Mercurial > repos > iuc > bioext_bealign

annotate bealign.xml @ 4:a287431cdf4f draft

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"planemo upload for repository https://github.com/davebx/bioext-gx/ commit c9002fa57e4d800f2c1c8d1dafbceb7681b0fcc2"
author iuc
date Tue, 05 Oct 2021 09:52:56 +0000
parents fb4975b507c6
children c239e93d9f04
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1 <?xml version="1.0"?>
2
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2 <tool id="bioext_bealign" name="Align sequences" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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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 <token name="@VERSION_SUFFIX@">2</token>
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7 </macros>
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8 <expand macro="requirements">
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9 <requirement type="package" version="5.1.0">gawk</requirement>
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10 <requirement type="package" version="1.13">samtools</requirement>
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11 </expand>
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12 <version_command>bealign --version</version_command>
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13 <command detect_errors="exit_code">
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14 <![CDATA[
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15 ## Some downstream tools, such as the TN-93 clustering tool and RAxML, might
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16 ## break if there are non-standard characters in the sequences or text other
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17 ## than alphanumerics in the sequence names, so we run the input dataset
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18 ## through a simple awk script to remove any non-IUPAC-standard nucleotides
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19 ## and replace any unwanted characters in the sequence names with underscores.
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20 ## This should not affect the actual alignment, since any non-standard character
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21 ## in the sequences is already ignored, but the possibility remains.
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22 set -o pipefail;
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23 cat '$input' @SANITIZE@ reads.fa &&
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24 ## bealign's parallel job executor uses the NCPU env variable
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25 NCPU=\${GALAXY_SLOTS:-2} bealign --reference '$select_reference.reference' --alphabet $advanced.alphabet
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26 #if $advanced.expected_identity:
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27 --expected-identity $advanced.expected_identity
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28 #end if
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29 #if $advanced.discard:
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30 $advanced.discard '$advanced.discarded_reads'
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31 #end if
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32 --score-matrix $advanced.score_matrix
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33 $advanced.reverse_complement
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34 $advanced.keep_reference
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35 ## bypass bealign's internal pysam-based, single-threaded BAM sorting
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36 --no-sort
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37 reads.fa bealign_out.bam &&
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38 samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output' bealign_out.bam
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39 #set $input_background = False
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40 #if $background_source.selection == 'history':
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41 #if $background_source.sequences:
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42 #set $input_background = $background_source.sequences
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43 #end if
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44 #else:
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45 #if $background_source.sequences:
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46 #set $input_background = $background_source.sequences.fields.path
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47 #end if
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48 #end if
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49 #if $input_background:
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50 && cat '$input_background' @SANITIZE@ background.fa &&
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51 NCPU=\${GALAXY_SLOTS:-2} bealign --reference '$select_reference.reference' --alphabet $advanced.alphabet
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52 #if $advanced.expected_identity:
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53 --expected-identity $advanced.expected_identity
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54 #end if
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55 --keep-reference --score-matrix $advanced.score_matrix $advanced.reverse_complement
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56 ## bypass bealign's internal pysam-based, single-threaded BAM sorting
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57 --no-sort
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58 background.fa bealign_background.bam &&
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59 samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$background' bealign_background.bam
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60 #end if
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61 #set $reference_name = str($select_reference.reference)
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62 #if $select_reference.reference_type == 'preset' and $select_reference.save_reference:
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63 && python '$__tool_directory__/copy_reference.py' --reference '$reference_name' --dataset '$saved_reference'
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64 #end if
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65 ]]>
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66 </command>
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67 <inputs>
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68 <param name="input" type="data" format="fasta" label="Input reads" help="For the benefit of certain tools that depend on this aligner, such as the TN-93 clustering tool, this dataset's sequence names will have non-alphanumeric characters replaced with underscores, and the sequences will be restricted to the set of IUPAC nucleotide characters." />
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69 <conditional name="select_reference">
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70 <param name="reference_type" type="select">
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71 <option value="preset">Select preset</option>
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72 <option value="dataset">Use a history dataset</option>
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73 </param>
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74 <when value="preset">
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75 <param argument="--reference" type="select">
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76 <option value="HXB2_tat">HXB2 tat</option>
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77 <option value="HXB2_gag">HXB2 gag</option>
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78 <option value="HXB2_pol">HXB2 polymerase</option>
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79 <option value="HXB2_int">HXB2 integrase</option>
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80 <option value="HXB2_vif">HXB2 vif</option>
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81 <option value="HXB2_pr">HXB2 protease</option>
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82 <option value="HXB2_vpr">HXB2 vpr</option>
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83 <option value="NL4-3_prrt">NL4-3 protease and reverse transcriptase</option>
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84 <option value="HXB2_nef">HXB2 nef</option>
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85 <option value="HXB2_env">HXB2 envelope</option>
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86 <option value="HXB2_rt">HXB2 reverse transcriptase</option>
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87 <option value="HXB2_prrt">HXB2 protease and reverse transcriptase</option>
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88 <option value="HXB2_rev">HXB2 rev</option>
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89 <option value="HXB2_vpu">HXB2 vpu</option>
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90 <option value="CoV2-3C">SARS-CoV-2: 3C</option>
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91 <option value="CoV2-S">SARS-CoV-2: Spike</option>
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92 <option value="CoV2-E">SARS-CoV-2: Envelope</option>
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93 <option value="CoV2-M">SARS-CoV-2: Membrane</option>
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94 <option value="CoV2-N">SARS-CoV-2: Nucleoprotein</option>
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95 <option value="CoV2-endornase">SARS-CoV-2: endornase</option>
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96 <option value="CoV2-exonuclease">SARS-CoV-2: exonuclease</option>
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97 <option value="CoV2-helicase">SARS-CoV-2: helicase</option>
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98 <option value="CoV2-leader">SARS-CoV-2: leader</option>
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99 <option value="CoV2-methyltransferase">SARS-CoV-2: methyltransferase</option>
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100 <option value="CoV2-nsp2">SARS-CoV-2: nsp2</option>
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101 <option value="CoV2-nsp3">SARS-CoV-2: nsp3</option>
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102 <option value="CoV2-nsp4">SARS-CoV-2: nsp4</option>
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103 <option value="CoV2-nsp6">SARS-CoV-2: nsp6</option>
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104 <option value="CoV2-nsp7">SARS-CoV-2: nsp7</option>
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105 <option value="CoV2-nsp8">SARS-CoV-2: nsp8</option>
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106 <option value="CoV2-nsp9">SARS-CoV-2: nsp9</option>
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107 <option value="CoV2-nsp10">SARS-CoV-2: nsp10</option>
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108 <option value="CoV2-ORF1a">SARS-CoV-2: ORF1a</option>
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109 <option value="CoV2-ORF1b">SARS-CoV-2: ORF1b</option>
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110 <option value="CoV2-ORF3a">SARS-CoV-2: ORF3a</option>
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111 <option value="CoV2-ORF5">SARS-CoV-2: ORF5</option>
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112 <option value="CoV2-ORF6">SARS-CoV-2: ORF6</option>
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113 <option value="CoV2-ORF7a">SARS-CoV-2: ORF7a</option>
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114 <option value="CoV2-ORF7b">SARS-CoV-2: ORF7b</option>
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115 <option value="CoV2-ORF8">SARS-CoV-2: ORF8</option>
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116 <option value="CoV2-ORF10">SARS-CoV-2: ORF10</option>
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117 <option value="CoV2-RdRp">SARS-CoV-2: RNA-dependent RNA polymerase</option>
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118 </param>
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119 <param name="save_reference" type="boolean" display="radio" label="Save this reference to your history" />
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120 </when>
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121 <when value="dataset">
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122 <param argument="--reference" type="data" format="fasta" label="Reference sequences" />
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123 </when>
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124 </conditional>
3
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125 <conditional name="background_source">
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126 <param name="selection" type="select" label="Source for the background" help="You can use a predefined background cached on this Galaxy server or select a dataset from your history">
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127 <option value="data_table">Use a predefined background</option>
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128 <option value="history">Select a dataset from your history</option>
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129 </param>
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130 <when value="data_table">
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131 <param name="sequences" type="select" optional="true" label="Select sequences from data table">
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132 <options from_data_table="bealign_selection" />
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133 </param>
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134 </when>
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135 <when value="history">
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136 <param name="sequences" type="data" format="fasta" optional="true" label="Select dataset with sequences" />
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137 </when>
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138 </conditional>
0
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139 <section name="advanced" title="Advanced options" expanded="False">
3
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140 <param argument="--expected-identity" type="float" min="0" max="1" optional="True" label="Discard sequences that are insufficiently identical to the reference" />
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141 <param argument="--alphabet" type="select" label="Alphabet to use for alignment">
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142 <option value="codon" selected="True">Codon</option>
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143 <option value="dna">DNA</option>
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144 <option value="amino">Amino acids</option>
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145 </param>
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146 <param name="score_matrix" argument="--score-matrix" type="select" label="Parametrize using score matrix">
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147 <option value="BLOSUM62" selected="True">Blocks substitution</option>
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148 <option value="DNA65">DNA, 65% expected identity</option>
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149 <option value="DNA70">DNA, 70% expected identity</option>
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150 <option value="DNA88">DNA, 88% expected identity</option>
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151 <option value="DNA80">DNA, 80% expected identity</option>
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152 <option value="DNA95">DNA, 95% expected identity</option>
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153 <option value="PAM200">PAM 200 substitution</option>
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154 <option value="PAM250">PAM 250 substitution</option>
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155 <option value="HIV_BETWEEN_F">HIV between+F</option>
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156 </param>
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157 <param argument="--discard" type="boolean" checked="False" truevalue="--discard" falsevalue="" label="Output discarded sequences to a separate dataset" />
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158 <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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159 <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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160 </section>
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161 </inputs>
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162 <outputs>
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163 <data name="output" format="bam" label="${tool.name} on ${on_string} - Aligned Sequences" />
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164 <data name="background" format="bam" label="${tool.name} on ${on_string} - Background" >
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165 <filter>background_source['sequences']</filter>
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166 </data>
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167 <data name="saved_reference" format="fasta" label="${tool.name} on ${on_string} - Reference" >
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168 <filter>select_reference['save_reference']</filter>
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169 </data>
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170 <data name="discarded_reads" format="fasta">
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171 <filter>advanced['discard']</filter>
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172 </data>
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173 </outputs>
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174 <tests>
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175 <test>
3
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176 <param name="input" ftype="fasta" value="query.fa" />
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177 <param name="reference_type" value="dataset" />
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178 <param name="score_matrix" value="HIV_BETWEEN_F" />
3
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179 <param name="reference" ftype="fasta" value="reference.fa" />
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180 <output name="output" file="bealign-out1.bam" ftype="bam" lines_diff="2" />
0
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181 </test>
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182 <test>
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183 <param name="input" ftype="fasta" value="query.fa" />
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184 <param name="reference_type" value="preset" />
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185 <param name="reference" value="CoV2-nsp8" />
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186 <param name="score_matrix" value="HIV_BETWEEN_F" />
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187 <output name="output" file="bealign-out2.bam" ftype="bam" lines_diff="2"/>
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188 </test>
3
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189 <test expect_num_outputs="2">
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190 <param name="input" ftype="fasta" value="query.fa" />
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191 <param name="reference_type" value="preset" />
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192 <param name="reference" value="CoV2-nsp8" />
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193 <param name="add_background" value="Yes" />
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194 <param name="background_source" value="data_table" />
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195 <param name="sequences" value="CoV2-nsp8" />
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196 <param name="alphabet" value="codon" />
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197 <param name="score_matrix" value="HIV_BETWEEN_F" />
2
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198 <output name="output" file="bealign-out3.bam" ftype="bam" lines_diff="2"/>
3
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199 <output name="background" file="bealign-out3-background.bam" ftype="bam" lines_diff="2"/>
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200 </test>
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201 <test expect_num_outputs="2">
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202 <param name="input" ftype="fasta" value="query.fa" />
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203 <param name="reference_type" value="preset" />
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204 <param name="reference" value="CoV2-nsp8" />
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205 <param name="save_reference" value="true" />
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206 <param name="add_background" value="No" />
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207 <param name="alphabet" value="codon" />
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208 <param name="score_matrix" value="HIV_BETWEEN_F" />
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209 <output name="output" file="bealign-out4.bam" ftype="bam" lines_diff="2"/>
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210 <output name="saved_reference" file="reference.fa" ftype="fasta"/>
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211 </test>
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212 </tests>
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213 <help>
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214 <![CDATA[
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215 bealign
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216 -------
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217
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218 Align sequences to a reference using a codon alignment algorithm.
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219
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220 NOTES
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221 -----
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222
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223 Reference can be one of the presets or a custom history reference.
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224 ]]></help>
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225 <expand macro="citations"/>
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226 </tool>