Mercurial > repos > iuc > miniprot_index

annotate miniprot_index.xml @ 3:3ccb407501d8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
author iuc
date Thu, 13 Jul 2023 09:37:48 +0000
parents b7b6b8188999
children 9e2772125405
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bd3dc3b5aea5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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1 <tool id="miniprot_index" name="Miniprot index" version="@TOOL_VERSION@+galaxy0" profile="21.05">
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2 <description>build a genome index for miniprot</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">miniprot</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
bd3dc3b5aea5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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10 miniprot -d '$output_index' '$input_genome'
bd3dc3b5aea5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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11 ]]></command>
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12 <inputs>
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13 <param name="input_genome" type="data" format="fasta,fasta.gz" label="Genomic sequence (FASTA)" help="Genomic contigs / scaffolds in FASTA format" />
bd3dc3b5aea5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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14 </inputs>
bd3dc3b5aea5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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15 <outputs>
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16 <!-- refine this when miniprot index format is in Galaxy datatypes -->
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17 <data name="output_index" format="binary" label="Miniprot index on ${on_string}" />
bd3dc3b5aea5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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18 </outputs>
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19 <tests>
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20 <test>
bd3dc3b5aea5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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21 <param name="input_genome" value="input_genome.fasta.gz" ftype="fasta" />
bd3dc3b5aea5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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22 <output name="output_index" ftype="binary">
bd3dc3b5aea5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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23 <assert_contents>
2
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24 <has_size value="69720149" delta="1000" />
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25 </assert_contents>
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26 </output>
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27 </test>
bd3dc3b5aea5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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28 </tests>
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29 <help><![CDATA[
bd3dc3b5aea5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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30 Pre-index genomic sequences (contigs, scaffolds or chromosomes) for use in the miniprot_ protein to genome alignment tool.
bd3dc3b5aea5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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31
bd3dc3b5aea5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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32 .. _miniprot: https://github.com/lh3/miniprot
bd3dc3b5aea5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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33 ]]></help>
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34 <expand macro="citation"></expand>
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bd3dc3b5aea5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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35 </tool>