Mercurial > repos > iuc > bioext_bam2msa

annotate bam2msa.xml @ 0:cf735919c2de draft

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planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
author iuc
date Wed, 16 May 2018 17:34:05 -0400
parents
children 31e5a2d73131
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cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
cf735919c2de 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">
cf735919c2de 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>
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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4 <macros>
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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5 <import>macros.xml</import>
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff changeset
6 </macros>
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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7 <expand macro="requirements"/>
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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8 <command detect_errors="exit_code"><![CDATA[
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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9 bam2msa
cf735919c2de 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:
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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11 -r $region_start:$region_end
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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12 #end if
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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13 '$input' '$output'
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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14 ]]></command>
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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15 <inputs>
cf735919c2de 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"/>
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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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"/>
cf735919c2de 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"/>
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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19 </inputs>
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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20 <outputs>
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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21 <data name="output" format="fasta"/>
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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22 </outputs>
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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23 <tests>
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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24 <test>
cf735919c2de 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"/>
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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26 <output name="output" file="bam2msa-out1.fa"/>
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff changeset
27 </test>
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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28 <test>
cf735919c2de 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"/>
cf735919c2de 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"/>
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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31 </test>
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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32 </tests>
cf735919c2de 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>
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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34 <expand macro="citations"/>
cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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35 </tool>