# HG changeset patch
# User petr-novak
# Date 1691136580 0
# Node ID f1738f8649b0acc6e7b894124e81870be3020d8d
# Parent  628b235d76c7fe9cc304e575582c78c0fa51f7fa
planemo upload commit 39094a128ea3dd2c39f4997c6de739c33c07e5f3-dirty

diff -r 628b235d76c7 -r f1738f8649b0 paired_fastq_filtering.R
--- a/paired_fastq_filtering.R	Fri Aug 04 07:37:49 2023 +0000
+++ b/paired_fastq_filtering.R	Fri Aug 04 08:09:40 2023 +0000
@@ -182,7 +182,7 @@
 
 
 cutadapt_cmd = function(input, output, cutadapt_arguments) {
-    cmds = paste("cutadapt --format=", "fastq", cutadapt_arguments, " ", c(input), 
+    cmds = paste("cutadapt ", cutadapt_arguments, " ", c(input),
         " -o ", c(output), sep = "")
 }
 
diff -r 628b235d76c7 -r f1738f8649b0 paired_fastq_filtering.xml
--- a/paired_fastq_filtering.xml	Fri Aug 04 07:37:49 2023 +0000
+++ b/paired_fastq_filtering.xml	Fri Aug 04 08:09:40 2023 +0000
@@ -9,7 +9,7 @@
     </description>
     <requirements>
         <requirement type="package">blast</requirement>
-        <requirement type="package">cutadapt</requirement>
+        <requirement type="package" version="4.4">cutadapt</requirement>
         <requirement type="package">bioconductor-shortread</requirement>
         <requirement type="package">r-optparse</requirement>
     </requirements>
@@ -19,6 +19,7 @@
         <include type="literal" path="fasta_interlacer.py"/>
     </required_files>
     <command>
+        cutadapt --version;
         bash '$__tool_directory__'/paired_fastq_filtering_wrapper.sh -a ${A} -b ${B} -o
         ${paired} -c ${cut_off} -p ${percent_above} -N ${max_n} $rename -G ${png_output}
 
diff -r 628b235d76c7 -r f1738f8649b0 single_fastq_filtering.R
--- a/single_fastq_filtering.R	Fri Aug 04 07:37:49 2023 +0000
+++ b/single_fastq_filtering.R	Fri Aug 04 08:09:40 2023 +0000
@@ -143,8 +143,7 @@
 
 
 cutadapt_cmd=function(input,output,cutadapt_arguments){
-	cmds=paste("cutadapt --format=",
-			"fastq",
+	cmds=paste("cutadapt ",
 			cutadapt_arguments,
 			" ",
 			c(input),
diff -r 628b235d76c7 -r f1738f8649b0 single_fastq_filtering.xml
--- a/single_fastq_filtering.xml	Fri Aug 04 07:37:49 2023 +0000
+++ b/single_fastq_filtering.xml	Fri Aug 04 08:09:40 2023 +0000
@@ -8,7 +8,7 @@
     </description>
     <requirements>
         <requirement type="package">blast</requirement>
-        <requirement type="package">cutadapt</requirement>
+        <requirement type="package" version="4.4">cutadapt</requirement>
         <requirement type="package">bioconductor-shortread</requirement>
         <requirement type="package">r-optparse</requirement>
     </requirements>
@@ -16,7 +16,7 @@
         <include type="literal" path="single_fastq_filtering_wrapper.sh"/>
         <include type="literal" path="single_fastq_filtering.R"/>
     </required_files>
-    <command interpreter="bash">
+    <command>
         bash '$__tool_directory__'/single_fastq_filtering_wrapper.sh -a ${A} -o ${output}
         -c ${cut_off} -p ${percent_above} -N ${max_n} -G ${png_output}