Mercurial > repos > rdvelazquez > bioext_bealign

annotate bealign.xml @ 3:f7866771310a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
2d9b98a2a0d6 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9a4a7b16c82dfaac1f49ba23a02560d6524233e3\n'-dirty
rdvelazquez
parents:
diff changeset
1 <?xml version="1.0"?>
2d9b98a2a0d6 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9a4a7b16c82dfaac1f49ba23a02560d6524233e3\n'-dirty
rdvelazquez
parents:
diff changeset
2 <tool id="bioext_bealign" name="Align sequences" version="@VERSION@.0">
2
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
3 <description>to a reference using a codon alignment
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
4 algorithm</description>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
5 <macros>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
6 <import>macros.xml</import>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
7 </macros>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
8 <expand macro="requirements"/>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
9 <version_command>bealign --version</version_command>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
1
d91cbcdac691 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
parents: 0
diff changeset
11 bealign --reference '$select_reference.reference' --alphabet $advanced.alphabet
d91cbcdac691 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
parents: 0
diff changeset
12 #if $advanced.expected_identity:
d91cbcdac691 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
parents: 0
diff changeset
13 --expected-identity $advanced.expected_identity
d91cbcdac691 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
parents: 0
diff changeset
14 #end if
0
2d9b98a2a0d6 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9a4a7b16c82dfaac1f49ba23a02560d6524233e3\n'-dirty
rdvelazquez
parents:
diff changeset
15 --score-matrix $advanced.score_matrix $advanced.reverse_complement $advanced.keep_reference
3
f7866771310a planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 2
diff changeset
16 #if $advanced.discard:
f7866771310a planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 2
diff changeset
17 --discard '$discarded_reads'
f7866771310a planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 2
diff changeset
18 #end if
2
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
19 '$input' '$output'
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
20 ]]></command>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
21 <inputs>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
22 <param name="input" type="data" format="fasta" label="Input reads"/>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
23 <conditional name="select_reference">
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
24 <param name="reference_type" type="select">
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
25 <option value="preset">Select preset</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
26 <option value="dataset">Use a history dataset</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
27 </param>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
28 <when value="preset">
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
29 <param argument="--reference" type="select">
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
30 <option value="HXB2_tat">HXB2 tat</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
31 <option value="HXB2_gag">HXB2 gag</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
32 <option value="HXB2_pol">HXB2 polymerase</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
33 <option value="HXB2_int">HXB2 integrase</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
34 <option value="HXB2_vif">HXB2 vif</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
35 <option value="HXB2_pr">HXB2 protease</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
36 <option value="HXB2_vpr">HXB2 vpr</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
37 <option value="NL4-3_prrt">NL4-3 protease and reverse
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
38 transcriptase</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
39 <option value="HXB2_nef">HXB2 nef</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
40 <option value="HXB2_env">HXB2 envelope</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
41 <option value="HXB2_rt">HXB2 reverse
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
42 transcriptase</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
43 <option value="HXB2_prrt">HXB2 protease and reverse
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
44 transcriptase</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
45 <option value="HXB2_rev">HXB2 rev</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
46 <option value="HXB2_vpu">HXB2 vpu</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
47 </param>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
48 </when>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
49 <when value="dataset">
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
50 <param argument="--reference" type="data" format="fasta" label="Reference sequences"/>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
51 </when>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
52 </conditional>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
53 <section name="advanced" title="Advanced options" expanded="False">
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
54 <param name="expected_identity" argument="--expected-identity" type="float" min="0" max="1" optional="True" label="Discard sequences that are insufficiently identical to the reference"/>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
55 <param argument="--alphabet" type="select" label="Alphabet to use for alignment">
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
56 <option value="codon" selected="True">Codon</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
57 <option value="dna">DNA</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
58 <option value="amino">Amino acids</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
59 </param>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
60 <param name="score_matrix" argument="--score-matrix" type="select" label="Parametrize using score matrix">
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
61 <option value="BLOSUM62" selected="True">Blocks
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
62 substitution</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
63 <option value="DNA65">DNA, 65% expected identity</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
64 <option value="DNA70">DNA, 70% expected identity</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
65 <option value="DNA88">DNA, 88% expected identity</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
66 <option value="DNA80">DNA, 80% expected identity</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
67 <option value="DNA95">DNA, 95% expected identity</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
68 <option value="PAM200">PAM 200 substitution</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
69 <option value="PAM250">PAM 250 substitution</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
70 <option value="HIV_BETWEEN_F">HIV between+F</option>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
71 </param>
3
f7866771310a planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 2
diff changeset
72 <param name="discard" argument="--discard" type="boolean" checked="False" truevalue="True" falsevalue="False" label="Output discarded sequences to a separate dataset"/>
2
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
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"/>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
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"/>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
75 </section>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
76 </inputs>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
77 <outputs>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
78 <data name="output" format="bam"/>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
79 <data name="discarded_reads" format="fasta">
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
80 <filter>advanced['discard']</filter>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
81 </data>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
82 </outputs>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
83 <tests>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
84 <test>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
85 <param name="input" ftype="fasta" value="bealign-in1.fa"/>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
86 <param name="reference_type" value="dataset"/>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
87 <param name="score_matrix" value="HIV_BETWEEN_F"/>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
88 <param name="reference" ftype="fasta" value="bealign-in-ref-1.fa"/>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
89 <output name="output" file="bealign-out1.bam"/>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
90 </test>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
91 <test>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
92 <param name="input" ftype="fasta" value="bealign-in2.fa"/>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
93 <param name="reference_type" value="dataset"/>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
94 <param name="score_matrix" value="BLOSUM62"/>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
95 <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa"/>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
96 <output name="output" file="bealign-out2.bam"/>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
97 </test>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
98 <test>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
99 <param name="input" ftype="fasta" value="bealign-in2.fa"/>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
100 <param name="reference_type" value="dataset"/>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
101 <param name="expected_identity" value="0.9"/>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
102 <param name="score_matrix" value="BLOSUM62"/>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
103 <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa"/>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
104 <output name="output" file="bealign-out3.bam"/>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
105 </test>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
106 </tests>
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
107 <help><![CDATA[
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
108 bealign
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
109 -------
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
110
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
111 Align sequences to a reference using a codon alignment algorithm.
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
112
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
113 NOTES
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
114 -----
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
115
85d823cf0872 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
rdvelazquez
parents: 1
diff changeset
116 Reference can be one of the presets or a custom history reference.
1
d91cbcdac691 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
parents: 0
diff changeset
117 ]]></help>
d91cbcdac691 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
rdvelazquez
parents: 0
diff changeset
118 <expand macro="citations"/>
0
2d9b98a2a0d6 planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9a4a7b16c82dfaac1f49ba23a02560d6524233e3\n'-dirty
rdvelazquez
parents:
diff changeset
119 </tool>