# HG changeset patch
# User kkonganti
# Date 1656607342 14400
# Node ID 8ea952e3726ebba8c640e827ada770df9151a51f
# Parent  36ca1a1156df2621dc18cb3905e3604bd2ed165a
"planemo upload"

diff -r 36ca1a1156df -r 8ea952e3726e cfsan_centriflaken.xml
--- a/cfsan_centriflaken.xml	Thu Jun 30 12:34:34 2022 -0400
+++ b/cfsan_centriflaken.xml	Thu Jun 30 12:42:22 2022 -0400
@@ -37,7 +37,7 @@
 	--input \${pwd_path}/cpipes-input
 	--output \${pwd_path}/cpipes-output
     --fq_suffix '${fq_suffix}'
-    #if ($fq_filter_by_len > 0):
+    #if ($fq_filter_by_len != "" and int($fq_filter_by_len) > 0):
         --fq_filter_by_len $fq_filter_by_len
     #end if
 	--fq_filename_delim '${fq_filename_delim}'
@@ -70,11 +70,11 @@
             <option value="pacbio_hifi">PacBio HiFi reads (&lt;1% error)</option>
         </param>
         <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/>
-        <param name="fq_filter_by_len" value="" type="integer" label="Enter minimum read length to retain before starting the analysis"
+        <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_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="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_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.">