<tool id="csp2-screen" name="CSP2 (Screening Mode)" version="0.9.7_Dev21">
        <description>Screen query assemblies against reference assemblies</description>
        <requirements>
                <requirement type="package" version="24.10.1">nextflow</requirement>
                <requirement type="package" version="1.5.8">micromamba</requirement>
        </requirements>
        <version_command>nextflow -version</version_command>
        <command detect_errors="aggressive"><![CDATA[

mkdir ./queries ./references;

#if (str($query_fasta.query_fasta_select) == "none"):
        export QUERY_FASTA_ARG="";
#elif (str($query_fasta.query_fasta_select) == "collection"):
        #for _, $query_assembly in enumerate($query_fasta.coll):
                ln -sf ${query_assembly} ./queries/${query_assembly.element_identifier};
        #end for
        export QUERY_FASTA_ARG="--fasta ./queries";
#else
        #for _, $query_assembly in enumerate($query_fasta.list):
                ln -sf ${query_assembly} ./queries/${query_assembly.element_identifier};
        #end for
        export QUERY_FASTA_ARG="--fasta ./queries";
#end if

#if (str($ref_fasta.ref_fasta_select) == "none"):
        export REF_FASTA_ARG="";
#elif (str($ref_fasta.ref_fasta_select) == "collection"):
        #for _, $ref_assembly in enumerate($ref_fasta.coll):
                ln -sf ${ref_assembly} ./references/${ref_assembly.element_identifier};
        #end for
        export REF_FASTA_ARG="--fasta ./references";
#else
        #for _, $ref_assembly in enumerate($ref_fasta.list):
                ln -sf ${ref_assembly} ./references/${ref_assembly.element_identifier};
        #end for
        export REF_FASTA_ARG="--fasta ./references";
#end if

#if (str($query_reads.query_reads_select) == "none"):
        export QUERY_READS_ARG="";
#elif (str($query_reads.query_reads_select) == "collection"):
        #for _, $pair in enumerate($query_reads.coll):
                ln -sf ${pair.forward} ./queries/${pair.forward.name};
                ln -sf ${pair.reverse} ./queries/${pair.reverse.name};
        #end for
        export QUERY_READS_ARG="--reads ./queries";
#else
        #for _, $read_file in enumerate($query_reads.list):
                ln -sf ${read_file} ./queries/${read_file.element_identifier};
        #end for
        export QUERY_READS_ARG="--reads ./queries";
#end if

#if (str($ref_reads.ref_reads_select) == "none"):
        export REF_READS_ARG="";
#elif (str($ref_reads.ref_reads_select) == "collection"):
        #for _, $pair in enumerate($ref_reads.coll):
                ln -sf ${pair.forward} ./references/${pair.forward.name};
                ln -sf ${pair.reverse} ./references/${pair.reverse.name};
        #end for
        export REF_READS_ARG="--ref_reads ./references";
#else
        #for _, $read_file in enumerate($ref_reads.list):
                ln -sf ${read_file} ./references/${read_file.element_identifier};
        #end for
        export REF_READS_ARG="--ref_reads ./references";
#end if

if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then
        export TRIM_ARG="--trim_name $trim_name";
else
        export TRIM_ARG="";
fi;

if [ -n "$ref_id" ] && [ "$ref_id" != "None" ]; then
        export REF_ID_ARG="--ref_id $ref_id";
else
        export REF_ID_ARG="";
fi;

nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --runmode screen \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$REF_ID_ARG \$TRIM_ARG --readext $readext --forward $forward --reverse $reverse --ref_readext $readext --ref_forward $forward --ref_reverse $reverse --min_cov $min_cov --min_iden $min_iden --min_len $min_len --ref_edge $ref_edge --query_edge $query_edge --dwin $dwin --wsnps $wsnps --out ./CSP2_Screen_Output > Nextflow_Log.txt 2>&1 &&
ls -la CSP2_Screen_Output;
]]>
        </command>
        <inputs>
                <conditional name="query_fasta">
                <param name="query_fasta_select" type="select" label="Get query assemblies from a collection or your history">
                        <option value="none" selected="true">Do not provide query assemblies</option>
                        <option value="collection">Query assemblies from a collection_type</option>
                        <option value="history">Query assemblies from your history</option>
                </param>
                <when value="none">
                </when>
                <when value="collection">
                        <param label="Query Assembly Collection" name="coll" type="data_collection" format="fasta" collection_type="list" />
                </when>
                <when value="history">
                        <param label="Query Assembly List" type="data" name="list" format="fasta"  multiple="true" />
                </when>
                </conditional>

                <conditional name="ref_fasta">
                <param name="ref_fasta_select" type="select" label="Get reference assemblies from a collection or your history">
                        <option value="none" selected="true">Do not provide reference assemblies</option>
                        <option value="collection">Reference assemblies from a collection_type</option>
                        <option value="history">Reference assemblies from your history</option>
                </param>
                <when value="none">
                </when>
                <when value="collection">
                        <param label="Reference Assembly Collection" name="coll" type="data_collection" format="fasta" collection_type="list" />
                </when>
                <when value="history">
                        <param label="Reference Assembly List" type="data" name="list" format="fasta"  multiple="true" />
                </when>
                </conditional>   
                <conditional name="query_reads">
                <param name="query_reads_select" type="select" label="Get query reads from a paired-end collection or your history">
                        <option value="none" selected="true">Do not provide query reads</option>
                        <option value="collection">Query reads from a collection_type</option>
                        <option value="history">Query reads from your history</option>
                </param>
                <when value="none">
                </when>
                <when value="collection">
                        <param label="Query Reads Collection" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="list:paired" />
                </when>
                <when value="history">
                        <param label="Query Reads List" type="data" name="list" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2"  multiple="true" />
                </when>
                </conditional>

                <conditional name="ref_reads">
                <param name="ref_reads_select" type="select" label="Get reference reads from a paired-end collection or your history">
                        <option value="none" selected="true">Do not provide reference reads</option>
                        <option value="collection">Refrence reads from a collection_type</option>
                        <option value="history">Refrence reads from your history</option>
                </param>
                <when value="none">
                </when>
                <when value="collection">
                        <param label="Refrence Reads Collection" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="list:paired" />
                </when>
                <when value="history">
                        <param label="Refrence Reads List" type="data" name="list" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2"  multiple="true" />
                </when>
                </conditional>             
                <param name="min_cov" type="float" value="85" label="Minimum reference genome coverage to proceed with distance estimation" optional="true" />
                <param name="min_iden" type="float" value="99" label="Minimum alignment percent identity to detect SNPs" optional="true" />
                <param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" />
                <param name="ref_edge" type="integer" value="150" label="Prune SNPs within this many bases of reference contig edge" optional="true" />
                <param name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" optional="true" />
                <param name="dwin" type="text" value="1000,125,15" label="Comma-separated set of window sizes for SNP density filtration (Set to 0 to disable density filtration)" optional="true" />
                <param name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" optional="true" />
                <param name="readext" type="text" value="fastq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" />
                <param name="forward" type="text" value="_1.fastq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" />
                <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" />
                <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" />
                <param name="ref_id" type="text" value="" label="Comma-separated list of desired Reference IDs (e.g., Sample_A,Sample_B)" optional="true" />
        </inputs>
        <outputs>
                <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_Screen_Output/Raw_MUMmer_Summary.tsv" />
                <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_Screen_Output/Isolate_Data.tsv" />
                <data name="screening_results" format="tabular" label="Screening Results" from_work_dir="CSP2_Screen_Output/Screening_Results.tsv" />
        </outputs>
        <tests>
                <test>
                        <param name="query_fasta">
                                <collection type="list">
                                        <element name="Sample_A" value="assemblies/Sample_A.fasta" />
                                        <element name="Sample_B" value="assemblies/Sample_B.fasta" />
                                        <element name="Sample_C" value="assemblies/Sample_C.fasta" />
                                        <element name="Sample_D" value="assemblies/Sample_D.fasta" />
                                        <element name="Sample_E" value="assemblies/Sample_E.fasta" />
                                        <element name="Sample_F" value="assemblies/Sample_F.fasta" />
                                        <element name="Sample_G" value="assemblies/Sample_G.fasta" />
                                        <element name="Sample_H" value="assemblies/Sample_H.fasta" />
                                        <element name="Sample_I" value="assemblies/Sample_I.fasta" />
                                        <element name="Sample_J" value="assemblies/Sample_J.fasta" />
                                        <element name="Sample_K" value="assemblies/Sample_K.fasta" />
                                        <element name="Sample_L" value="assemblies/Sample_L.fasta" />
                                        <element name="Sample_M" value="assemblies/Sample_M.fasta" />
                                        <element name="Sample_N" value="assemblies/Sample_N.fasta" />
                                        <element name="Sample_O" value="assemblies/Sample_O.fasta" />
                                </collection>
                        </param>
                        <param name="query_reads">
                                <collection type="list">
                                        <element name="Forward" value="reads/Week_42_Reads_1.fq.gz" />
                                        <element name="Reverse" value="reads/Week_42_Reads_2.fq.gz" />
                                </collection>
                        </param>

                        <param name="ref_id" value="Sample_A,Sample_B" />
                        <param name="readext" value="fq.gz" />
                        <param name="forward" value="_1.fq.gz" />
                        <param name="reverse" value="_2.fq.gz" />

                        <output name="screening_results" value="Screening_Results.tsv" />
                        <output name="isolate_data" value="Isolate_Data.tsv" />
                </test>
        </tests>
        <help>
        This tool takes query assemblies and reference assemblies and calculates the pairwise distance between each query/reference combination. If no reference is provided, all queries are compared to all other queries.
        </help>
        <citations>
                <citation type="doi">10.XXXX/placeholder.doi</citation>
                <citation type="bibtex">@article{example2024,title={CFSAN SNP Pipeline 2 (CSP2): a pipeline for fast and accurate SNP distance estimation from bacterial genome assemblies.},author={Doe, John and Smith, Jane},journal={Submitted},year={2024}}
                </citation>
        </citations>
</tool>