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comparison bealign.xml @ 0:6ef10b28e967 draft

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planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
author iuc
date Wed, 16 May 2018 17:34:42 -0400
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children f9b72a376ec9
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1 <?xml version="1.0"?>
2 <tool id="bioext_bealign" name="Align sequences" version="@VERSION@.0">
3 <description>to a reference using a codon alignment algorithm</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <version_command>bealign --version</version_command>
9 <command detect_errors="exit_code">
10 <![CDATA[
11 bealign --reference '$select_reference.reference' --alphabet $advanced.alphabet
12 #if $advanced.expected_identity:
13 --expected-identity $advanced.expected_identity
14 #end if
15 --score-matrix $advanced.score_matrix $advanced.reverse_complement $advanced.keep_reference
16 #if $advanced.discard:
17 $advanced.discard '$advanced.discarded_reads'
18 #end if
19 '$input' '$output'
20 ]]>
21 </command>
22 <inputs>
23 <param name="input" type="data" format="fasta" label="Input reads" />
24 <conditional name="select_reference">
25 <param name="reference_type" type="select">
26 <option value="preset">Select preset</option>
27 <option value="dataset">Use a history dataset</option>
28 </param>
29 <when value="preset">
30 <param argument="--reference" type="select">
31 <option value="HXB2_tat">HXB2 tat</option>
32 <option value="HXB2_gag">HXB2 gag</option>
33 <option value="HXB2_pol">HXB2 polymerase</option>
34 <option value="HXB2_int">HXB2 integrase</option>
35 <option value="HXB2_vif">HXB2 vif</option>
36 <option value="HXB2_pr">HXB2 protease</option>
37 <option value="HXB2_vpr">HXB2 vpr</option>
38 <option value="NL4-3_prrt">NL4-3 protease and reverse transcriptase</option>
39 <option value="HXB2_nef">HXB2 nef</option>
40 <option value="HXB2_env">HXB2 envelope</option>
41 <option value="HXB2_rt">HXB2 reverse transcriptase</option>
42 <option value="HXB2_prrt">HXB2 protease and reverse transcriptase</option>
43 <option value="HXB2_rev">HXB2 rev</option>
44 <option value="HXB2_vpu">HXB2 vpu</option>
45 </param>
46 </when>
47 <when value="dataset">
48 <param argument="--reference" type="data" format="fasta" label="Reference sequences" />
49 </when>
50 </conditional>
51 <section name="advanced" title="Advanced options" expanded="False">
52 <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" />
53 <param argument="--alphabet" type="select" label="Alphabet to use for alignment">
54 <option value="codon" selected="True">Codon</option>
55 <option value="dna">DNA</option>
56 <option value="amino">Amino acids</option>
57 </param>
58 <param name="score_matrix" argument="--score-matrix" type="select" label="Parametrize using score matrix">
59 <option value="BLOSUM62" selected="True">Blocks substitution</option>
60 <option value="DNA65">DNA, 65% expected identity</option>
61 <option value="DNA70">DNA, 70% expected identity</option>
62 <option value="DNA88">DNA, 88% expected identity</option>
63 <option value="DNA80">DNA, 80% expected identity</option>
64 <option value="DNA95">DNA, 95% expected identity</option>
65 <option value="PAM200">PAM 200 substitution</option>
66 <option value="PAM250">PAM 250 substitution</option>
67 <option value="HIV_BETWEEN_F">HIV between+F</option>
68 </param>
69 <param argument="--discard" type="boolean" checked="False" truevalue="--discard" falsevalue="" label="Output discarded sequences to a separate dataset" />
70 <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" />
71 <param name="keep_reference" argument="--keep-reference" type="boolean" checked="False" truevalue="--keep-reference" falsevalue="" label="Include reference as first sequence in aligned BAM" />
72 </section>
73 </inputs>
74 <outputs>
75 <data name="output" format="bam" />
76 <data name="discarded_reads" format="fasta">
77 <filter>advanced['discard']</filter>
78 </data>
79 </outputs>
80 <tests>
81 <test>
82 <param name="input" ftype="fasta" value="bealign-in1.fa" />
83 <param name="reference_type" value="dataset" />
84 <param name="score_matrix" value="HIV_BETWEEN_F" />
85 <param name="reference" ftype="fasta" value="bealign-in-ref-1.fa" />
86 <output name="output" file="bealign-out1.bam" />
87 </test>
88 <test>
89 <param name="input" ftype="fasta" value="bealign-in2.fa" />
90 <param name="reference_type" value="dataset" />
91 <param name="score_matrix" value="BLOSUM62" />
92 <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" />
93 <output name="output" file="bealign-out2.bam" />
94 </test>
95 <test>
96 <param name="input" ftype="fasta" value="bealign-in2.fa" />
97 <param name="reference_type" value="dataset" />
98 <param name="expected_identity" value="0.9" />
99 <param name="score_matrix" value="BLOSUM62" />
100 <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" />
101 <output name="output" file="bealign-out3.bam" />
102 </test>
103 </tests>
104 <help>
105 <![CDATA[
106 bealign
107 -------
108
109 Align sequences to a reference using a codon alignment algorithm.
110
111 NOTES
112 -----
113
114 Reference can be one of the presets or a custom history reference.
115 ]]></help>
116 <expand macro="citations"/>
117 </tool>