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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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1 <tool id="fargene" name="fARGene" version="0.1">
2 <description>Fragmented Antibiotic Resistance Gene iENntifiEr </description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <version_command>fargene --version</version_command>
8 <command detect_errors="exit_code">
9 <![CDATA[
10 #import re
11 #if $inputs.input_type == 'paired':
12 #set $safename_R1 = re.sub('[^\w\-_\.]', '_', $inputs.R1.element_identifier)
13 #set $safename_R2 = re.sub('[^\w\-_\.]', '_', $inputs.R2.element_identifier)
14 ln -fs '$inputs.R1' ${safename_R1}.fastq &&
15 ln -fs '$inputs.R2' ${safename_R2}.fastq &&
16 #elif $inputs.input_type == 'collection':
17 #for $input in $inputs.input_collection
18 #set $safename_fwd = re.sub('[^\w\-_\.]', '_', $input.forward.element_identifier)
19 ln -fs $input.forward ${safename_fwd}.fastq &&
20 #set $safename_rvs = re.sub('[^\w\-_\.]', '_', $input.reverse.element_identifier)
21 ln -fs $input.reverse ${safename_rvs}.fastq &&
22 #end for
23 #elif $inputs.input_type == 'sequence':
24 #for $input in $inputs.input_sequence
25 #set $safename_seq = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
26 ln -fs $input ${safename_seq}.fasta &&
27 #end for
28 #end if
29
30 fargene
31 --infiles
32 #if $inputs.input_type in ('paired', 'collection'):
33 *.fastq
34 --meta
35 #elif $inputs.input_type == 'sequence':
36 *.fasta
37 #end if
38 --hmm-model $models
39 --output fargene_output
40 --tmp-dir tmp
41 -p \${GALAXY_SLOTS:-4}
42 #if $meta_score != 0.0:
43 --meta-score '$meta_score'
44 #end if
45 #if $score != 0.0:
46 --score '$score'
47 #end if
48 #if $protein:
49 '$protein'
50 #end if
51 #if $min_orf_length != 90:
52 --min-orf-length '$min_orf_length'
53 #end if
54 #if $retrieve_whole:
55 '$retrieve_whole'
56 #end if
57 #if $no_orf_predict:
58 '$no_orf_predict'
59 #end if
60 #if $no_quality_filtering:
61 '$no_quality_filtering'
62 #end if
63 #if $no_assembly:
64 '$no_assembly'
65 #end if
66 #if $orf_finder:
67 '$orf_finder'
68 #end if
69 #if $store_peptides:
70 '$store_peptides'
71 #end if
72 &&
73 #if $inputs.input_type in ('paired', 'collection'):
74 tar czf retrievedFragments.tar.gz fargene_output/retrievedFragments
75 #end if
76 2>&1
77 ]]></command>
78 <inputs>
79 <conditional name="inputs">
80 <param name="input_type" type="select" label="Input type" help="Select 'paired end' reads or 'sequence' for genomes/contigs">
81 <option value="paired" selected="true">Paired End</option>
82 <option value="collection">Collection</option>
83 <option value="sequence">Contigs/Genomes</option>
84 </param>
85 <when value="paired">
86 <param name="R1" type="data" format="fastqsanger,fastqsanger.gz" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/>
87 <param name="R2" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>
88 </when>
89 <when value="collection">
90 <param name="input_collection" format="fastqsanger" type="data_collection" collection_type="list:paired" label="Paired collection"/>
91 </when>
92 <when value="sequence">
93 <param name="input_sequence" type="data" format="fasta" multiple="true" label="Input contigs/genomes" />
94 </when>
95 </conditional>
96
97 <param name="models" type="select" label="Resistance Genes">
98 <option value="class_a">Class A beta-lactamases</option>
99 <option value="class_b_1_2">Subclass B1 and B2 beta-lactamases</option>
100 <option value="class_b_3">Subclass B3 beta-lactamases</option>
101 <option value="class_c">Class C beta-lactamases</option>
102 <option value="class_d_1">Class D beta-lactamases-1</option>
103 <option value="class_d_2">Class D beta-lactamases-2</option>
104 <option value="qnr">QNR</option>
105 </param>
106 <param name="score" argument="--score" type="float" value="0.0" label="The threshold score for a sequence to be classified as
107 a (almost) complete gene" />
108 <param name="meta_score" argument="--meta-score" type="float" value="0.0" label="The threshold score for a fragment to be classified as
109 a positive. Expressed as score per amino acid" />
110 <param name="protein" argument="--protein" type="boolean" truevalue="--protein" falsevalue="" checked="False" label="Rescue short unassmebled plasmids" />
111 <param name="min_orf_length" argument="--min-orf-length" type="integer" value="90" label="The minimal length for a retrieved predicted ORF (nt)" />
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
113 detected should be retrieved" />
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" />
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
116 metagenomic data" />
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
118 contigs for metagenomic data" />
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
120 prediction of genomes/contigs" />
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
122 redo the analysis using a different model and want to
123 skip the preprocessing steps" />
124
125 </inputs>
126 <outputs>
127 <data name="summary" format="txt" from_work_dir="fargene_output/results_summary.txt" label="${tool.name} on ${on_string} (Summary)"/>
128 <data name="retrievedFragments" format="gz" from_work_dir="retrievedFragments.tar.gz" label="${tool.name} on ${on_string} (Retrieved Fragments)">
129 <filter>inputs["input_type"] in ['paired', 'collection']</filter>
130 </data>
131 <data name="fargene_log" format="txt" from_work_dir="fargene_analysis.log" label="${tool.name} on ${on_string} (log)"/>
132 <collection name="hmmsearchresults" type="list" label="HMM Search Result">
133 <discover_datasets pattern="__name__" directory="fargene_output/hmmsearchresults" format="txt" ext="out" visible="false" />
134 </collection>
135 <collection name="predictedGenes" type="list" label="Predicted Genes">
136 <discover_datasets pattern="__name__" directory="fargene_output/predictedGenes" ext="fasta" format="fasta" visible="false" />
137 </collection>
138 </outputs>
139 <tests>
140 <test>
141 <conditional name="inputs">
142 <param name="input_type" value="paired"/>
143 <param name="R1" value="reads_1.fastq"/>
144 <param name="R2" value="reads_2.fastq"/>
145 </conditional>
146 <output name="summary" file="paired/results_summary.txt" compare="sim_size"/>
147 </test>
148 <test>
149 <conditional name="inputs">
150 <param name="input_type" value="sequence"/>
151 <param name="input_sequence" value="klebsiella_plasmid.fasta"/>
152 <param name="models" value="class_b_1_2" />
153 </conditional>
154 <output name="summary" file="contigs/results_summary.txt" compare="sim_size"/>
155 </test>
156 </tests>
157 <help><![CDATA[
158
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.
160
161 The current version of the tool includes developed and optimized models for identification of the following resistance genes
162
163 - Class A beta-lactamases
164 - Subclass B1 and B2 beta-lactamases
165 - Subclass B3 beta-lactamases
166 - Class C beta-lactamases
167 - Class D beta-lactamases
168 - qnr
169 ]]></help>
170 <expand macro="citations" />
171 </tool>