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annotate samtools_faidx.xml @ 0:91ebd197998b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
author iuc
date Mon, 12 May 2025 18:06:27 +0000
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91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
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1 <tool id="samtools_faidx" name="Samtools faidx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
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2 <description>Index a FASTA file</description>
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
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3 <macros>
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
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4 <import>macros.xml</import>
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
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5 </macros>
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
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6 <expand macro="requirements"/>
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
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7 <expand macro="stdio"/>
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
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8 <expand macro="version_command"/>
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
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9 <command><![CDATA[
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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10 samtools
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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11 faidx
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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12 '$in_fasta'
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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13 --fai-idx '$output'
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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14 ]]></command>
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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15 <inputs>
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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16 <param name="in_fasta" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="dataset with sequences" />
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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17 </inputs>
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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18 <outputs>
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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19 <data name="output" format="tabular"/>
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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20 </outputs>
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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21 <tests>
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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22 <test expect_num_outputs="1">
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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23 <param name="in_fasta" value="samtools_fastx-out1-2.fasta" />
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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24 <output name="output" file="out.tabular" />
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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25 </test>
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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26 </tests>
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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27 <help><![CDATA[
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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28 **What it does**
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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29
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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30 Runs the ``samtools faidx`` command to index reference sequence in the FASTA format reference sequence.
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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31
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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32 Full `documentation <https://www.htslib.org/doc/samtools-faidx.html>`_ for the faidx command.
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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33 ]]></help>
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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34 <expand macro="citations"/>
91ebd197998b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
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35 </tool>