--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hfp_bettercallsal.xml	Thu May 28 20:31:42 2026 +0000
@@ -0,0 +1,218 @@
+<tool id="hfp_bettercallsal_awsbatch" name="bettercallsal" version="1.0.0+awsbatch">
+    <description>An automated workflow to assign Salmonella serotype based on NCBI Pathogen Detection Project for Salmonella.</description>
+    <requirements>
+        <container type="docker">quay.io/galaxytrakr/mulled-v2-ebd88135862aa647eeae73d4d8e6ea8ec81245cd:v5.0</container>
+    </requirements>
+    <version_command>nextflow -version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    export MAMBA_ROOT_PREFIX="/server/galaxy/data/nextflow-micromamba-cache";
+    export NXF_HOME=\$(pwd)"/.nextflow-home";
+    input_path=\$(pwd)"/cpipes-input";
+    workdir_path=\$(pwd)"/work";
+    mkdir -p "\${input_path}" || exit 1;
+    #import re
+    #if (str($input_read_type_cond.input_read_type) == "single_long" or str($input_read_type_cond.input_read_type) == "long_long"):
+	    #for _, $unpaired in enumerate($input_read_type_cond.input):
+            #set read1 = str($unpaired.name)
+            #if not str($unpaired.name).endswith(('.fastq', '.fastq.gz')):
+                #set read1_ext = re.sub('fastqsanger', 'fastq', str($unpaired.ext))
+                #set read1 = str($unpaired.name) + str('.') + $read1_ext
+            #end if
+            ln -sf '$unpaired' "\${input_path}/$read1";
+	    #end for
+    #elif (str($input_read_type_cond.input_read_type) == "paired"):
+	    #for _, $pair in enumerate($input_read_type_cond.input_pair)
+            #set read_R1 = re.sub('\:forward', '_forward', str($pair.forward.name))
+            #set read_R2 = re.sub('\:reverse', '_reverse', str($pair.reverse.name))
+            #set read_R1_ext = re.sub('fastqsanger', 'fastq', str($pair.forward.ext))
+            #set read_R2_ext = re.sub('fastqsanger', 'fastq', str($pair.reverse.ext))
+            #if not str($pair.forward.name).endswith(('.fastq', '.fastq.gz')):
+	            #set read_R1 = $read_R1 + str('.') + $read_R1_ext
+            #end if
+            #if not str($pair.reverse.name).endswith(('.fastq', '.fastq.gz')):
+                #set read_R2 = $read_R2 + str('.') + $read_R2_ext
+            #end if
+	        ln -sf '$pair.forward' "\${input_path}/$read_R1";
+	        ln -sf '$pair.reverse' "\${input_path}/$read_R2";
+	    #end for
+    #end if
+	$__tool_directory__/1.0.0/cpipes
+    #if (str($input_read_type_cond.input_read_type) == "long_long"):
+        --pipeline bettercallsal_lr
+    #else
+        --pipeline bettercallsal
+    #end if
+    --input \${input_path}
+	--output cpipes-output
+    --fq_suffix '${input_read_type_cond.fq_suffix}'
+    #if (str($input_read_type_cond.input_read_type) == "long_long"):
+        --fq_single_end true
+    #elif (str($input_read_type_cond.input_read_type) == "single_long"):
+        --fq_single_end true
+    #elif (str($input_read_type_cond.input_read_type) == "paired"):
+        --fq_single_end false --fq2_suffix '${input_read_type_cond.fq2_suffix}'
+    #end if
+    --tuspy_n $tuspy_n
+    #if ($sourmash_cond.run == "true"):
+        --sfhpy_fcv $sourmash_cond.sfhpy_fcv
+    #end if
+    #if ($bcs_thresholds != 'relax' and str($input_read_type_cond.input_read_type) != "long_long"):
+        --kmaalign_ID $kma_id
+    #end if
+    #if ($sourmash_cond.run == "true"):
+        --sfhpy_fcv $sourmash_cond.sfhpy_fcv
+    #end if
+    --bcs_db_mode $bcs_db_mode
+    --bcs_thresholds $bcs_thresholds
+	--fq_filename_delim '${fq_filename_delim}'
+	--fq_filename_delim_idx $fq_filename_delim_idx
+    -work-dir "\${workdir_path}"
+	-profile stdkondagac;
+    #if (str($input_read_type_cond.input_read_type) == "long_long"):
+        mv './cpipes-output/bettercallsal_lr-multiqc/CPIPES-Report_multiqc_report.html' './multiqc_report.html' || exit 1;
+    #else
+        mv './cpipes-output/bettercallsal-multiqc/CPIPES-Report_multiqc_report.html' './multiqc_report.html' || exit 1;
+    #end if
+    rm -rf ./cpipes-output || exit 1;
+    rm -rf ./work || exit 1;
+    ]]></command>
+    <inputs>
+        <conditional name="input_read_type_cond">
+            <param name="input_read_type" type="select" label="Select the read collection type">
+                <option value="single_long" selected="true">Single-End short reads</option>
+                <option value="paired">Paired-End short reads</option>
+                <option value="long_long">Long reads</option>
+            </param>
+            <when value="single_long">
+                <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz"
+                    label="Dataset list of unpaired short reads" />
+                <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the Single-End FASTQ"/>
+            </when>
+            <when value="long_long">
+                <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz"
+                    label="Dataset list of long reads" />
+                <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the long read FASTQ"/>
+            </when>
+            <when value="paired">
+                <param name="input_pair" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz" label="List of Dataset pairs" />
+                <param name="fq_suffix" value="_R1_001.fastq.gz" type="text" label="Suffix of the R1 FASTQ"
+                    help="For any data sets downloaded from NCBI into Galaxy, change this to _forward.fastq.gz suffix."/>
+                <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ"
+                    help="For any data sets downloaded from NCBI into Galaxy, change this to _reverse.fastq.gz suffix."/>
+            </when>
+        </conditional>
+        <param name="bcs_db_mode" type="select" label="Select the database mode with bettercallsal"
+            help="Refer to `Database generation` section in our manuscript: https://doi.org/10.3389/fmicb.2023.1200983">
+            <option value="snp" selected="true">per_snp_cluster</option>
+            <option value="comp">per_computed_type</option>
+        </param>
+        <param name="tuspy_n" optional="true" value="10" type="integer" label="Enter the number of top unique serotypes to retain after initial MASH screen step"
+            help="The default value of 10 is suitable for almost all scenarios."/>
+        <param name="bcs_thresholds" type="select" label="Enter the type of base quality thresholds to be set with bettercallsal"
+            help="The default value sets strictest thresholds that tends to filter out most of the false positive hits.">
+            <option value="strict" selected="true">strict</option>
+            <option value="relax">relax</option>
+        </param>
+        <param name="kma_id" optional="true" value="10.0" type="text" label="Enter the %ID threshold for KMA alignments of samples against genomes"
+            help="The default value of 10% works well for enrichment samples tested within FDA. The 'relax' preset for base quality thresholds automatically sets this value to 5%."/>
+        <conditional name="sourmash_cond">
+            <param name="run" type="select" label="Run sourmash"
+                help="Should sourmash be used for additional genome fraction filtering">
+                <option value="true" selected="true">yes</option>
+                <option value="false">no</option>
+            </param>
+            <when value="true">
+                <param name="sfhpy_fcv" type="text" value="0.1" label="Enter the minimum coverage match with sourmash before a serotype hit is considered for further processing"
+                        help="The default value is set at 10% coverage threshold."/>
+            </when>
+            <when value="false">
+                <param name="sfhpy_fcv" type="select" label="Enter the minimum coverage match with sourmash before a serotype hit is considered for further processing"
+                    help="THIS OPTION IS IGNORED IF SOURMASH TOOL IS NOT RUN.">
+                    <option value="NA" selected="true">N/A</option>
+                </param>
+            </when>
+        </conditional>
+        <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)" 
+            help="This is the delimitor by which samples are grouped together to display in the final MultiQC report. For example, if your input data sets are mango_replicate1.fastq.gz, mango_replicate2.fastq.gz, orange_replicate1_maryland.fastq.gz, orange_replicate2_maryland.fastq.gz, then to create 2 samples mango and orange, the value for --fq_filename_delim would be _ (underscore) and the value for --fq_filename_delim_idx would be 1, since you want to group by the first word (i.e. mango or orange) after splitting the filename based on _ (underscore)."/>
+        <param name="fq_filename_delim_idx" type="integer" value="1" label="File name delimitor index (--fq_filename_delim_idx)" />
+        <!-- <param name="runtime_profile" type="select" label="Run time profile">
+            <option value="kondagac" selected="true">conda</option>
+            <option value="cingularitygac">singularity</option>
+        </param> -->
+    </inputs>
+    <outputs>
+        <data name="multiqc_report" format="html" label="bettercallsal: MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/>
+    </outputs>
+    <tests>
+        <!--Test 01: long reads-->
+        <test expect_num_outputs="2">
+            <param name="input">
+                <collection type="list">
+                    <element name="FAL11127.fastq.gz" value="FAL11127.fastq.gz" />
+                    <element name="FAL11341.fastq.gz" value="FAL11341.fastq.gz" />
+                    <element name="FAL11342.fastq.gz" value="FAL11342.fastq.gz" />
+                </collection>
+            </param>
+            <param name="fq_suffix" value=".fastq.gz"/>
+            <output name="multiqc_report" file="multiqc_report.html" ftype="html" compare="sim_size"/>
+            <!-- <output name="assembled_mags" file="FAL11127.assembly_filtered.contigs.fasta" ftype="fasta" compare="sim_size"/> -->
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**Purpose**
+
+bettercallsal is an automated workflow to assign Salmonella serotype based on NCBI Pathogen Detection Project for Salmonella. 
+It uses MASH to reduce the search space followed by additional genome filtering with sourmash. It then performs genome based 
+alignment with kma followed by count generation using salmon. This workflow can be used to analyze shotgun metagenomics 
+datasets, quasi-metagenomic datasets (enriched for Salmonella) and target enriched datasets (enriched with molecular baits specific for Salmonella) 
+and is especially useful in a case where a sample is of multi-serovar mixture.
+
+It is written in Nextflow and is part of the modular data analysis pipelines (CFSAN PIPELINES or CPIPES for short) at CFSAN.
+
+
+----
+
+.. class:: infomark
+
+**Testing and Validation**
+
+The CPIPES - bettercallsal Nextflow pipeline has been wrapped to make it work in Galaxy. It takes in either paired or unpaired short reads list as an input 
+and generates a MultiQC report in the final step. The pipeline has been tested on 2x300 bp MiSeq and 2x150 bp NextSeq simulated reads and has been shown to call multiple
+Salmonella serotypes with up to ~95% accuracy. The pipeline has also been tested on metagenomics data sets from Peach and Papaya outbreaks as discussed in 
+our publication (https://www.frontiersin.org/articles/10.3389/fmicb.2023.1200983/full). All the original testing and validation was 
+done on the command line on the CFSAN Raven2 HPC Cluster.
+
+
+----
+
+.. class:: infomark
+
+**Outputs**
+
+The main output file is a:
+
+    ::
+
+        - MultiQC Report: Contains a brief summary report including any serotyping and AMR result tables.
+                          Please note that due to MultiQC customizations, the preview (eye icon) will not
+                          work within Galaxy for the MultiQC report. Please download the file by clicking
+                          on the floppy icon and view it in your browser on your local desktop/workstation.
+                          You can export the tables and plots from the downloaded MultiQC report.
+
+  ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @article{bettercallsal,
+            author = {Konganti, Kranti},
+            year = {2023},
+            month = {August},
+            title = {bettercallsal: better calling of Salmonella serotypes from enrichment cultures using shotgun metagenomic profiling and its application in an outbreak setting},
+            journal = {Frontiers in Microbiology},
+            doi = {10.3389/fmicb.2023.1200983},
+            url = {https://www.frontiersin.org/articles/10.3389/fmicb.2023.1200983/full}}
+        </citation>
+    </citations>
+</tool>