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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampligone commit 5bd763da003ce033467702f2fb4dca5264e0be43
author iuc
date Tue, 29 Jul 2025 10:18:37 +0000
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0
d5fc5d888a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampligone commit 5bd763da003ce033467702f2fb4dca5264e0be43
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1 <tool id="ampligone" name="AmpliGone" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
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2 <description>Find and remove primers from NGS amplicon reads</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">2.0.1</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">AmpliGone</requirement>
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9 </requirements>
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10 <version_command>ampligone --version</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 #import re
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13
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14 #set $inputs_map = {
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15 'input': 'reads',
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16 'reference': 'reference',
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17 'primers': 'primers'
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18 }
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19
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20 #for $key, $short in $inputs_map.items()
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21 #set $ds = $inputs[$key]
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22 #set $ext = re.sub("sanger", "", $ds.ext)
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23 #set $is_gz = str($ds.ext).endswith('.gz') and $ext != 'bam'
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24 #set $filename = $short + '.' + $ext
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25
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26 ln -sf '$ds' '$filename' &&
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27 #silent $inputs_map[$key] = $filename
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28
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29 #if $key == 'input'
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30 #set $output_name = 'output.fastq' + ('.gz' if $is_gz else '')
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31 touch '$cleaned' &&
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32 ln -sf '$cleaned' $output_name &&
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33 #end if
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34 #end for
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35
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36 #if $inputs.primers.ext == 'fasta' and $inputs.export_primers == 'yes'
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37 #set $primer_filename = 'primers.bed'
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38 touch '$exp_prim' &&
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39 ln -sf '$exp_prim' $primer_filename &&
d5fc5d888a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampligone commit 5bd763da003ce033467702f2fb4dca5264e0be43
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40 #end if
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41
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42 ## --- Run the tool using clean and predictable filenames ---
d5fc5d888a46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampligone commit 5bd763da003ce033467702f2fb4dca5264e0be43
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43 ampligone
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44 ##add input files
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45 --input '$inputs_map['input']'
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46 --reference '$inputs_map['reference']'
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47 --primers '$inputs_map['primers']'
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48
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49 ## Compute options
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50 --threads "\${GALAXY_SLOTS:-2}"
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51
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52 ##optional arguments
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53
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54 #if $opt_args.ampli_type.amplicon_type
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55 --amplicon-type $opt_args.ampli_type.amplicon_type
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56 #end if
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57 #if $opt_args.ampli_type.amplicon_type == 'fragmented'
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58 --fragment-lookaround-size $opt_args.ampli_type.fragment_lookaround_size
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59 #end if
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60 #if $opt_args.error_rate
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61 --error-rate $opt_args.error_rate
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62 #end if
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63
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64 ##output options
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65 #if $inputs.primers.ext == 'fasta' and $inputs.export_primers == 'yes'
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66 --export-primers '$primer_filename'
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67 #end if
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68
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69 --output '$output_name'
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70
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71 ]]></command>
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72 <inputs>
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73 <section name="inputs" title="Inputs" expanded="true">
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74 <param argument="--input" type="data" format="fastqsanger,fastqsanger.gz,bam" label="Input file" help="Input file with reads in FASTQ format."/>
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75 <param argument="--reference" type="data" format="fasta" label="Reference genome" help="Input Reference genome in FASTA format." />
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76 <param argument="--primers" type="data" format="fasta,bed" label="Used primer sequences" help="Used primer sequences in FASTA or BED format." />
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77 <param argument="--export-primers" type="boolean" checked="false" truevalue="yes" falsevalue="no" optional="true" label="Output cut primers coordinates" help="Output BED file with found primer coordinates if they are actually cut from the reads."/>
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78 </section>
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79
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80 <section name="opt_args" title="Optional Arguments" expanded="false">
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81 <conditional name="ampli_type">
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82 <param argument="--amplicon-type" type="select" label="Define the amplicon-type" help="Define the amplicon-type, either being 'end-to-end', 'end-to-mid', or 'fragmented'. See the docs for more info.">
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83 <option value="end-to-end" selected="true">end-to-end</option>
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84 <option value="end-to-mid">end-to-mid</option>
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85 <option value="fragmented">fragmented</option>
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86 </param>
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87 <when value="fragmented">
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88 <param argument="--fragment-lookaround-size" type="integer" value="10" optional="true" label="Fragment lookaround size" help="The number of bases to look around a primer-site to consider it part of a fragment." />
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89 </when>
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90 <when value="end-to-end"/>
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91 <when value="end-to-mid"/>
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92 </conditional>
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93 <param argument="--error-rate" type="float" min="0" max="1" value="0.1" label="Error rate" help="The maximum allowed error rate for the primer search. Use 0 for exact primer matches." />
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94 </section>
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95 </inputs>
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96
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97 <outputs>
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98 <data name="cleaned" format="fastqsanger" label="${tool.name} on ${inputs.input.name} ($on_string): Cleaned reads"/>
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99 <data name="exp_prim" format="bed" label="${tool.name} on ${on_string}: Detected primer coordinates">
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100 <filter>inputs['primers'].ext == 'fasta' and inputs['export_primers'] is True</filter>
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101 </data>
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102 </outputs>
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103 <tests>
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104 <test expect_num_outputs="1">
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105 <section name="inputs">
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106 <param name="input" value="sars-cov-2.fastq"/>
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107 <param name="reference" value="SARS-CoV-2-reference.fasta"/>
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108 <param name="primers" value="SARS-CoV-2-ARTIC-V5.3.2.scheme.bed" />
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109 </section>
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110 <output name="cleaned">
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111 <assert_contents>
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112 <has_text text="@SRR30635841.1"/>
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113 <has_text text="@SRR30635841.2"/>
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114 <has_text text="@SRR30635841.3"/>
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115 <has_text text="@SRR30635841.4"/>
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116 <has_text text="@SRR30635841.5"/>
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117 </assert_contents>
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118 </output>
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119 </test>
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120 <test expect_num_outputs="2">
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121 <section name="inputs">
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122 <param name="input" value="sars-cov-2.fastq"/>
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123 <param name="reference" value="SARS-CoV-2-reference.fasta"/>
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124 <param name="primers" value="ARTIC-V5.3.2.fasta" />
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125 <param name="export_primers" value="yes"/>
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126 </section>
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127 <output name="cleaned">
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128 <assert_contents>
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129 <has_text text="@SRR30635841.1"/>
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130 <has_text text="@SRR30635841.2"/>
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131 <has_text text="@SRR30635841.3"/>
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132 <has_text text="@SRR30635841.4"/>
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133 <has_text text="@SRR30635841.5"/>
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134 </assert_contents>
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135 </output>
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136 <output name="exp_prim">
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137 <assert_contents>
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138 <has_text text="MN908947.3:6204-6237_LEFT"/>
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139 <has_text text="MN908947.3:25744-25777_RIGHT"/>
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140 </assert_contents>
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141 </output>
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142 </test>
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143 <test expect_num_outputs="1">
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144 <section name="inputs">
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145 <param name="input" value="synthetic.bam"/>
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146 <param name="reference" value="synthetic.fasta"/>
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147 <param name="primers" value="synthetic.bed" />
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148 </section>
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149 <output name="cleaned">
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150 <assert_contents>
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151 <has_text text="read_number_2_last_120_of_ref"/>
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152 <has_text text="read_number_1_first_120_of_ref"/>
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153 </assert_contents>
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154 </output>
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155 </test>
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156 </tests>
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157 <help><![CDATA[
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158 **AmpliGone**
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159
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160 In contrast to a lot of other primer-removal tools, AmpliGone does not actively look for primer sequences within the NGS reads. When providing BED input, reads are trimmed based on primer sequence coordinates in relation to a given reference sequence. Additionally, AmpliGone is able to compensate for, and therefore properly clean, reads that start or end outside of a primer-region as this is a common occurrence in amplicon-based sequencing data.
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161 AmpliGone works with both reads in FASTQ format, as well as aligned data in BAM-format. However, when data is presented in the BAM-format then only read-data (sequence and quality scores) will be used. Other data present in the BAM-format will not be used in this version of AmpliGone.
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162
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163 Currently, AmpliGone supports Nanopore data and Illumina data. The Illumina platform (NextSeq/MiSeq/HiSeq/other) does not matter.
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164
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165 It is however important that you know the read-length in relation to the amplicon length. AmpliGone expects this information in the form of an 'amplicon-type'.
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166
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167 AmpliGone is build and tested with Nanopore and Illumina data (fastq) in mind and supports 'end-to-end', 'end-to-mid' and 'fragmented' amplicons to be cleaned.
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168
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169
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170 **More Information**
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171
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172 - **Official Repository**: https://github.com/RIVM-bioinformatics/AmpliGone
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173 - **Extended User Guide**: https://rivm-bioinformatics.github.io/AmpliGone/@TOOL_VERSION@/
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174
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175 ]]></help>
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176 <citations>
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177 <citation type="doi">10.5281/zenodo.7684307</citation>
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178 </citations>
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179 </tool>