Mercurial > repos > thanhlv > fargene

annotate fargene.xml @ 0:6f78bc71eb12 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
author thanhlv
date Fri, 19 Jul 2019 08:42:37 -0400
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6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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1 <tool id="fargene" name="fARGene" version="0.1">
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2 <description>Fragmented Antibiotic Resistance Gene iENntifiEr </description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <version_command>fargene --version</version_command>
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8 <command detect_errors="exit_code">
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9 <![CDATA[
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10 #import re
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11 #if $inputs.input_type == 'paired':
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12 #set $safename_R1 = re.sub('[^\w\-_\.]', '_', $inputs.R1.element_identifier)
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13 #set $safename_R2 = re.sub('[^\w\-_\.]', '_', $inputs.R2.element_identifier)
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14 ln -fs '$inputs.R1' ${safename_R1}.fastq &&
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15 ln -fs '$inputs.R2' ${safename_R2}.fastq &&
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16 #elif $inputs.input_type == 'collection':
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17 #for $input in $inputs.input_collection
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18 #set $safename_fwd = re.sub('[^\w\-_\.]', '_', $input.forward.element_identifier)
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19 ln -fs $input.forward ${safename_fwd}.fastq &&
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20 #set $safename_rvs = re.sub('[^\w\-_\.]', '_', $input.reverse.element_identifier)
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21 ln -fs $input.reverse ${safename_rvs}.fastq &&
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22 #end for
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23 #elif $inputs.input_type == 'sequence':
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24 #for $input in $inputs.input_sequence
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25 #set $safename_seq = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
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26 ln -fs $input ${safename_seq}.fasta &&
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27 #end for
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28 #end if
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29
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30 fargene
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31 --infiles
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32 #if $inputs.input_type in ('paired', 'collection'):
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33 *.fastq
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34 --meta
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35 #elif $inputs.input_type == 'sequence':
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36 *.fasta
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37 #end if
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38 --hmm-model $models
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39 --output fargene_output
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40 --tmp-dir tmp
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41 -p \${GALAXY_SLOTS:-4}
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42 #if $meta_score != 0.0:
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43 --meta-score '$meta_score'
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44 #end if
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45 #if $score != 0.0:
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46 --score '$score'
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47 #end if
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48 #if $protein:
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49 '$protein'
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50 #end if
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51 #if $min_orf_length != 90:
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52 --min-orf-length '$min_orf_length'
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53 #end if
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54 #if $retrieve_whole:
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55 '$retrieve_whole'
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56 #end if
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57 #if $no_orf_predict:
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58 '$no_orf_predict'
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59 #end if
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60 #if $no_quality_filtering:
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61 '$no_quality_filtering'
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62 #end if
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63 #if $no_assembly:
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64 '$no_assembly'
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65 #end if
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66 #if $orf_finder:
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67 '$orf_finder'
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68 #end if
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69 #if $store_peptides:
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70 '$store_peptides'
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71 #end if
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72 &&
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73 #if $inputs.input_type in ('paired', 'collection'):
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74 tar czf retrievedFragments.tar.gz fargene_output/retrievedFragments
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75 #end if
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76 2>&1
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77 ]]></command>
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78 <inputs>
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79 <conditional name="inputs">
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80 <param name="input_type" type="select" label="Input type" help="Select 'paired end' reads or 'sequence' for genomes/contigs">
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81 <option value="paired" selected="true">Paired End</option>
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82 <option value="collection">Collection</option>
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83 <option value="sequence">Contigs/Genomes</option>
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84 </param>
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85 <when value="paired">
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86 <param name="R1" type="data" format="fastqsanger,fastqsanger.gz" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/>
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87 <param name="R2" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>
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88 </when>
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89 <when value="collection">
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90 <param name="input_collection" format="fastqsanger" type="data_collection" collection_type="list:paired" label="Paired collection"/>
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91 </when>
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92 <when value="sequence">
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93 <param name="input_sequence" type="data" format="fasta" multiple="true" label="Input contigs/genomes" />
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94 </when>
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95 </conditional>
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96
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97 <param name="models" type="select" label="Resistance Genes">
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98 <option value="class_a">Class A beta-lactamases</option>
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99 <option value="class_b_1_2">Subclass B1 and B2 beta-lactamases</option>
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100 <option value="class_b_3">Subclass B3 beta-lactamases</option>
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101 <option value="class_c">Class C beta-lactamases</option>
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102 <option value="class_d_1">Class D beta-lactamases-1</option>
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103 <option value="class_d_2">Class D beta-lactamases-2</option>
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104 <option value="qnr">QNR</option>
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105 </param>
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106 <param name="score" argument="--score" type="float" value="0.0" label="The threshold score for a sequence to be classified as
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107 a (almost) complete gene" />
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108 <param name="meta_score" argument="--meta-score" type="float" value="0.0" label="The threshold score for a fragment to be classified as
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109 a positive. Expressed as score per amino acid" />
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110 <param name="protein" argument="--protein" type="boolean" truevalue="--protein" falsevalue="" checked="False" label="Rescue short unassmebled plasmids" />
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111 <param name="min_orf_length" argument="--min-orf-length" type="integer" value="90" label="The minimal length for a retrieved predicted ORF (nt)" />
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112 <param name="retrieve_whole" argument="--retrieve-whole" type="boolean" truevalue="--retrieve-whole " falsevalue="" checked="False" label="Use this flag if the whole sequence where a hit is
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113 detected should be retrieved" />
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114 <param name="no_orf_predict" argument="--no-orf-predict" type="boolean" truevalue="--no-orf-predict" falsevalue="" checked="False" label="Do not perform ORF prediction" />
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115 <param name="no_quality_filtering" argument="--no-quality-filtering" type="boolean" truevalue="--no-quality-filtering" falsevalue="" checked="False" label="Use if no quality control should be performed on the
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116 metagenomic data" />
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117 <param name="no_assembly" argument="--no-assembly" type="boolean" truevalue="--no-assembly" falsevalue="" checked="False" label="Use if you want to skip the assembly and retrieval of
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118 contigs for metagenomic data" />
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119 <param name="orf_finder" argument="--orf-finder" type="boolean" truevalue="--orf-finder" falsevalue="" checked="False" label="Use NCBI ORFfinder instead of prodigal for ORF
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120 prediction of genomes/contigs" />
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121 <param name="store_peptides" argument="--store-peptides" type="boolean" truevalue="--store-peptides" falsevalue="" checked="False" label="Store the translated sequences. Useful if you plan to
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122 redo the analysis using a different model and want to
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123 skip the preprocessing steps" />
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124
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125 </inputs>
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126 <outputs>
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127 <data name="summary" format="txt" from_work_dir="fargene_output/results_summary.txt" label="${tool.name} on ${on_string} (Summary)"/>
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128 <data name="retrievedFragments" format="gz" from_work_dir="retrievedFragments.tar.gz" label="${tool.name} on ${on_string} (Retrieved Fragments)">
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129 <filter>inputs["input_type"] in ['paired', 'collection']</filter>
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130 </data>
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131 <data name="fargene_log" format="txt" from_work_dir="fargene_analysis.log" label="${tool.name} on ${on_string} (log)"/>
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132 <collection name="hmmsearchresults" type="list" label="HMM Search Result">
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133 <discover_datasets pattern="__name__" directory="fargene_output/hmmsearchresults" format="txt" ext="out" visible="false" />
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134 </collection>
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135 <collection name="predictedGenes" type="list" label="Predicted Genes">
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136 <discover_datasets pattern="__name__" directory="fargene_output/predictedGenes" ext="fasta" format="fasta" visible="false" />
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137 </collection>
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138 </outputs>
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139 <tests>
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140 <test>
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141 <conditional name="inputs">
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142 <param name="input_type" value="paired"/>
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143 <param name="R1" value="reads_1.fastq"/>
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144 <param name="R2" value="reads_2.fastq"/>
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145 </conditional>
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146 <output name="summary" file="paired/results_summary.txt" compare="sim_size"/>
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147 </test>
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148 <test>
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149 <conditional name="inputs">
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150 <param name="input_type" value="sequence"/>
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151 <param name="input_sequence" value="klebsiella_plasmid.fasta"/>
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152 <param name="models" value="class_b_1_2" />
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153 </conditional>
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154 <output name="summary" file="contigs/results_summary.txt" compare="sim_size"/>
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155 </test>
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156 </tests>
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157 <help><![CDATA[
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158
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159 fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. The tool includes developed and optimized models for a number or resistance gene types, and the functionality to create and optimize models of your own choice of resistance genes.
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160
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161 The current version of the tool includes developed and optimized models for identification of the following resistance genes
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162
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163 - Class A beta-lactamases
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164 - Subclass B1 and B2 beta-lactamases
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165 - Subclass B3 beta-lactamases
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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166 - Class C beta-lactamases
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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167 - Class D beta-lactamases
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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168 - qnr
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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169 ]]></help>
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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170 <expand macro="citations" />
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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171 </tool>