# HG changeset patch
# User kkonganti
# Date 1686059185 14400
# Node ID 4678c2cd1c9e7b1093ce6325caa8c62d124045e0
# Parent  365849f031fd016a10a7e21eac315d224a912e44
"planemo upload"

diff -r 365849f031fd -r 4678c2cd1c9e cfsan_bettercallsal.xml
--- a/cfsan_bettercallsal.xml	Mon Jun 05 18:48:51 2023 -0400
+++ b/cfsan_bettercallsal.xml	Tue Jun 06 09:46:25 2023 -0400
@@ -36,7 +36,7 @@
 	    #end for
     #end if
 	$__tool_directory__/0.5.0/cpipes
-    --pipeline $input_read_type_cond.pipeline_cond.pipeline
+    --pipeline bettercallsal
     --input \${pwd_path}/cpipes-input
 	--output \${pwd_path}/cpipes-output
     --fq_suffix '${input_read_type_cond.fq_suffix}'
@@ -53,7 +53,7 @@
 	--fq_filename_delim '${fq_filename_delim}'
 	--fq_filename_delim_idx $fq_filename_delim_idx
 	-profile kondagac;
-    mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html' './multiqc_report.html' > /dev/null 2>&1 || exit 1;
+    mv './cpipes-output/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
     ]]></command>
@@ -74,25 +74,25 @@
                 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ"/>
             </when>
         </conditional>
-        <param name="tuspy_n" optional="true" value="10" type="integer" label="Enter the number of top unique serotypes to retain after initial MASH screen step."
+        <param name="tuspy_n" optional="true" value="10" type="integer" label="Enter the number of top unique serotypes to retain after initial MASH screen step"
             help="The default value of 10 is suitable for almost all scenarios."/>
-        <param name="bcs_thresholds" type="select" label="Enter the type of base quality thresholds to be set with bettercallsal."
+        <param name="bcs_thresholds" type="select" label="Enter the type of base quality thresholds to be set with bettercallsal"
             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>
         <conditional name="sourmash_cond">
             <param name="run" type="select" label="Run sourmash"
-                help="Should sourmash be used for additional genome fraction filtering.">
+                help="Should sourmash be used for additional genome fraction filtering">
                 <option value="true" selected="true">yes</option>
                 <option value="false">no</option>
             </param>
             <when value="true">
-                <param name="sfhpy_fcv" type="text" value="0.1" label="Enter the minimum coverage match with sourmash before a serotype hit is considered for further processing."
+                <param name="sfhpy_fcv" type="text" value="0.1" label="Enter the minimum coverage match with sourmash before a serotype hit is considered for further processing"
                         help="The default value is set at 10% coverage threshold."/>
             </when>
             <when value="false">
-                <param name="sfhpy_fcv" type="select" label="Enter the minimum coverage match with sourmash before a serotype hit is considered for further processing."
+                <param name="sfhpy_fcv" type="select" label="Enter the minimum coverage match with sourmash before a serotype hit is considered for further processing"
                     help="THIS OPTION IS IGNORED IF SOURMASH TOOL IgreS DISABLED.">
                     <option value="NA" selected="true">N/A</option>
                 </param>
@@ -107,7 +107,7 @@
         </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"/>
+        <data name="multiqc_report" format="html" label="bettercallsal: MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/>
     </outputs>
     <tests>
         <!--Test 01: long reads-->