Mercurial > repos > iuc > bioext_bam2msa
annotate bam2msa.xml @ 0:12729213b4ae draft
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
author | iuc |
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date | Wed, 16 May 2018 17:34:58 -0400 |
parents | |
children | 0a4ad829d87a |
rev | line source |
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0
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
changeset
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1 <?xml version="1.0"?> |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
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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:
diff
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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:
diff
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4 <macros> |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
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5 <import>macros.xml</import> |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
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|
6 </macros> |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
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7 <expand macro="requirements"/> |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
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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
parents:
diff
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|
9 bam2msa |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
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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
parents:
diff
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11 -r $region_start:$region_end |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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12 #end if |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
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13 '$input' '$output' |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
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|
14 ]]></command> |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
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|
15 <inputs> |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
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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
parents:
diff
changeset
|
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:
diff
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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:
diff
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|
19 </inputs> |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
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20 <outputs> |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
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21 <data name="output" format="fasta"/> |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
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|
22 </outputs> |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
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|
23 <tests> |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
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|
24 <test> |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
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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
parents:
diff
changeset
|
26 <output name="output" file="bam2msa-out1.fa"/> |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
changeset
|
27 </test> |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
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|
28 <test> |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
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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:
diff
changeset
|
30 <output name="output" file="bam2msa-out2.fa"/> |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
changeset
|
31 </test> |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
changeset
|
32 </tests> |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
changeset
|
33 <help>Extract MSA from a BAM file</help> |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
changeset
|
34 <expand macro="citations"/> |
12729213b4ae
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff
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|
35 </tool> |