Mercurial > repos > rdvelazquez > bioext_bam2msa

annotate bam2msa.xml @ 2:80fc71979f19 draft default tip

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planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
author rdvelazquez
date Fri, 22 Mar 2019 11:43:12 -0400
parents c7c46222ee0c
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72b7678b5b09 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9a4a7b16c82dfaac1f49ba23a02560d6524233e3\n'-dirty
rdvelazquez
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1 <?xml version="1.0"?>
72b7678b5b09 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9a4a7b16c82dfaac1f49ba23a02560d6524233e3\n'-dirty
rdvelazquez
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2 <tool id="bioext_bam2msa" name="Convert BAM" version="@VERSION@.0">
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c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
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3 <description>to FASTA multiple sequence alignment</description>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
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4 <macros>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
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5 <import>macros.xml</import>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
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6 </macros>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
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7 <expand macro="requirements"/>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
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8 <command detect_errors="exit_code"><![CDATA[
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72b7678b5b09 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9a4a7b16c82dfaac1f49ba23a02560d6524233e3\n'-dirty
rdvelazquez
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9 bam2msa
72b7678b5b09 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9a4a7b16c82dfaac1f49ba23a02560d6524233e3\n'-dirty
rdvelazquez
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10 #if $region_start and $region_end:
72b7678b5b09 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9a4a7b16c82dfaac1f49ba23a02560d6524233e3\n'-dirty
rdvelazquez
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11 -r $region_start:$region_end
72b7678b5b09 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9a4a7b16c82dfaac1f49ba23a02560d6524233e3\n'-dirty
rdvelazquez
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12 #end if
1
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
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13 '$input' '$output'
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
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14 ]]></command>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
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15 <inputs>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
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16 <param name="input" type="data" format="bam,sam" label="Input BAM file"/>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
parents: 0
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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"/>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
parents: 0
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18 <param name="region_end" type="integer" value="0" optional="True" label="End coordinate"/>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
parents: 0
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19 </inputs>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
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20 <outputs>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
parents: 0
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21 <data name="output" format="fasta"/>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
parents: 0
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22 </outputs>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
parents: 0
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23 <tests>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
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24 <test>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
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25 <param name="input" ftype="bam" value="bealign-out1.bam"/>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
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26 <output name="output" file="bam2msa-out1.fa"/>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
parents: 0
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27 </test>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
parents: 0
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28 <test>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
parents: 0
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29 <param name="input" ftype="bam" value="bealign-out2.bam"/>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
parents: 0
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30 <output name="output" file="bam2msa-out2.fa"/>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
parents: 0
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31 </test>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
parents: 0
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32 </tests>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
parents: 0
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33 <help>Extract MSA from a BAM file</help>
c7c46222ee0c planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
parents: 0
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34 <expand macro="citations"/>
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72b7678b5b09 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9a4a7b16c82dfaac1f49ba23a02560d6524233e3\n'-dirty
rdvelazquez
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35 </tool>