# HG changeset patch
# User kkonganti
# Date 1685996243 14400
# Node ID a4b1ee4b68b1f0a9914fd7821030cdfbb99c8530

"planemo upload"

diff -r 000000000000 -r a4b1ee4b68b1 cfsan_bettercallsal.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cfsan_bettercallsal.xml	Mon Jun 05 16:17:23 2023 -0400
@@ -0,0 +1,232 @@
+<tool id="cfsan_centriflaken" name="Centriflaken" version="0.2.0+galaxy0">
+    <description>An automated pipeline to generate a MAG of interest (E.coli or Salmonella) and perform serotyping.</description>
+    <requirements>
+	<requirement type="package" version="22.04">nextflow</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__/0.4.0/cpipes
+    --pipeline $input_read_type_cond.pipeline_cond.pipeline
+    #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"):
+        --fq_single_end true
+        --flye_genome_size '${genome_size}'
+        #if ($input_read_type_cond.pipeline_cond.long_read_platform == "nanopore_corr"):
+            --flye_nano_corr true --flye_nano_raw false
+        #elif ($input_read_type_cond.pipeline_cond.long_read_platform == "nanopore_hq"):
+            --flye_nano_hq true --flye_nano_raw false
+        #elif ($input_read_type_cond.pipeline_cond.long_read_platform == "pacbio_raw"):
+            --flye_pacbio_raw true --flye_nano_raw false
+        #elif ($input_read_type_cond.pipeline_cond.long_read_platform == "pacbio_corr"):
+            --flye_pacbio_corr true --flye_nano_raw false
+        #elif ($input_read_type_cond.pipeline_cond.long_read_platform == "pacbio_hifi"):
+            --flye_pacbio_hifi true --flye_nano_raw false
+        #end if
+    #elif ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken_hy"):
+        #if (str($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
+    #end if
+	--input \${pwd_path}/cpipes-input
+	--output \${pwd_path}/cpipes-output
+    --fq_suffix '${input_read_type_cond.fq_suffix}'
+    #if ($fq_filter_by_len != ""):
+        --fq_filter_by_len $fq_filter_by_len
+    #end if
+	--fq_filename_delim '${fq_filename_delim}'
+	--fq_filename_delim_idx $fq_filename_delim_idx
+	--centrifuge_extract_bug '${centrifuge_extract_bug}'
+    #if (str($input_read_type_cond.pipeline_cond.rm_dup_seqs) == "true"):
+        --seqkit_rmdup_run true
+    #end if
+	-profile kondagac;
+    mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html' './multiqc_report.html' > /dev/null 2>&1 || exit 1;
+    mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs > /dev/null 2>&1 || exit 1;
+    rm -rf ./cpipes-output > /dev/null 2>&1 || exit 1;
+    rm -rf ./work > /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">Unpaired reads (i.e. Single-End short reads or Long reads)</option>
+                <option value="paired">Paired-End 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" />
+                <conditional name="pipeline_cond">
+                    <param name="pipeline" type="select" label="CPIPES Workflow name"
+                        help="centriflaken: for long reads (Nanopore or PacBio). centriflaken_hy: for unpaired short reads. Default: centriflaken">
+                        <option value="centriflaken" selected="true">centriflaken</option>
+                        <option value="centriflaken_hy">centriflaken_hy</option>
+                    </param>
+                    <when value="centriflaken">
+                        <param name="long_read_platform" type="select" label="Mention long read sequencing platform and type">
+                            <option value="nanopore_raw" selected="true">Nanopore raw reads, pre-Guppy5 (&lt;20% error)</option>
+                            <option value="nanopore_corr">Nanopore reads that were corrected with other methods (&lt;3% error)</option>
+                            <option value="nanopore_hq">Nanopore high-quality reads, Guppy5+ SUP or Q20 (5% error)</option>
+                            <option value="pacbio_raw">PacBio regular CLR reads (&lt;20% error)</option>
+                            <option value="pacbio_corr">PacBio reads that were corrected with other methods (&lt;3% error)</option>
+                            <option value="pacbio_hifi">PacBio HiFi reads (&lt;1% error)</option>
+                        </param>
+                        <param name="rm_dup_seqs" type="select" label="Remove duplicate sequences"
+                            help="THIS OPTION IS IGNORED IF THE INPUT READS ARE LONG READS.">
+                            <option value="NA" selected="true">N/A</option>
+                        </param>
+                    </when>
+                    <when value="centriflaken_hy">
+                        <param name="long_read_platform" type="select" label="Mention long read sequencing platform and type"
+                            help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS.">
+                                <option value="NA" selected="true">N/A</option>
+                        </param>
+                        <param name="rm_dup_seqs" type="select" label="Remove duplicate sequences"
+                            help="Selecting yes will compare sequence content and remove identical sequences i.e. only the first occured sequence record will be saved.">
+                            <option value="true">yes</option>
+                            <option value="false" selected="true">no</option>
+                        </param>
+                    </when>
+                </conditional>
+                <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the Unpaired 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" />
+                <conditional name="pipeline_cond">
+                    <param name="pipeline" type="select" label="CPIPES Workflow name"
+                        help="Auto selected centriflaken_hy workflow for paired-end short reads.">
+                        <option value="centriflaken_hy" selected="true">centriflaken_hy</option>
+                    </param>
+                    <when value="centriflaken_hy">
+                        <param name="long_read_platform" type="select" label="Mention long read sequencing platform and type"
+                            help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS.">
+                                <option value="NA" selected="true">N/A</option>
+                        </param>
+                        <param name="rm_dup_seqs" type="select" label="Remove duplicate sequences"
+                            help="Selecting yes will compare sequence content and remove identical sequences i.e. only the first occured sequence record will be saved.">
+                            <option value="true">yes</option>
+                            <option value="false" selected="true">no</option>
+                        </param>
+                    </when>
+                </conditional>
+                <param name="fq_suffix" value="_R1_001.fastq.gz" type="text" label="Suffix of the R1 FASTQ"/>
+                <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ"/>
+            </when>
+        </conditional>
+        <param name="fq_filter_by_len" optional="true" value="" type="integer" label="Enter minimum read length to retain before starting the analysis"
+            help="Keep this option empty to use default values. Default for centriflaken (long reads) is 4000 bp and for centriflaken_hy (short reads) is 75 bp."/>
+        <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="centrifuge_extract_bug" type="text" value="Escherichia coli" label="Reads belonging to this taxa are extracted and a MAG is generated to allow for serotyping"/>
+        <param name="genome_size" type="text" optional="true" value="5.5m" label="Estimated genome size" help="For example, 5m or 2.6g.">
+            <validator type="regex" message="Genome size must be a float  or integer, optionally followed by the a unit prefix (kmg)">^([0-9]*[.])?[0-9]+[kmg]?$</validator>
+        </param>
+        <!-- <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="${input_read_type_cond.pipeline_cond.pipeline}: MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/>
+        <collection name="assembled_mags" type="list" label="${input_read_type_cond.pipeline_cond.pipeline}: Assembled MAGs on ${on_string}">
+            <discover_datasets pattern="(?P&lt;name&gt;.*)\.assembly_filtered_contigs\.fasta" ext="fasta" directory="kraken2_extract_contigs"/>
+        </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**
+
+Centriflaken suite of automated data analysis pipelines are based on Nextflow DSL2 developed at CFSAN, FDA. These pipelines allow rapid 
+and effective construction of metagenomic assembled genomes (MAGs) to enable bacterial source-tracking. It is based on methods described in our 
+previous publication (Maguire *et al*, 2021. doi: https://doi.org/10.1371/journal.pone.0245172).
+
+----
+
+.. class:: infomark
+
+**Testing and Validation**
+
+The CPIPES - Centriflaken Nextflow pipeline has been wrapped to make it work in Galaxy. It takes in either paired or unpaired short reads or long reads, generates MAGs and performs 
+in silico-based analysis (i.e., virulence gene finding). Additionally, AMR gene finding analysis is also included in Centriflaken and performed on MAGs 
+of interest. The final summary plots and tables can be downloaded from the provided MultiQC HTML report generated as part of the pipeline. 
+The Centriflaken pipeline was validated with data from our previously published method (Maguire *et al*, 2021. doi: https://doi.org/10.1371/journal.pone.0245172) and was able to replicate the detection 
+and classification of STECs for each sample. We tested the pipeline with Nanopore data obtained from 21 additional enriched samples from 
+irrigation water and was able to perform the entire precision metagenomics analysis in less than 5 hours for all of them. All the original testing and validation was 
+done on the command line on the CFSAN Raven2 HPC Cluster.
+
+
+----
+
+.. class:: infomark
+
+**Outputs**
+
+The main output files are:
+
+    ::
+
+        - 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.
+        - Final assembly: contains contigs and possibly scaffolds.
+
+  ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @misc{gitlabCPIPES,
+            author = {Konganti, Kranti},
+            year = {2022},
+            title = {CPIPES - Centriflaken},
+            publisher = {GitLab},
+            journal = {GitLab repository},
+            url = {https://cfsan-git.fda.gov/Kranti.Konganti/cpipes}}
+        </citation>
+    </citations>
+</tool>