--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hfp_nowayout.xml	Mon Mar 31 14:50:40 2025 -0400
@@ -0,0 +1,199 @@
+<tool id="hfp_nowayout" name="nowayout" version="0.5.0+galaxy24">
+    <description>An automated workflow to identify Mitochondrial reads and classify Eukaryotes.</description>
+    <requirements>
+        <container type="docker">quay.io/biocontainers/nextflow:24.10.4--hdfd78af_0</container>
+    </requirements> 
+    <version_command>nextflow -version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+	input_path=\$(pwd)"/cpipes-input";
+    mkdir -p "\${input_path}" || exit 1;
+    #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' "\${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
+	$__tool_directory__/0.5.0/cpipes
+    --pipeline nowayout
+    --input \${input_path}
+	--output cpipes-output
+    --fq_suffix '${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
+    --db_mode $nowo_db_mode
+    --nowo_thresholds $nowo_thresholds
+	--fq_filename_delim '${fq_filename_delim}'
+	--fq_filename_delim_idx $fq_filename_delim_idx
+	-profile gxkubernetes;
+    mv './cpipes-output/nowayout-multiqc/multiqc_report.html' './multiqc_report.html' || exit 1;
+    mv './cpipes-output/krona_ktimporttext/CPIPES_nowayout_krona.html './CPIPES_nowayout_krona.html' || exit 1;
+    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>
+            </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="nowo_db_mode" type="select" label="Select the database with nowayout"
+            help="Please see below about different databases.">
+            <option value="mitomine" selected="true">mitomine</option>
+            <option value="cytox1">cytox1</option>
+            <option value="voucher">voucher</option>
+            <option value="ganoderma">ganoderma</option>
+            <option value="listeria">listeria</option>
+        </param>
+        <param name="nowo_thresholds" type="select" label="Enter the type of base quality thresholds to be set with nowayout"
+            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="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="krona_chart" format="html" label="nowayout: Krona Chart on ${on_string}" from_work_dir="CPIPES_nowayout_krona.html"/>
+        <data name="multiqc_report" format="html" label="nowayout: 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**
+
+nowayout is a mitochondrial metagenomics classifier for Eukaryotes. 
+It uses a custom kma database to identify mitochondrial reads and 
+performs read classification followed by further read classification 
+reinforcement using sourmash.
+
+It is written in Nextflow and is part of the modular data analysis pipelines (CFSAN PIPELINES or CPIPES for short) at HFP.
+
+
+----
+
+.. class:: infomark
+
+** Databases **
+
+    - mitomine: Big database that works in almost all scenarios.
+    - cytox1: Collection of only non-redundant COXI genes from NCBI.
+    - voucher: Collection of only non-redundant voucher sequences from NCBI.
+    - ganoderma: Collection of only non-redundant mtDNA sequences of Ganoderma fungi.
+    - listeria: Collection of organelle sequences and other rRNA genes for Listeria.
+
+
+----
+
+.. class:: infomark
+
+**Testing and Validation**
+
+The CPIPES - nowayout 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 
+which contains relative abundances in context of number of mitochondrial reads identified. It also 
+generates a Krona chart for each sample. The pipeline has been tested on multiple internal insect 
+mixture samples. All the original testing and validation was done on the command line on the 
+HFP Reedling HPC Cluster.
+
+
+----
+
+.. class:: infomark
+
+** Please note **
+
+    ::
+    
+        - nowayout only works on Illumina short reads (paired or unpaired).
+        - nowayout uses a custom kma database named mitomine.
+        - The custom database will be incrementally augmented and refined over time.
+        - mitomine stats:
+            Contains ~ 2.93M non-redundant mitochondrial and voucher sequences.
+            Represents ~ 717K unique species.
+        - Other databases are also available but will be seldom updated.
+
+----
+
+.. class:: infomark
+
+**Outputs**
+
+The main output file is a:
+
+    ::
+
+        - MultiQC Report: Contains a brief summary report including individual Mitochondrial reads identified
+                          per sample and relative abundances in context of the total number of Mitochondrial reads
+                          identified.
+                          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{nowayout,
+            author = {Konganti, Kranti},
+            year = {2025},
+            month = {May},
+            title = {nowayout: An automated mitrochiondrial read classifier for Eukaryotes.},
+            journal = {Manuscript in preparation},
+            doi = {10.3389/xxxxxxxxxxxxxxxxxx},
+            url = {https://xxxxxxx/articles/10.3389/xxxxxxxxxxxx/full}}
+        </citation>
+    </citations>
+</tool>