Mercurial > repos > iuc > bioext_bam2msa

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planemo upload for repository https://github.com/davebx/bioext-gx/ commit e5a0f251aae89a83d154836029701bbf1c5a17fe
author iuc
date Fri, 10 Oct 2025 13:28:24 +0000
parents a6baa8728699
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cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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1 <?xml version="1.0"?>
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iuc
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2 <tool id="bioext_bam2msa" name="Convert BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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3 <description>to FASTA multiple sequence alignment</description>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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4 <macros>
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5 <import>macros.xml</import>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
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6 </macros>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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iuc
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9 ## avoid bam2msa to create .bai in inputdir
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a6baa8728699 planemo upload for repository https://github.com/davebx/bioext-gx/ commit a7729ad7789e8b120055a9a9b53494acb826b371
iuc
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10 ln -sf '$input' input_bam &&
a6baa8728699 planemo upload for repository https://github.com/davebx/bioext-gx/ commit a7729ad7789e8b120055a9a9b53494acb826b371
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11 ln -sf '$input.metadata.bam_index' input_bam.bai &&
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31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
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12 bam2msa
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13 #if $region_start and $region_end:
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
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14 -r $region_start:$region_end
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
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15 #end if
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a6baa8728699 planemo upload for repository https://github.com/davebx/bioext-gx/ commit a7729ad7789e8b120055a9a9b53494acb826b371
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16 'input_bam'
a6baa8728699 planemo upload for repository https://github.com/davebx/bioext-gx/ commit a7729ad7789e8b120055a9a9b53494acb826b371
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17 '$output'
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18 ]]></command>
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19 <inputs>
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20 <param name="input" type="data" format="bam,sam" label="Input BAM file"/>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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21 <param name="region_start" type="integer" value="0" optional="True" label="Starting coordinate" help="Leave blank to extract all sequences"/>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
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22 <param name="region_end" type="integer" value="0" optional="True" label="End coordinate"/>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
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23 </inputs>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
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24 <outputs>
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25 <data name="output" format="fasta"/>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
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26 </outputs>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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27 <tests>
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28 <test>
3
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29 <param name="input" ftype="bam" value="bam2msa-in1.bam"/>
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30 <output name="output" file="bam2msa-out1.fa"/>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
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31 </test>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
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32 <test>
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33 <param name="input" ftype="bam" value="bam2msa-in2.bam"/>
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34 <output name="output" file="bam2msa-out2.fa"/>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
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35 </test>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
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36 </tests>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
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37 <help>Extract MSA from a BAM file</help>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
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38 <expand macro="citations"/>
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cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
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39 </tool>