to_fasta_python_1.out" />
74831e85c49b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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37 </test>
74831e85c49b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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38 </tests>
74831e85c49b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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39 <help><![CDATA[
0
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40 **What it does**
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41
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42 This tool converts FASTQ sequencing reads to FASTA sequences.
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43 ]]></help>
74831e85c49b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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44 <citations>
74831e85c49b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit f2582539542b33240234e8ea6093e25d0aee9b6a
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45 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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46 </citations>
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47 </tool>