--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cfsan_cronology.xml	Mon Nov 27 12:37:44 2023 -0500
@@ -0,0 +1,169 @@
+<tool id="cfsan_cronology" name="cronology" version="0.1.0">
+    <description>An automated workflow for Cronobacter isolate assembly, sequence typing and traceback.</description>
+    <requirements>
+	<requirement type="package" version="23.04">nextflow</requirement>
+    <requirement type="package" version="1.0.0">micromamba</requirement>
+	<requirement type="package">graphviz</requirement>
+    </requirements>    
+    <version_command>nextflow -version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+	mkdir -p cpipes-input || exit 1;
+    pwd_path=\$(pwd);
+    #import re
+    #if (str($input_read_type_cond.input_read_type) == "single_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' './cpipes-input/$read1';
+	    #end for
+    #elif (str($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' './cpipes-input/$read_R1';
+	        ln -sf '$pair.reverse' './cpipes-input/$read_R2';
+	    #end for
+    #end if
+	$__tool_directory__/0.1.0/cpipes
+    --pipeline cronology
+    --input \${pwd_path}/cpipes-input
+	--output \${pwd_path}/cpipes-output
+    --fq_suffix '${input_read_type_cond.fq_suffix}'
+    #if (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
+    --ref_acc $refgenome
+    --tuspy_n $tuspy_n
+	--fq_filename_delim '${fq_filename_delim}'
+	--fq_filename_delim_idx $fq_filename_delim_idx
+	-profile kondagac;
+    mv './cpipes-output/cronology-multiqc/multiqc_report.html' './multiqc_report.html' > /dev/null 2>&1 || exit 1;
+    mv './cpipes-output/mashtree/hitsTree.dnd' './hitsTree.dnd' > /dev/null 2>&1 || 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>
+            </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 or long reads" />
+                <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the Single-End 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="refgenome" optional="true" value="GCF_003516125" type="text"
+                label="NCBI reference genome accession"
+                help="Is the reference genome other than <i>Cronobacter sakazakii</i>? Reference genome FASTA is used as a model for gene prediction. DO NOT ENTER THE DECIMAL PART (Ex: GCF_003516125.1)." />
+        <param name="tuspy_n" optional="true" value="10" type="integer" label="Enter the number of top unique hits to retain after initial MASH screen step"
+            help="These hits will be used to build a genome distance based tree for your experiment run. Default value of 2 is suitable for almost all scenarios."/>
+        <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)" />
+    </inputs>
+    <outputs>
+        <data name="multiqc_report" format="html" label="cronology: MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/>
+        <data name="mashtree" format="nwk" label="cronology: Genome distance based tree on ${on_string}" from_work_dir="hitsTree.dnd"/>
+        <collection name="itol_metadata" type="list" label="cronology: iTOL Metadata: ${on_string}">
+            <discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" ext="txt" match_relative_path="true" directory="./cpipes-output/cat_unique"/>
+        </collection>
+        <collection name="gene_models" type="list" label="cronology: Predicted gene models: ${on_string}">
+            <discover_datasets pattern="(?P&lt;name&gt;.*)\.gff" ext="gff" match_relative_path="true" recurse="true" directory="./cpipes-output/prokka"/>
+        </collection>
+        <collection name="assemblies" type="list" label="cronology: Polished genome assemblies: ${on_string}">
+            <discover_datasets pattern="(?P&lt;name&gt;.*)\.fa" ext="fa" match_relative_path="true" directory="./cpipes-output/polypolish"/>
+        </collection>
+    </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**
+
+cronology 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 - cronology 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{cronology,
+            author = {Konganti, Kranti},
+            year = {2023},
+            month = {August},
+            title = {cronology: 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>