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annotate rgi.xml @ 0:715bc9aeef69 draft

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planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
author card
date Wed, 27 Feb 2019 09:08:21 -0500
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children f96cbb663aa9
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0
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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1 <tool id="rgi" name="Resistance Gene Identifier (RGI)" version="4.2.2">
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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="4.2.2">rgi</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <command><![CDATA[
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10 #if $db_opts.db_opts_selector != "default":
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11 rgi load
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12 #if $db_opts.db_opts_selector == "local":
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13 -i "${__tool_data_path__}/rgi_databases/$db_opts.rgi_db_local/card.json"
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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14 #else:
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15 -i "$db_opts.rgi_db_hist"
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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16 #end if
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17 --local
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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18 &&
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19 #end if
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20
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21 rgi main
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22 -i '$input_sequence'
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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23 -o out
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24 -t $input_type
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25 -a $alignment_tool
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26 -n "\${GALAXY_SLOTS:-1}"
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27 $include_loose
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28 $low_quality
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29 -d $data
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30
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31 #if $db_opts.db_opts_selector != "default":
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32 --local
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33 #end if
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34 ]]></command>
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35 <inputs>
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36 <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"/>
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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37 <param argument="--input_type" type="select" multiple="false" label="Input type" help="specify data input type (default = contig)">
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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38 <option value="contig" selected="true">CONTIG (Nucleotide Sequence)</option>
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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39 <option value="protein">PROTEIN (Protein Sequence)</option>
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40 </param>
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41 <param argument="--alignment_tool" type="select" label="Alignment tool" help="specify alignment tool (default = BLAST)">
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42 <option value="blast" selected="true">BLAST</option>
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43 <option value="diamond">DIAMOND</option>
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44 </param>
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45 <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"/>
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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46 <param argument="--low_quality" type="boolean" checked="false" truevalue="--low_quality" falsevalue="" label="Low quality" help="use for short contigs to predict partial genes"/>
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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47 <param argument="--data" type="select" multiple="false" label="Data type" help="specify a data-type (default = NA)">
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48 <option value="wgs">WGS</option>
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49 <option value="plasmid">PLASMID</option>
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50 <option value="chromosome">CHROMOSOME</option>
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51 <option value="NA" selected="true">NA</option>
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52 </param>
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53 <conditional name="db_opts">
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54 <param name="db_opts_selector" type="select" label="Select an RGI database">
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55 <option value="default" selected="true">Default RGI database</option>
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56 <option value="local">Locally installed RGI database</option>
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57 <option value="hist">RGI database from your history</option>
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58 </param>
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59 <when value="default">
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60 <param name="rgi_db_local" type="hidden" value="" />
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61 <param name="rgi_db_hist" type="hidden" value="" />
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62 </when>
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63 <when value="local">
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64 <param name="rgi_db_local" type="select" multiple="false" label="Locally installed RGI database">
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65 <options from_data_table="rgi_databases">
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66 <validator type="no_options" message="No databases are available built-in"/>
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67 </options>
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68 </param>
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69 <param name="rgi_db_hist" type="hidden" value="" />
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70 </when>
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71 <when value="hist">
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72 <param name="rgi_db_local" type="hidden" value="" />
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73 <param name="rgi_db_hist" type="data" format="json" label="RGI database from your history" />
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74 </when>
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75 </conditional>
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76 </inputs>
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77 <outputs>
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78 <data name="report" format="json" from_work_dir="out.json" label="${tool.name} on ${on_string}: report.json"/>
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79 <data name="summary" format="tabular" from_work_dir="out.txt" label="${tool.name} on ${on_string}: summary.txt"/>
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80 </outputs>
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81 <tests>
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82 <test>
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83 <param name="input_sequence" value="test1.fasta" />
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84 <param name="input_type" value="contig" />
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85 <param name="alignment_tool" value="blast" />
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86 <param name="include_loose" value="false" />
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87 <param name="low_quality" value="false" />
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88 <param name="data" value="NA" />
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89 <conditional name="db_opts">
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90 <param name="db_opts_selector" value="default" />
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91 </conditional>
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92 <output name="summary">
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93 <assert_contents>
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94 <has_text text="AY123251" />
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95 </assert_contents>
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96 </output>
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97 </test>
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98 </tests>
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99 <help>
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100 <![CDATA[
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101 Resistance Gene Identifier (RGI)
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102 ================================
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103
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104 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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105
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106 Usage
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107 -----
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108
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109 1. Select your input sequence (in FASTA format).
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110 2. Select your input type (CONTIG or PROTEIN).
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111 3. Select your alignment tool (DIAMOND or BLAST).
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112 4. Specify if you want to include loose hits (YES or NO).
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113 5. Specify if you want to remove temporary files (YES or NO).
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114 6. Specify if you want to low quality predictions (YES or NO).
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115 7. Select your data type (WGS, PLASMID, CHROMOSOME or NA).
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116 8. Run the tool.
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117
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118 Output
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119 ------
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120
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121 There are 2 different output files produced by `rgi`.
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122
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123 summary.txt
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124 ^^^^^^^^^^^
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125
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126 A tabular file of all detected resistance genes, one gene per line.
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127
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128 +--------------------------------------------------------------------------------------------------------------------------+---------------+-------+------+-------------+----------+----------------+---------------------+----------------+------------------+----------+-----------------------+--------------------------+-------------+------------+-------------------------+----------------------+---------------------------+------------------------+---------------------------+-----------------------------------------+--------------------------------+-----------+
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129 | 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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130 +==========================================================================================================================+===============+=======+======+=============+==========+================+=====================+================+==================+==========+=======================+==========================+=============+============+=========================+======================+===========================+========================+===========================+=========================================+================================+===========+
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131 | 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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132 +--------------------------------------------------------------------------------------------------------------------------+---------------+-------+------+-------------+----------+----------------+---------------------+----------------+------------------+----------+-----------------------+--------------------------+-------------+------------+-------------------------+----------------------+---------------------------+------------------------+---------------------------+-----------------------------------------+--------------------------------+-----------+
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133
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134 report.json
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135 ^^^^^^^^^^^
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136
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137 A json version of summary.txt.
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138
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139 Help
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140 ----
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141
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142 **usage:**
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143 ``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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144
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145 **optional arguments:**
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146
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147 - ``-h, --help``
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148 show this help message and exit
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149 - ``-i INPUT_SEQUENCE, --input_sequence INPUT_SEQUENCE``
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150 input file must be in either FASTA (contig and protein) or gzip format e.g myFile.fasta, myFasta.fasta.gz
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151 - ``-o OUTPUT_FILE, --output_file OUTPUT_FILE``
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152 output folder and base filename
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153 - ``-t {read,contig,protein,wgs}, --input_type {read,contig,protein,wgs}``
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154 specify data input type (default = contig)
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155 - ``-a {DIAMOND,BLAST}, --alignment_tool {DIAMOND,BLAST}``
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156 specify alignment tool (default = BLAST)
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157 - ``-n THREADS, --num_threads THREADS``
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158 number of threads (CPUs) to use in the BLAST search (default=8)
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159 - ``--include_loose``
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160 include loose hits in addition to strict and perfect hits
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161 - ``--local``
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162 use local database (default: uses database in executable directory)
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163 - ``--clean``
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164 removes temporary files
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165 - ``--debug``
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166 debug mode
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167 - ``--low_quality``
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168 use for short contigs to predict partial genes
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169 - ``-d {wgs,plasmid,chromosome,NA}, --data {wgs,plasmid,chromosome,NA}``
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170 specify a data-type (default = NA)
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171 - ``-v, --version``
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172 prints software version number
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173
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174 Links
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175 -----
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176
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177 RGI: https://card.mcmaster.ca/analyze/rgi
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178
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179 Github: https://github.com/arpcard/rgi
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180
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181 CARD database: https://card.mcmaster.ca
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182 ]]>
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183 </help>
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184 <citations>
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185 <citation type="doi">10.1093/nar/gkw1004</citation>
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186 </citations>
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187 </tool>