Mercurial > repos > iuc > bioext_bam2msa

annotate bam2msa.xml @ 1:f5792425ea50 draft

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"planemo upload for repository https://github.com/davebx/bioext-gx/ commit 9a163dd8880c14f371e2603389f4951881a74b25"
author iuc
date Thu, 13 May 2021 16:57:46 +0000
parents 12729213b4ae
children 0a4ad829d87a
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12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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2 <tool id="bioext_bam2msa" name="Convert BAM" version="@VERSION@.0">
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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3 <description>to FASTA multiple sequence alignment</description>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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4 <macros>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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5 <import>macros.xml</import>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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6 </macros>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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7 <expand macro="requirements"/>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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8 <command detect_errors="exit_code"><![CDATA[
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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9 bam2msa
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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10 #if $region_start and $region_end:
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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11 -r $region_start:$region_end
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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12 #end if
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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13 '$input' '$output'
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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14 ]]></command>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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15 <inputs>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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16 <param name="input" type="data" format="bam,sam" label="Input BAM file"/>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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17 <param name="region_start" type="integer" value="0" optional="True" label="Starting coordinate" help="Leave blank to extract all sequences"/>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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18 <param name="region_end" type="integer" value="0" optional="True" label="End coordinate"/>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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19 </inputs>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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20 <outputs>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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21 <data name="output" format="fasta"/>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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22 </outputs>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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23 <tests>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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24 <test>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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25 <param name="input" ftype="bam" value="bealign-out1.bam"/>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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26 <output name="output" file="bam2msa-out1.fa"/>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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27 </test>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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28 <test>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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29 <param name="input" ftype="bam" value="bealign-out2.bam"/>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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30 <output name="output" file="bam2msa-out2.fa"/>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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31 </test>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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32 </tests>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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33 <help>Extract MSA from a BAM file</help>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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34 <expand macro="citations"/>
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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35 </tool>