Mercurial > repos > thanhlv > fargene
diff fargene.xml @ 0:6f78bc71eb12 draft default tip
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 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fargene.xml Fri Jul 19 08:42:37 2019 -0400 @@ -0,0 +1,171 @@ +<tool id="fargene" name="fARGene" version="0.1"> + <description>Fragmented Antibiotic Resistance Gene iENntifiEr </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <version_command>fargene --version</version_command> + <command detect_errors="exit_code"> + <![CDATA[ + #import re + #if $inputs.input_type == 'paired': + #set $safename_R1 = re.sub('[^\w\-_\.]', '_', $inputs.R1.element_identifier) + #set $safename_R2 = re.sub('[^\w\-_\.]', '_', $inputs.R2.element_identifier) + ln -fs '$inputs.R1' ${safename_R1}.fastq && + ln -fs '$inputs.R2' ${safename_R2}.fastq && + #elif $inputs.input_type == 'collection': + #for $input in $inputs.input_collection + #set $safename_fwd = re.sub('[^\w\-_\.]', '_', $input.forward.element_identifier) + ln -fs $input.forward ${safename_fwd}.fastq && + #set $safename_rvs = re.sub('[^\w\-_\.]', '_', $input.reverse.element_identifier) + ln -fs $input.reverse ${safename_rvs}.fastq && + #end for + #elif $inputs.input_type == 'sequence': + #for $input in $inputs.input_sequence + #set $safename_seq = re.sub('[^\w\-_\.]', '_', $input.element_identifier) + ln -fs $input ${safename_seq}.fasta && + #end for + #end if + + fargene + --infiles + #if $inputs.input_type in ('paired', 'collection'): + *.fastq + --meta + #elif $inputs.input_type == 'sequence': + *.fasta + #end if + --hmm-model $models + --output fargene_output + --tmp-dir tmp + -p \${GALAXY_SLOTS:-4} + #if $meta_score != 0.0: + --meta-score '$meta_score' + #end if + #if $score != 0.0: + --score '$score' + #end if + #if $protein: + '$protein' + #end if + #if $min_orf_length != 90: + --min-orf-length '$min_orf_length' + #end if + #if $retrieve_whole: + '$retrieve_whole' + #end if + #if $no_orf_predict: + '$no_orf_predict' + #end if + #if $no_quality_filtering: + '$no_quality_filtering' + #end if + #if $no_assembly: + '$no_assembly' + #end if + #if $orf_finder: + '$orf_finder' + #end if + #if $store_peptides: + '$store_peptides' + #end if + && + #if $inputs.input_type in ('paired', 'collection'): + tar czf retrievedFragments.tar.gz fargene_output/retrievedFragments + #end if + 2>&1 + ]]></command> + <inputs> + <conditional name="inputs"> + <param name="input_type" type="select" label="Input type" help="Select 'paired end' reads or 'sequence' for genomes/contigs"> + <option value="paired" selected="true">Paired End</option> + <option value="collection">Collection</option> + <option value="sequence">Contigs/Genomes</option> + </param> + <when value="paired"> + <param name="R1" type="data" format="fastqsanger,fastqsanger.gz" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/> + <param name="R2" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/> + </when> + <when value="collection"> + <param name="input_collection" format="fastqsanger" type="data_collection" collection_type="list:paired" label="Paired collection"/> + </when> + <when value="sequence"> + <param name="input_sequence" type="data" format="fasta" multiple="true" label="Input contigs/genomes" /> + </when> + </conditional> + + <param name="models" type="select" label="Resistance Genes"> + <option value="class_a">Class A beta-lactamases</option> + <option value="class_b_1_2">Subclass B1 and B2 beta-lactamases</option> + <option value="class_b_3">Subclass B3 beta-lactamases</option> + <option value="class_c">Class C beta-lactamases</option> + <option value="class_d_1">Class D beta-lactamases-1</option> + <option value="class_d_2">Class D beta-lactamases-2</option> + <option value="qnr">QNR</option> + </param> + <param name="score" argument="--score" type="float" value="0.0" label="The threshold score for a sequence to be classified as + a (almost) complete gene" /> + <param name="meta_score" argument="--meta-score" type="float" value="0.0" label="The threshold score for a fragment to be classified as + a positive. Expressed as score per amino acid" /> + <param name="protein" argument="--protein" type="boolean" truevalue="--protein" falsevalue="" checked="False" label="Rescue short unassmebled plasmids" /> + <param name="min_orf_length" argument="--min-orf-length" type="integer" value="90" label="The minimal length for a retrieved predicted ORF (nt)" /> + <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 + detected should be retrieved" /> + <param name="no_orf_predict" argument="--no-orf-predict" type="boolean" truevalue="--no-orf-predict" falsevalue="" checked="False" label="Do not perform ORF prediction" /> + <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 + metagenomic data" /> + <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 + contigs for metagenomic data" /> + <param name="orf_finder" argument="--orf-finder" type="boolean" truevalue="--orf-finder" falsevalue="" checked="False" label="Use NCBI ORFfinder instead of prodigal for ORF + prediction of genomes/contigs" /> + <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 + redo the analysis using a different model and want to + skip the preprocessing steps" /> + + </inputs> + <outputs> + <data name="summary" format="txt" from_work_dir="fargene_output/results_summary.txt" label="${tool.name} on ${on_string} (Summary)"/> + <data name="retrievedFragments" format="gz" from_work_dir="retrievedFragments.tar.gz" label="${tool.name} on ${on_string} (Retrieved Fragments)"> + <filter>inputs["input_type"] in ['paired', 'collection']</filter> + </data> + <data name="fargene_log" format="txt" from_work_dir="fargene_analysis.log" label="${tool.name} on ${on_string} (log)"/> + <collection name="hmmsearchresults" type="list" label="HMM Search Result"> + <discover_datasets pattern="__name__" directory="fargene_output/hmmsearchresults" format="txt" ext="out" visible="false" /> + </collection> + <collection name="predictedGenes" type="list" label="Predicted Genes"> + <discover_datasets pattern="__name__" directory="fargene_output/predictedGenes" ext="fasta" format="fasta" visible="false" /> + </collection> + </outputs> + <tests> + <test> + <conditional name="inputs"> + <param name="input_type" value="paired"/> + <param name="R1" value="reads_1.fastq"/> + <param name="R2" value="reads_2.fastq"/> + </conditional> + <output name="summary" file="paired/results_summary.txt" compare="sim_size"/> + </test> + <test> + <conditional name="inputs"> + <param name="input_type" value="sequence"/> + <param name="input_sequence" value="klebsiella_plasmid.fasta"/> + <param name="models" value="class_b_1_2" /> + </conditional> + <output name="summary" file="contigs/results_summary.txt" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ + + 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. + + The current version of the tool includes developed and optimized models for identification of the following resistance genes + + - Class A beta-lactamases + - Subclass B1 and B2 beta-lactamases + - Subclass B3 beta-lactamases + - Class C beta-lactamases + - Class D beta-lactamases + - qnr + ]]></help> + <expand macro="citations" /> +</tool>