# HG changeset patch
# User petr-novak
# Date 1691134669 0
# Node ID 628b235d76c7fe9cc304e575582c78c0fa51f7fa
# Parent  be1f407e101813680a4786aa6a41c063ff7d027d
planemo upload commit 39094a128ea3dd2c39f4997c6de739c33c07e5f3-dirty

diff -r be1f407e1018 -r 628b235d76c7 RM_custom_search.py
--- a/RM_custom_search.py	Thu Aug 03 10:54:34 2023 +0000
+++ b/RM_custom_search.py	Fri Aug 04 07:37:49 2023 +0000
@@ -57,10 +57,11 @@
 
 def summarizeRepeatMaskerOutput(htmlout = "summary.html"):
     cmd = os.path.dirname(os.path.abspath(__file__))+"/rmsk_summary_table_multiple.r"
-    args = [ cmd, "dir_CL*/reads.fas", "dir_CL*/reads.fas.out", "RM-custom_output_table"  ]
+    args = [ "Rscript", cmd, "dir_CL*/reads.fas", "dir_CL*/reads.fas.out",
+             "RM-custom_output_table" ]
     status=subprocess.call(args)
-    cmd = cmd = os.path.dirname(os.path.abspath(__file__))+"/RM_html_report.R"
-    args = [cmd, htmlout]
+    cmd = os.path.dirname(os.path.abspath(__file__))+"/RM_html_report.R"
+    args = ["Rscript", cmd, htmlout]
     status=subprocess.call(args)
     return status
     
diff -r be1f407e1018 -r 628b235d76c7 RM_custom_search.xml
--- a/RM_custom_search.xml	Thu Aug 03 10:54:34 2023 +0000
+++ b/RM_custom_search.xml	Fri Aug 04 07:37:49 2023 +0000
@@ -12,6 +12,8 @@
     <required_files>
         <include type="literal" path="RM_custom_search.py"/>
         <include type="literal" path="parallel.py"/>
+        <include type="literal" path="rmsk_summary_table_multiple.r"/>
+        <include type="literal" path="RM_html_report.R"/>
     </required_files>
 
 
diff -r be1f407e1018 -r 628b235d76c7 fasta_interlacer.xml
--- a/fasta_interlacer.xml	Thu Aug 03 10:54:34 2023 +0000
+++ b/fasta_interlacer.xml	Fri Aug 04 07:37:49 2023 +0000
@@ -1,7 +1,7 @@
 <tool id="fasta_interlacer" name="FASTA interlacer" version="1.0.0.4">
     <description>Join pared reads into single file</description>
     <requirements>
-        <container type="package" version="3">python</container>
+        <requirement type="package" version="3">python</requirement>
     </requirements>
     <required_files>
         <include type="literal" path="fasta_interlacer.py"/>
diff -r be1f407e1018 -r 628b235d76c7 fastq_name_affixer.xml
--- a/fastq_name_affixer.xml	Thu Aug 03 10:54:34 2023 +0000
+++ b/fastq_name_affixer.xml	Fri Aug 04 07:37:49 2023 +0000
@@ -7,7 +7,7 @@
         <include type="literal" path="name_affixer.py"/>
     </required_files>
     <command>
-        ${__tool_directory__}/name_affixer.py -f $input -p "$prefix" -s "$suffix" -n
+        python ${__tool_directory__}/name_affixer.py -f $input -p "$prefix" -s "$suffix" -n
         $nspace > $output
     </command>
 
diff -r be1f407e1018 -r 628b235d76c7 paired_fastq_filtering_wrapper.sh
--- a/paired_fastq_filtering_wrapper.sh	Thu Aug 03 10:54:34 2023 +0000
+++ b/paired_fastq_filtering_wrapper.sh	Fri Aug 04 07:37:49 2023 +0000
@@ -52,14 +52,14 @@
 
 if [ -z "$CUTADAPT" ] # test if$CUTADAPT is empty
 then
-    ${WD}/paired_fastq_filtering.R -a $FASTAA -b $FASTAB -x $fasta_tmp_fileX -y $fasta_tmp_fileY  ${SAMPLING[@]} -c $CUT_OFF -G $PNG_OUTPUT\
+    Rscript ${WD}/paired_fastq_filtering.R -a $FASTAA -b $FASTAB -x $fasta_tmp_fileX -y $fasta_tmp_fileY  ${SAMPLING[@]} -c $CUT_OFF -G $PNG_OUTPUT\
          -p $PERCENT_ABOVE  ${TRIM_START[@]}  ${TRIM_END[@]} -N $MAX_N $RENAME ${FILTER_SEQ[@]}
 else
-    ${WD}/paired_fastq_filtering.R -a $FASTAA -b $FASTAB -x $fasta_tmp_fileX -y $fasta_tmp_fileY  ${SAMPLING[@]} -c $CUT_OFF -G $PNG_OUTPUT\
+    Rscript ${WD}/paired_fastq_filtering.R -a $FASTAA -b $FASTAB -x $fasta_tmp_fileX -y $fasta_tmp_fileY  ${SAMPLING[@]} -c $CUT_OFF -G $PNG_OUTPUT\
          -p $PERCENT_ABOVE  ${TRIM_START[@]}  ${TRIM_END[@]} -N $MAX_N "${CUTADAPT[@]}" $RENAME ${FILTER_SEQ[@]}
 fi
 
-${WD}/fasta_interlacer.py -a $fasta_tmp_fileX -b $fasta_tmp_fileY -p $PAIRED_OUTPUT -x fasta_tmp_single
+python ${WD}/fasta_interlacer.py -a $fasta_tmp_fileX -b $fasta_tmp_fileY -p $PAIRED_OUTPUT -x fasta_tmp_single
 
 
 rm $fasta_tmp_fileX
diff -r be1f407e1018 -r 628b235d76c7 sampleFasta.xml
--- a/sampleFasta.xml	Thu Aug 03 10:54:34 2023 +0000
+++ b/sampleFasta.xml	Fri Aug 04 07:37:49 2023 +0000
@@ -2,6 +2,7 @@
   <description> Tool for randomly sampling subsets of reads from large datasets</description>
   <requirements>
     <requirement type="package">seqkit</requirement>
+    <requirement type="package" version="3">python</requirement>
   </requirements>
   <stdio>
     <exit_code range="1:" level="fatal" description="Error" />
diff -r be1f407e1018 -r 628b235d76c7 single_fastq_filtering_wrapper.sh
--- a/single_fastq_filtering_wrapper.sh	Thu Aug 03 10:54:34 2023 +0000
+++ b/single_fastq_filtering_wrapper.sh	Fri Aug 04 07:37:49 2023 +0000
@@ -47,10 +47,10 @@
 
 if [ -z "$CUTADAPT" ] # test if $CUTADAPT is empty
 then
-    ${WD}/single_fastq_filtering.R -a $FASTAA -x $OUTPUT  ${SAMPLING[@]} -c $CUT_OFF\
+    Rscript ${WD}/single_fastq_filtering.R -a $FASTAA -x $OUTPUT  ${SAMPLING[@]} -c $CUT_OFF\
          -p $PERCENT_ABOVE  ${TRIM_START[@]}  ${TRIM_END[@]} -N $MAX_N -G $PNG_OUTPUT ${FILTER_SEQ[@]}
 else
-    ${WD}/single_fastq_filtering.R -a $FASTAA -x $OUTPUT  ${SAMPLING[@]} -c $CUT_OFF -G $PNG_OUTPUT\
+    Rscript ${WD}/single_fastq_filtering.R -a $FASTAA -x $OUTPUT  ${SAMPLING[@]} -c $CUT_OFF -G $PNG_OUTPUT\
          -p $PERCENT_ABOVE  ${TRIM_START[@]}  ${TRIM_END[@]} -N $MAX_N "${CUTADAPT[@]}" ${FILTER_SEQ[@]}
 fi
 
diff -r be1f407e1018 -r 628b235d76c7 summarize_cluster_table.xml
--- a/summarize_cluster_table.xml	Thu Aug 03 10:54:34 2023 +0000
+++ b/summarize_cluster_table.xml	Fri Aug 04 07:37:49 2023 +0000
@@ -9,7 +9,7 @@
     <required_files>
         <include type="literal" path="summarize_cluster_table.R"/>
     </required_files>
-    <command interpreter="Rscript" detect_errors="exit_code">
+    <command detect_errors="exit_code">
         Rscript $__tool_directory__/summarize_cluster_table.R
         --cluster_table=$cluster_table
         --output=$output