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comparison bealign.xml @ 0:2d9b98a2a0d6 draft

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planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9a4a7b16c82dfaac1f49ba23a02560d6524233e3\n'-dirty
author rdvelazquez
date Wed, 14 Mar 2018 14:44:06 -0400
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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' $advanced.expected_identity --alphabet $advanced.alphabet
12 --score-matrix $advanced.score_matrix $advanced.reverse_complement $advanced.keep_reference
13 #if $advanced.discard:
14 $advanced.discard $advanced.discarded_reads
15 #end if
16 $input $output
17 ]]>
18 </command>
19 <inputs>
20 <param name="input" type="data" format="fasta" label="Input reads" />
21 <conditional name="select_reference">
22 <param name="reference_type" type="select">
23 <option value="preset">Select preset</option>
24 <option value="dataset">Use a history dataset</option>
25 </param>
26 <when value="preset">
27 <param argument="--reference" type="select">
28 <option value="HXB2_tat">HXB2 tat</option>
29 <option value="HXB2_gag">HXB2 gag</option>
30 <option value="HXB2_pol">HXB2 polymerase</option>
31 <option value="HXB2_int">HXB2 integrase</option>
32 <option value="HXB2_vif">HXB2 vif</option>
33 <option value="HXB2_pr">HXB2 protease</option>
34 <option value="HXB2_vpr">HXB2 vpr</option>
35 <option value="NL4-3_prrt">NL4-3 protease and reverse transcriptase</option>
36 <option value="HXB2_nef">HXB2 nef</option>
37 <option value="HXB2_env">HXB2 envelope</option>
38 <option value="HXB2_rt">HXB2 reverse transcriptase</option>
39 <option value="HXB2_prrt">HXB2 protease and reverse transcriptase</option>
40 <option value="HXB2_rev">HXB2 rev</option>
41 <option value="HXB2_vpu">HXB2 vpu</option>
42 </param>
43 </when>
44 <when value="dataset">
45 <param argument="--reference" type="data" format="fasta" label="Reference sequences" />
46 </when>
47 </conditional>
48 <section name="advanced" title="Advanced options" expanded="False">
49 <param name="expected_identity" argument="--expected-identity" type="boolean" checked="False" truevalue="--expected-identity" falsevalue="" label="Discard sequences that are insufficiently identical to the reference" />
50 <param argument="--alphabet" type="select" label="Alphabet to use for alignment">
51 <option value="codon" selected="True">Codon</option>
52 <option value="dna">DNA</option>
53 <option value="amino">Amino acids</option>
54 </param>
55 <param name="score_matrix" argument="--score-matrix" type="select" label="Parametrize using score matrix">
56 <option value="BLOSUM62" selected="True">Blocks substitution</option>
57 <option value="DNA65">DNA, 65% expected identity</option>
58 <option value="DNA70">DNA, 70% expected identity</option>
59 <option value="DNA88">DNA, 88% expected identity</option>
60 <option value="DNA80">DNA, 80% expected identity</option>
61 <option value="DNA95">DNA, 95% expected identity</option>
62 <option value="PAM200">PAM 200 substitution</option>
63 <option value="PAM250">PAM 250 substitution</option>
64 <option value="HIV_BETWEEN_F">HIV between+F</option>
65 </param>
66 <param argument="--discard" type="boolean" checked="False" truevalue="--discard" falsevalue="" label="Output discarded sequences to a separate dataset" />
67 <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" />
68 <param name="keep_reference" argument="--keep-reference" type="boolean" checked="False" truevalue="--keep-reference" falsevalue="" label="Include reference as first sequence in aligned BAM" />
69 </section>
70 </inputs>
71 <outputs>
72 <data name="output" format="bam"/>
73 <data name="discarded_reads" format="fasta">
74 <filter>discard</filter>
75 </data>
76 </outputs>
77 <tests>
78 <test>
79 <param name="input" ftype="fasta" value="bealign-in1.fa" />
80 <param name="reference_type" value="dataset" />
81 <param name="score_matrix" value="HIV_BETWEEN_F" />
82 <param name="reference" ftype="fasta" value="bealign-in-ref-1.fa" />
83 <output name="output" file="bealign-out1.bam" />
84 </test>
85 <test>
86 <param name="input" ftype="fasta" value="bealign-in2.fa" />
87 <param name="reference_type" value="dataset" />
88 <param name="score_matrix" value="BLOSUM62" />
89 <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" />
90 <output name="output" file="bealign-out2.bam" />
91 </test>
92 </tests>
93 <help>
94 <![CDATA[
95 -r REFERENCE, --reference REFERENCE
96 REFERENCE FASTA file or {HXB2_tat, HXB2_nef, HXB2_vpu,
97 HXB2_vif, HXB2_env, HXB2_vpr, HXB2_rev, HXB2_pol,
98 HXB2_prrt, NL4-3_prrt, HXB2_rt, HXB2_gag, HXB2_pr,
99 HXB2_int}
100 -e EXPECTED_IDENTITY, --expected-identity EXPECTED_IDENTITY
101 discard sequences that are insufficiently identical to
102 the reference
103 -a ALPHABET, --alphabet ALPHABET
104 perform an alignment using one of {amino, dna, codon}
105 [default=codon]
106 -m SCOREMATRIX, --score-matrix SCOREMATRIX
107 parameterize using one of {PAM250, DNA80,
108 HIV_BETWEEN_F, BLOSUM62, DNA70, DNA88, PAM200, DNA95,
109 DNA65} [default=BLOSUM62]
110 -D DISCARD, --discard DISCARD
111 discarded sequences are sent to DISCARD
112 -R, --reverse-complement
113 also align the reverse complement of each query
114 sequence, returning it if the alignment is superior
115 -S, --no-sort do NOT sort the resulting BAM file [the default is to
116 sort]
117 -q, --quiet do not print status update messages
118 -v, --version print version information and exit
119 -K, --keep-reference include the reference sequence as the first one in the
120 resulting BAM file [the default is to strip it]
121 ]]>
122 </help>
123 <expand macro="citations" />
124 </tool>