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planemo upload commit 02a9d915c5d4ee1e01a76d230a3c7196caf732f0
author galaxytrakr
date Thu, 26 Mar 2026 18:55:33 +0000
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1 <tool id="rgi" name="Resistance Gene Identifier (RGI)" profile="23" version="6.0.5+gt_0.1">
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2 <description>This tool predicts resistome(s) from protein or nucleotide data based on homology and SNP models.</description>
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3 <requirements>
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4 <requirement type="package" version="6.0.5">rgi</requirement>
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5 </requirements>
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6 <command detect_errors="aggressive"><![CDATA[
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7 #if $db_opts.db_opts_selector == "default":
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8 export DB_PATH='${__tool_data_path__}/rgi_databases/_default' &&
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9 export DATA_PATH="\$_GALAXY_JOB_TMP_DIR" &&
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10 mkdir -p "\$DB_PATH" &&
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11 #end if
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12
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13 #if $db_opts.db_opts_selector != "default":
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14 rgi load
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15 #if $db_opts.db_opts_selector == "local":
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16 -i "${__tool_data_path__}/rgi_databases/$db_opts.rgi_db_local/card.json"
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17 #else:
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18 -i "$db_opts.rgi_db_hist"
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19 #end if
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20 --local
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21 &&
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22 #end if
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23
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24 rgi main
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25 -i '$input_sequence'
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26 -o out
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27 -t $input_type
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28 -a $alignment_tool
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29 -n "\${GALAXY_SLOTS:-1}"
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30 $include_loose
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31 $low_quality
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32 -d $data
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33
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34 #if $db_opts.db_opts_selector != "default":
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35 --local
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36 #end if
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37 ]]></command>
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38 <inputs>
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39 <param argument="--input_sequence" type="data" format="fastq,fasta" label="Input sequence" help="input file must be in either FASTA (contig and protein) or gzip format e.g myFile.fasta, myFasta.fasta.gz"/>
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40 <param argument="--input_type" type="select" multiple="false" label="Input type" help="specify data input type (default = contig)">
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41 <option value="contig" selected="true">CONTIG (Nucleotide Sequence)</option>
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42 <option value="protein">PROTEIN (Protein Sequence)</option>
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43 </param>
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44 <param argument="--alignment_tool" type="select" label="Alignment tool" help="specify alignment tool (default = BLAST)">
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45 <option value="blast" selected="true">BLAST</option>
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46 <option value="diamond">DIAMOND</option>
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47 </param>
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48 <param argument="--include_loose" type="boolean" checked="false" truevalue="--include_loose" falsevalue="" label="Include loose hits" help="include loose hits in addition to strict and perfect hits"/>
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49 <param argument="--low_quality" type="boolean" checked="false" truevalue="--low_quality" falsevalue="" label="Low quality" help="use for short contigs to predict partial genes"/>
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50 <param argument="--data" type="select" multiple="false" label="Data type" help="specify a data-type (default = NA)">
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51 <option value="wgs">WGS</option>
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52 <option value="plasmid">PLASMID</option>
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53 <option value="chromosome">CHROMOSOME</option>
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54 <option value="NA" selected="true">NA</option>
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55 </param>
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56 <conditional name="db_opts">
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57 <param name="db_opts_selector" type="select" label="Select an RGI database">
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58 <option value="default" selected="true">Default RGI database</option>
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59 <option value="local">Locally installed RGI database</option>
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60 <option value="hist">RGI database from your history</option>
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61 </param>
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62 <when value="default">
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63 <param name="rgi_db_local" type="hidden" value="" />
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64 <param name="rgi_db_hist" type="hidden" value="" />
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65 </when>
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66 <when value="local">
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67 <param name="rgi_db_local" type="select" multiple="false" label="Locally installed RGI database">
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68 <options from_data_table="rgi_databases">
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69 <validator type="no_options" message="No databases are available built-in"/>
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70 </options>
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71 </param>
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72 <param name="rgi_db_hist" type="hidden" value="" />
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73 </when>
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74 <when value="hist">
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75 <param name="rgi_db_local" type="hidden" value="" />
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76 <param name="rgi_db_hist" type="data" format="json" label="RGI database from your history" />
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77 </when>
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78 </conditional>
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79 </inputs>
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80 <outputs>
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81 <data name="report" format="json" from_work_dir="out.json" label="${tool.name} on ${on_string}: report.json"/>
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82 <data name="summary" format="tabular" from_work_dir="out.txt" label="${tool.name} on ${on_string}: summary.txt"/>
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83 </outputs>
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84 <tests>
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85 <test>
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86 <param name="input_sequence" value="test1.fasta" />
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87 <param name="input_type" value="contig" />
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88 <param name="alignment_tool" value="blast" />
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89 <param name="include_loose" value="false" />
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90 <param name="low_quality" value="false" />
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91 <param name="data" value="NA" />
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92 <conditional name="db_opts">
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93 <param name="db_opts_selector" value="default" />
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94 </conditional>
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95 <output name="summary">
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96 <assert_contents>
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97 <has_text text="AY123251" />
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98 </assert_contents>
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99 </output>
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100 </test>
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101 </tests>
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102 <help>
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103 <![CDATA[
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104 Resistance Gene Identifier (RGI)
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105 ================================
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106
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107 RGI is used to predict resistome(s) from protein or nucleotide data based on homology and SNP models. The tool uses data from the CARD database.
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108
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109 Usage
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110 -----
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111
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112 1. Select your input sequence (in FASTA format).
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113 2. Select your input type (CONTIG or PROTEIN).
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114 3. Select your alignment tool (DIAMOND or BLAST).
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115 4. Specify if you want to include loose hits (YES or NO).
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116 5. Specify if you want to remove temporary files (YES or NO).
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117 6. Specify if you want to low quality predictions (YES or NO).
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118 7. Select your data type (WGS, PLASMID, CHROMOSOME or NA).
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119 8. Run the tool.
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120
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121 Output
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122 ------
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123
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124 There are 2 different output files produced by `rgi`.
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125
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126 summary.txt
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127 ^^^^^^^^^^^
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128
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129 A tabular file of all detected resistance genes, one gene per line.
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130
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131 +--------------------------------------------------------------------------------------------------------------------------+---------------+-------+------+-------------+----------+----------------+---------------------+----------------+------------------+----------+-----------------------+--------------------------+-------------+------------+-------------------------+----------------------+---------------------------+------------------------+---------------------------+-----------------------------------------+--------------------------------+-----------+
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132 | ORF_ID | Contig | Start | Stop | Orientation | Cut_Off | Pass_Bitscore | Best_Hit_Bitscore | Best_Hit_ARO | Best_Identities | ARO | Model_type | SNPs_in_Best_Hit_ARO | Other_SNPs | Drug Class | Resistance Mechanism | AMR Gene Family | Predicted_DNA | Predicted_Protein | CARD_Protein_Sequence | Percentage Length of Reference Sequence | ID | Model_ID |
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133 +==========================================================================================================================+===============+=======+======+=============+==========+================+=====================+================+==================+==========+=======================+==========================+=============+============+=========================+======================+===========================+========================+===========================+=========================================+================================+===========+
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134 | AY123251.1_6 # 3575 # 4489 # 1 # ID=1_6;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.399 | AY123251.1_6 | 3575 | 4489 | \+ | Strict | 500 | 506.908 | CARB-7 | 83.68 | 3002246 | protein homolog model | n/a | n/a | penam | antibiotic inactivation | CARB beta-lactamase | ATGC | MLLYKMCDNQNYGVTYMKFLLV | MKSLLVFALLMPSVVFASSSKFQSV | 105.56 | gnl|BL_ORD_ID|589|hsp_num:0 | 1443 |
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135 +--------------------------------------------------------------------------------------------------------------------------+---------------+-------+------+-------------+----------+----------------+---------------------+----------------+------------------+----------+-----------------------+--------------------------+-------------+------------+-------------------------+----------------------+---------------------------+------------------------+---------------------------+-----------------------------------------+--------------------------------+-----------+
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136
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137 report.json
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138 ^^^^^^^^^^^
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139
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140 A json version of summary.txt.
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141
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142 Help
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143 ----
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144
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145 **usage:**
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146 ``rgi main [-h] -i INPUT_SEQUENCE -o OUTPUT_FILE [-t {read,contig,protein,wgs}] [-a {DIAMOND,BLAST}] [-n THREADS] [--include_loose] [--local] [--clean] [--debug] [--low_quality] [-d {wgs,plasmid,chromosome,NA}] [-v]``
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147
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148 **optional arguments:**
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149
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150 - ``-h, --help``
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151 show this help message and exit
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152 - ``-i INPUT_SEQUENCE, --input_sequence INPUT_SEQUENCE``
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153 input file must be in either FASTA (contig and protein) or gzip format e.g myFile.fasta, myFasta.fasta.gz
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154 - ``-o OUTPUT_FILE, --output_file OUTPUT_FILE``
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155 output folder and base filename
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156 - ``-t {read,contig,protein,wgs}, --input_type {read,contig,protein,wgs}``
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157 specify data input type (default = contig)
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158 - ``-a {DIAMOND,BLAST}, --alignment_tool {DIAMOND,BLAST}``
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159 specify alignment tool (default = BLAST)
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160 - ``-n THREADS, --num_threads THREADS``
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161 number of threads (CPUs) to use in the BLAST search (default=8)
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162 - ``--include_loose``
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163 include loose hits in addition to strict and perfect hits
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164 - ``--local``
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165 use local database (default: uses database in executable directory)
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166 - ``--clean``
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167 removes temporary files
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168 - ``--debug``
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169 debug mode
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170 - ``--low_quality``
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171 use for short contigs to predict partial genes
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172 - ``-d {wgs,plasmid,chromosome,NA}, --data {wgs,plasmid,chromosome,NA}``
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173 specify a data-type (default = NA)
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174 - ``-v, --version``
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175 prints software version number
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176
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177 Links
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178 -----
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179
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180 RGI: https://card.mcmaster.ca/analyze/rgi
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181
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182 Github: https://github.com/arpcard/rgi
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183
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184 CARD database: https://card.mcmaster.ca
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185 ]]>
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186 </help>
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187 <citations>
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188 <citation type="doi">10.1093/nar/gkw1004</citation>
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189 </citations>
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190 </tool>