Mercurial > repos > rdvelazquez > bioext_bealign

comparison bealign.xml @ 3:f7866771310a 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 13:03:03 -0400
parents 85d823cf0872
children
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2:85d823cf0872 3:f7866771310a
11 bealign --reference '$select_reference.reference' --alphabet $advanced.alphabet 11 bealign --reference '$select_reference.reference' --alphabet $advanced.alphabet
12 #if $advanced.expected_identity: 12 #if $advanced.expected_identity:
13 --expected-identity $advanced.expected_identity 13 --expected-identity $advanced.expected_identity
14 #end if 14 #end if
15 --score-matrix $advanced.score_matrix $advanced.reverse_complement $advanced.keep_reference 15 --score-matrix $advanced.score_matrix $advanced.reverse_complement $advanced.keep_reference
16 #if $advanced.discard:
17 --discard '$discarded_reads'
18 #end if
16 '$input' '$output' 19 '$input' '$output'
17 ]]></command> 20 ]]></command>
18 <inputs> 21 <inputs>
19 <param name="input" type="data" format="fasta" label="Input reads"/> 22 <param name="input" type="data" format="fasta" label="Input reads"/>
20 <conditional name="select_reference"> 23 <conditional name="select_reference">
64 <option value="DNA95">DNA, 95% expected identity</option> 67 <option value="DNA95">DNA, 95% expected identity</option>
65 <option value="PAM200">PAM 200 substitution</option> 68 <option value="PAM200">PAM 200 substitution</option>
66 <option value="PAM250">PAM 250 substitution</option> 69 <option value="PAM250">PAM 250 substitution</option>
67 <option value="HIV_BETWEEN_F">HIV between+F</option> 70 <option value="HIV_BETWEEN_F">HIV between+F</option>
68 </param> 71 </param>
72 <param name="discard" argument="--discard" type="boolean" checked="False" truevalue="True" falsevalue="False" label="Output discarded sequences to a separate dataset"/>
69 <param name="reverse_complement" argument="--reverse-complement" type="boolean" checked="False" truevalue="--reverse-complement" falsevalue="" label="Also try to align against reverse complement of reference"/> 73 <param name="reverse_complement" argument="--reverse-complement" type="boolean" checked="False" truevalue="--reverse-complement" falsevalue="" label="Also try to align against reverse complement of reference"/>
70 <param name="keep_reference" argument="--keep-reference" type="boolean" checked="False" truevalue="--keep-reference" falsevalue="" label="Include reference as first sequence in aligned BAM"/> 74 <param name="keep_reference" argument="--keep-reference" type="boolean" checked="False" truevalue="--keep-reference" falsevalue="" label="Include reference as first sequence in aligned BAM"/>
71 </section> 75 </section>
72 </inputs> 76 </inputs>
73 <outputs> 77 <outputs>