Commit 2911096e authored by Jerome Mariette's avatar Jerome Mariette
Browse files

add quality_threshold to pyrocleaner options

parent 357e1453
......@@ -36,6 +36,8 @@ $;WINDOW$;=100
$;STEP$;=5
; Minimal complexity/length ratio (used with --clean-complexity-win and --clean-complexity-full)
$;COMPLEXITY$;=40
; At least one base pair has to be equal or higher than this value (used with --clean-quality)
$;QUALITY_THRESHOLD$; = 35
; Can be : -q path/to/qual_file
$;OTHERS$;=
; The analyse name to display in ng6
......
......@@ -36,6 +36,8 @@ $;WINDOW$;=100
$;STEP$;=5
; Minimal complexity/length ratio (used with --clean-complexity-win and --clean-complexity-full)
$;COMPLEXITY$;=40
; At least one base pair has to be equal or higher than this value (used with --clean-quality)
$;QUALITY_THRESHOLD$; = 35
; Can be : -q path/to/qual_file
$;OTHERS$;=
; The analyse name to display in ng6
......
......@@ -36,6 +36,8 @@ $;WINDOW$;=100
$;STEP$;=5
; Minimal complexity/length ratio (used with --clean-complexity-win and --clean-complexity-full)
$;COMPLEXITY$;=40
; At least one base pair has to be equal or higher than this value (used with --clean-quality)
$;QUALITY_THRESHOLD$; = 35
; Can be : -q path/to/qual_file
$;OTHERS$;=
; The analyse name to display in ng6
......
......@@ -36,6 +36,8 @@ $;WINDOW$;=100
$;STEP$;=5
; Minimal complexity/length ratio (used with --clean-complexity-win and --clean-complexity-full)
$;COMPLEXITY$;=40
; At least one base pair has to be equal or higher than this value (used with --clean-quality)
$;QUALITY_THRESHOLD$; = 35
; Can be : -q path/to/qual_file
$;OTHERS$;=
; The analyse name to display in ng6
......
......@@ -36,6 +36,8 @@ $;WINDOW$;=100
$;STEP$;=5
; Minimal complexity/length ratio (used with --clean-complexity-win and --clean-complexity-full)
$;COMPLEXITY$;=40
; At least one base pair has to be equal or higher than this value (used with --clean-quality)
$;QUALITY_THRESHOLD$; = 35
; Can be : -q path/to/qual_file
$;OTHERS$;=
; The analyse name to display in ng6
......
......@@ -36,6 +36,8 @@ $;WINDOW$;=100
$;STEP$;=5
; Minimal complexity/length ratio (used with --clean-complexity-win and --clean-complexity-full)
$;COMPLEXITY$;=40
; At least one base pair has to be equal or higher than this value (used with --clean-quality)
$;QUALITY_THRESHOLD$; = 35
; Can be : -q path/to/qual_file
$;OTHERS$;=
; The analyse name to display in ng6
......
......@@ -36,6 +36,8 @@ $;WINDOW$;=100
$;STEP$;=5
; Minimal complexity/length ratio (used with --clean-complexity-win and --clean-complexity-full)
$;COMPLEXITY$;=40
; At least one base pair has to be equal or higher than this value (used with --clean-quality)
$;QUALITY_THRESHOLD$; = 35
; Can be : -q path/to/qual_file
$;OTHERS$;=
; The analyse name to display in ng6
......
......@@ -36,6 +36,8 @@ $;WINDOW$; = 100
$;STEP$; = 5
; Minimal complexity/length ratio (used with --clean-complexity-win and --clean-complexity-full)
$;COMPLEXITY$; = 40
; At least one base pair has to be equal or higher than this value (used with --clean-quality)
$;QUALITY_THRESHOLD$; = 35
; Can be : --aggressive, --acpus
$;OTHERS$; =
; The analyse name to display in ng6
......
......@@ -25,6 +25,10 @@
<key>--format</key>
<value>"$;FORMAT$;"</value>
</param>
<param>
<key>--quality-threshold</key>
<value>"$;QUALITY_THRESHOLD$;"</value>
</param>
<param>
<key>--recursion</key>
<value>"$;RECURSION_LIMIT$;"</value>
......@@ -86,7 +90,7 @@
<type>RunUnixCommand</type>
<name>extract results</name>
<state>incomplete</state>
<executable>if [ "$;FORMAT$;"="sff" ]; then `python $;BIN_DIR$;/sff_extract.py -c -s $;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.clean.sff_extract.fasta -q $;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.clean.sff_extract.qual -x $;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.clean.sff_extract.xml $;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.clean.sff`; elif [ "$;FORMAT$;"="fastq" ]; then `python $;BIN_DIR$;/fastq_extract.py --in $;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.clean.fastq --fasta $;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.clean.fastq_extract.fasta --qual $;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.clean.fastq_extract.qual`; fi;</executable>
<executable>if [ "$;FORMAT$;"="sff" ]; then `python $;BIN_DIR$;/sff_extract.py -c -s $;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.clean.fasta -q $;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.clean.qual -x $;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.clean.xml $;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.clean.sff`; elif [ "$;FORMAT$;"="fastq" ]; then `python $;BIN_DIR$;/fastq_extract.py --in $;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.clean.fastq --fasta $;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.clean.fasta --qual $;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.clean.qual`; fi;</executable>
<arg></arg>
<param>
<key>stdout</key>
......
......@@ -43,7 +43,7 @@
</param>
<param>
<key>--analyse-software-parameters</key>
<value>"-f $;FORMAT$; $;CLEANING_OPTIONS$; -r $;RECURSION_LIMIT$; -b $;BORDER_LIMIT$; -e $;MISSMATCH$; -j $;STD$; -k $;MIN_LENGTH$; -m $;MAX_LENGTH$; -s $;NS_PERCENT$; -t $;DUPLICATION_LIMIT$; -v $;WINDOW$; -x $;STEP$; -y $;COMPLEXITY$; $;OTHERS$;"</value>
<value>"--format $;FORMAT$; $;CLEANING_OPTIONS$; --recursion $;RECURSION_LIMIT$; --border-limit $;BORDER_LIMIT$; --missmatch $;MISSMATCH$; --std $;STD$; --min $;MIN_LENGTH$; --max $;MAX_LENGTH$; --ns_percent $;NS_PERCENT$; --duplication_limit $;DUPLICATION_LIMIT$; --window $;WINDOW$; --step $;STEP$; --complexity $;COMPLEXITY$; --quality-threshold $;QUALITY_THRESHOLD$; $;OTHERS$;"</value>
</param>
<param>
<key>stdout</key>
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment