Mercurial > repos > iuc > bioext_bam2msa

annotate bam2msa.xml @ 2:31e5a2d73131 draft

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"planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
author iuc
date Fri, 09 Jul 2021 15:17:20 +0000
parents cf735919c2de
children 3afd5c92b4a1
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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"?>
2
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
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>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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5 <import>macros.xml</import>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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6 <token name="@VERSION_SUFFIX@">0</token>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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7 </macros>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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8 <expand macro="requirements"/>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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9 <command detect_errors="exit_code"><![CDATA[
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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10 bam2msa
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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11 #if $region_start and $region_end:
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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12 -r $region_start:$region_end
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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13 #end if
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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14 '$input' '$output'
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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15 ]]></command>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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16 <inputs>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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17 <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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18 <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"
iuc
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19 <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"
iuc
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20 </inputs>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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21 <outputs>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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22 <data name="output" format="fasta"/>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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23 </outputs>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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24 <tests>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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25 <test>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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26 <param name="input" ftype="bam" value="bealign-out1.bam"/>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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27 <output name="output" file="bam2msa-out1.fa"/>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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28 </test>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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29 <test>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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30 <param name="input" ftype="bam" value="bealign-out2.bam"/>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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31 <output name="output" file="bam2msa-out2.fa"/>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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32 </test>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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33 </tests>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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34 <help>Extract MSA from a BAM file</help>
31e5a2d73131 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
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35 <expand macro="citations"/>
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cf735919c2de planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
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36 </tool>