--- a/cfsan_bettercallsal.xml	Thu Sep 07 15:22:10 2023 -0400
+++ b/cfsan_bettercallsal.xml	Mon Jul 15 10:42:02 2024 -0400
@@ -1,14 +1,12 @@
-<tool id="cfsan_bettercallsal" name="bettercallsal" version="0.6.1">
+<tool id="cfsan_bettercallsal" name="bettercallsal" version="0.7.0+galaxy23.1">
     <description>An automated workflow to assign Salmonella serotype based on NCBI Pathogen Detection Project for Salmonella.</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>    
+        <container type="docker">quay.io/biocontainers/nextflow:24.04.2--hdfd78af_0</container>
+    </requirements> 
     <version_command>nextflow -version</version_command>
     <command detect_errors="exit_code"><![CDATA[
-	mkdir -p cpipes-input || exit 1;
-    pwd_path=\$(pwd);
+	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):
@@ -17,7 +15,7 @@
                 #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/$read1';
+            ln -sf '$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)
@@ -31,13 +29,13 @@
             #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/$read_R2';
+	        ln -sf '$pair.forward' "\${input_path}/$read_R1";
+	        ln -sf '$pair.reverse' "\${input_path}/$read_R2";
 	    #end for
     #end if
-	$__tool_directory__/0.6.1/cpipes
+	$__tool_directory__/0.7.0/cpipes
     --pipeline bettercallsal
-    --input \${pwd_path}/cpipes-input
+    --input \${input_path}
 	--output \${pwd_path}/cpipes-output
     --fq_suffix '${input_read_type_cond.fq_suffix}'
     #if (str($input_read_type_cond.input_read_type) == "single_long"):
@@ -49,14 +47,20 @@
     #if ($sourmash_cond.run == "true"):
         --sfhpy_fcv $sourmash_cond.sfhpy_fcv
     #end if
+    #if ($bcs_thresholds != 'relax'):
+        --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
-	-profile kondagac;
-    mv './cpipes-output/bettercallsal-multiqc/multiqc_report.html' './multiqc_report.html' > /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
+	-profile gxkubernetes;
+    mv './cpipes-output/bettercallsal-multiqc/multiqc_report.html' './multiqc_report.html' || exit 1;
+    rm -rf ./cpipes-output > || exit 1;
+    rm -rf ./work || exit 1
     ]]></command>
     <inputs>
         <conditional name="input_read_type_cond">
@@ -89,6 +93,8 @@
             <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">
@@ -154,7 +160,10 @@
 **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.
+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.
 
 
 ----