Mercurial > repos > veg > bioext_bealign

annotate bealign.xml @ 1:787baac95405 draft default tip

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planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'1e1a1e37fa621df190621f5c95c00fb9d31d9a60\n'-dirty
author veg
date Thu, 08 Mar 2018 13:06:02 -0500
parents c6f0b318bc03
children
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1 <?xml version="1.0"?>
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2 <tool id="bioext_bealign" name="Align sequences" version="@VERSION@.0">
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3 <description>to a reference using a codon alignment algorithm</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <version_command>bealign --version</version_command>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
1
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11 bealign --reference '$select_reference.reference' $advanced.expected_identity --alphabet $advanced.alphabet
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12 --score-matrix $advanced.score_matrix $advanced.reverse_complement $advanced.keep_reference
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13 #if $advanced.discard:
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14 $advanced.discard $advanced.discarded_reads
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15 #end if
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16 $input $output
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param name="input" type="data" format="fasta" label="Input reads" />
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21 <conditional name="select_reference">
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22 <param name="reference_type" type="select">
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23 <option value="preset">Select preset</option>
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24 <option value="dataset">Use a history dataset</option>
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25 </param>
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26 <when value="preset">
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27 <param argument="--reference" type="select">
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28 <option value="HXB2_tat">HXB2 tat</option>
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29 <option value="HXB2_gag">HXB2 gag</option>
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30 <option value="HXB2_pol">HXB2 polymerase</option>
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31 <option value="HXB2_int">HXB2 integrase</option>
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32 <option value="HXB2_vif">HXB2 vif</option>
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33 <option value="HXB2_pr">HXB2 protease</option>
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34 <option value="HXB2_vpr">HXB2 vpr</option>
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35 <option value="NL4-3_prrt">NL4-3 protease and reverse transcriptase</option>
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36 <option value="HXB2_nef">HXB2 nef</option>
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37 <option value="HXB2_env">HXB2 envelope</option>
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38 <option value="HXB2_rt">HXB2 reverse transcriptase</option>
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39 <option value="HXB2_prrt">HXB2 protease and reverse transcriptase</option>
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40 <option value="HXB2_rev">HXB2 rev</option>
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41 <option value="HXB2_vpu">HXB2 vpu</option>
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42 </param>
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43 </when>
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44 <when value="dataset">
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45 <param argument="--reference" type="data" format="fasta" label="Reference sequences" />
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46 </when>
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47 </conditional>
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48 <section name="advanced" title="Advanced options" expanded="False">
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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" />
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50 <param argument="--alphabet" type="select" label="Alphabet to use for alignment">
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51 <option value="codon" selected="True">Codon</option>
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52 <option value="dna">DNA</option>
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53 <option value="amino">Amino acids</option>
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54 </param>
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55 <param name="score_matrix" argument="--score-matrix" type="select" label="Parametrize using score matrix">
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56 <option value="BLOSUM62" selected="True">Blocks substitution</option>
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57 <option value="DNA65">DNA, 65% expected identity</option>
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58 <option value="DNA70">DNA, 70% expected identity</option>
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59 <option value="DNA88">DNA, 88% expected identity</option>
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60 <option value="DNA80">DNA, 80% expected identity</option>
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61 <option value="DNA95">DNA, 95% expected identity</option>
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62 <option value="PAM200">PAM 200 substitution</option>
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63 <option value="PAM250">PAM 250 substitution</option>
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64 <option value="HIV_BETWEEN_F">HIV between+F</option>
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65 </param>
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66 <param argument="--discard" type="boolean" checked="False" truevalue="--discard" falsevalue="" label="Output discarded sequences to a separate dataset" />
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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" />
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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" />
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69 </section>
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70 </inputs>
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71 <outputs>
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72 <data name="output" format="bam"/>
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73 <data name="discarded_reads" format="fasta">
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74 <filter>discard</filter>
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75 </data>
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76 </outputs>
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77 <tests>
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78 <test>
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79 <param name="input" ftype="fasta" value="bealign-in1.fa" />
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80 <param name="reference_type" value="dataset" />
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81 <param name="score_matrix" value="HIV_BETWEEN_F" />
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82 <param name="reference" ftype="fasta" value="bealign-in-ref-1.fa" />
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83 <output name="output" file="bealign-out1.bam" />
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84 </test>
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85 <test>
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86 <param name="input" ftype="fasta" value="bealign-in2.fa" />
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87 <param name="reference_type" value="dataset" />
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88 <param name="score_matrix" value="BLOSUM62" />
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89 <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" />
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90 <output name="output" file="bealign-out2.bam" />
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91 </test>
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92 </tests>
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93 <help>
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94 <![CDATA[
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95 -r REFERENCE, --reference REFERENCE
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96 REFERENCE FASTA file or {HXB2_tat, HXB2_nef, HXB2_vpu,
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97 HXB2_vif, HXB2_env, HXB2_vpr, HXB2_rev, HXB2_pol,
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98 HXB2_prrt, NL4-3_prrt, HXB2_rt, HXB2_gag, HXB2_pr,
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99 HXB2_int}
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100 -e EXPECTED_IDENTITY, --expected-identity EXPECTED_IDENTITY
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101 discard sequences that are insufficiently identical to
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102 the reference
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103 -a ALPHABET, --alphabet ALPHABET
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104 perform an alignment using one of {amino, dna, codon}
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105 [default=codon]
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106 -m SCOREMATRIX, --score-matrix SCOREMATRIX
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107 parameterize using one of {PAM250, DNA80,
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108 HIV_BETWEEN_F, BLOSUM62, DNA70, DNA88, PAM200, DNA95,
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109 DNA65} [default=BLOSUM62]
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110 -D DISCARD, --discard DISCARD
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111 discarded sequences are sent to DISCARD
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112 -R, --reverse-complement
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113 also align the reverse complement of each query
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114 sequence, returning it if the alignment is superior
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115 -S, --no-sort do NOT sort the resulting BAM file [the default is to
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116 sort]
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117 -q, --quiet do not print status update messages
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118 -v, --version print version information and exit
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119 -K, --keep-reference include the reference sequence as the first one in the
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120 resulting BAM file [the default is to strip it]
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121 ]]>
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122 </help>
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123 </tool>
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124
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125
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126
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127
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128