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planemo upload for repository https://github.com/phac-nml/galaxy_tools commit c32ec4a9284ec939d001bd7d7d551c15feaa5333
author nml
date Mon, 07 Nov 2022 23:40:55 +0000
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4b00d869c8c0 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit c32ec4a9284ec939d001bd7d7d551c15feaa5333
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1 <tool id="spades_header_fixer" name="SPAdes fasta header fixer" version="1.1.2+galaxy1">
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2 <description>Fixes Spades Fasta ids</description>
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3 <requirements>
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4 <requirement type="package" version="4.7.0">sed</requirement>
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5 </requirements>
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6 <command >sed -r "s/>NODE(_[0-9]+)_(.*)|>contig/>${input.element_identifier}\1_\2/g" $input >$output</command>
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7 <inputs>
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8 <param name="input" type="data" format="fasta" label="Fix these fasta headers"/>
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9 </inputs>
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10 <outputs>
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11 <data name="output" format="fasta"/>
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12 </outputs>
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13 <tests>
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14 <test>
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15 <param name="input" value="spades_before_1.fasta" />
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16 <output name="output" file="spades_header_fixed_1.fasta" ftype="fasta"/>
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17 </test>
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18 <test>
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19 <param name="input" value="spades_before_2.fasta" />
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20 <output name="output" file="spades_header_fixed_2.fasta" ftype="fasta"/>
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21 </test>
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22 </tests>
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24 <help><![CDATA[
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25 SPAdes fasta header fixer
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26 =======
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27
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28 The SPAdes header fixer tool replaces the default value of NODE from SPAdes fasta header(s) to either a filename or a collection identifier.
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29 ]]></help>
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30
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31 <citations>
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32 <citation type="bibtex">@ARTICLE{a1,
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33 title = {SPAdes fasta header fixer},
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34 author = {Philip Mabon},
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35 url = {https://github.com/phac-nml/galaxy_tools}
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36 }
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37 }</citation>
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38 </citations>
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39 </tool>