--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fargene.xml	Thu Nov 28 14:39:41 2019 -0500
@@ -0,0 +1,189 @@
+<tool id="fargene" name="fargene" version="@VERSION@">
+    <description>Fragmented antibiotic resistance gene identifier </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 $i, $input in enumerate($inputs.input_collection)
+            #set $safename_fwd = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
+            ln -fs '${input.forward}' ${safename_fwd}_1.fastq &&
+            #set $safename_rvs = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
+            ln -fs '${input.reverse}' ${safename_rvs}_2.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</option>
+                <option value="collection">Paired 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" min="1" 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 ${on_string} (Summary)">
+        </data>
+        <data name="retrievedFragments" format="tar.gz" from_work_dir="retrievedFragments.tar.gz" label="${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)">
+        </data>
+        <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 expect_num_outputs="5">
+            <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 expect_num_outputs="5">
+            <conditional name="inputs">
+                <param name="input_type" value="collection"/>
+                <param name="input_collection">
+                    <collection type="list:paired">
+                        <element name="Pair1">
+                            <collection type="paired">
+                                <element name="forward" value="reads_1.fastq" ftype="fastqsanger"/>
+                                <element name="reverse" value="reads_2.fastq" ftype="fastqsanger"/>
+                            </collection>
+                        </element>
+                    </collection>
+                </param>
+            </conditional>
+            <output name="summary" file="paired/results_summary.txt" compare="sim_size"/>
+        </test>
+        <test expect_num_outputs="4">
+            <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>