# HG changeset patch
# User kkonganti
# Date 1656427011 14400
# Node ID 1e19594944c5ebd5983acbbf33da9e36de31f308
# Parent  8ab30c459b5371bd909ce038c3ea8d67c14d86fd
"planemo upload"

diff -r 8ab30c459b53 -r 1e19594944c5 cfsan_centriflaken.xml
--- a/cfsan_centriflaken.xml	Tue Jun 28 10:22:03 2022 -0400
+++ b/cfsan_centriflaken.xml	Tue Jun 28 10:36:51 2022 -0400
@@ -48,8 +48,8 @@
         <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/>
         <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ R2"/>
         <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_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_delimitor_idx)" />
+            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>
@@ -88,7 +88,7 @@
 
 **Purpose**
 
-Centriflaken suite of automated data analysis pipelines based on Nextflow DSL2 developed at CFSAN, FDA. Thess piepelines allow rapid 
+Centriflaken suite of automated data analysis pipelines are based on Nextflow DSL2 developed at CFSAN, FDA. These piepelines 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 (https://doi.org/10.1371/journal.pone.0245172).
 ----