# HG changeset patch
# User lecorguille
# Date 1492001584 14400
# Node ID dd0a593dded1a682d10dd78e56de3b18bcbc1776
# Parent 03fdfbd914ab0c64d514002f177aa4ba122513b8
planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd
diff -r 03fdfbd914ab -r dd0a593dded1 ipo4retgroup.xml
--- a/ipo4retgroup.xml Thu Mar 30 11:27:09 2017 -0400
+++ b/ipo4retgroup.xml Wed Apr 12 08:53:04 2017 -0400
@@ -4,6 +4,14 @@
macros.xml
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@@ -24,43 +32,27 @@
sleep 0.001
#if $group.methods.method == "density":
- bw "c($group.methods.bw)"
- minfrac "c($group.methods.minfrac)"
- mzwid "c($group.methods.mzwid)"
- ## minsamp "c($group.methods.minsamp)"
- #if $group.methods.density_options.option == "show":
- max "c($group.methods.density_options.max)"
- #end if
+ bw "c($group.methods.section_group_density_optiomizable.conditional_parameter.bw)"
+ mzwid "c($group.methods.section_group_density_optiomizable.conditional_parameter.mzwid)"
+
+ minfrac $group.methods.section_group_density_non_optimizable.minfrac
+ max $group.methods.section_group_density_non_optimizable.max
#end if
-
-
## retcor methods
#if $retcor.methods.method == "obiwarp":
retcorMethod obiwarp
- profStep "c($methods.profStep)"
-
- ## $distFunc [1] "cor_opt"
- ## $gapInit [1] 0.0 0.4
- ## $gapExtend [1] 2.1 2.7
- ## $$plottype [1] "none"
- ## $response [1] 1
- ## $factorDiag [1] 2
- ## $factorGap [1] 1
- ## $localAlignment [1] 0
+ profStep $methods.section_retcor_obiwarp_non_optimizable.profStep
#elif $retcor.methods.method == "peakgroups":
- ## smooth loess
retcorMethod loess
- smooth loess
- extra "c($retcor.methods.extra)"
- missing "c($retcor.methods.missing)"
- #if $retcor.methods.options.option == "show":
- span "c($retcor.methods.options.span)"
- family "$retcor.methods.options.family"
- plottype "$retcor.methods.options.plottype"
- #end if
+ smooth $retcor.methods.section_retcor_peakgroups_non_optimizable.smooth
+ extra $retcor.methods.section_retcor_peakgroups_non_optimizable.extra
+ missing $retcor.methods.section_retcor_peakgroups_non_optimizable.missing
+ span $retcor.methods.section_retcor_peakgroups_non_optimizable.span
+ family $retcor.methods.section_retcor_peakgroups_non_optimizable.family
+ plottype $retcor.methods.section_retcor_peakgroups_non_optimizable.plottype
#elif $retcor.methods.method == "none":
retcorMethod none
#end if
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diff -r 03fdfbd914ab -r dd0a593dded1 ipo4xcmsSet.xml
--- a/ipo4xcmsSet.xml Thu Mar 30 11:27:09 2017 -0400
+++ b/ipo4xcmsSet.xml Wed Apr 12 08:53:04 2017 -0400
@@ -1,21 +1,39 @@
-
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IPO optimization process for xcms.xcmsSet
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- #if $file_load_conditional.file_load_select == "yes":
- #if $file_load_conditional.inputs.input == "zip_file":
- zipfile $file_load_conditional.inputs.zip_file
+ #if $file_load_section.file_load_conditional.file_load_select == "yes":
+ #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"):
+ #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
+ #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
+
+ singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
#else
- #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_conditional.inputs.single_file ] )
- #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_conditional.inputs.single_file ] )
-
- singlefile_galaxyPath $singlefile_galaxyPath singlefile_sampleName $singlefile_sampleName
+ zipfile '$file_load_section.file_load_conditional.input'
#end if
#end if
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diff -r 03fdfbd914ab -r dd0a593dded1 test-data/MM14_IPO_parameters4xcmsSet.tsv
--- a/test-data/MM14_IPO_parameters4xcmsSet.tsv Thu Mar 30 11:27:09 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-min_peakwidth 5.275
-max_peakwidth 13.5
-mzdiff 0.01
-ppm 56
-snthresh 10
-noise 0
-prefilter 3
-value_of_prefilter 100
-mzCenterFun wMean
-integrate 1
-fitgauss FALSE
diff -r 03fdfbd914ab -r dd0a593dded1 test-data/MM14_IPO_parameters4xcmsSet_peakwidth.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/MM14_IPO_parameters4xcmsSet_peakwidth.tsv Wed Apr 12 08:53:04 2017 -0400
@@ -0,0 +1,11 @@
+min_peakwidth 3.325
+max_peakwidth 11
+prefilter 3
+ppm 56
+mzdiff -0.001
+snthresh 10
+integrate 1
+noise 0
+value_of_prefilter 100
+mzCenterFun wMean
+fitgauss FALSE
diff -r 03fdfbd914ab -r dd0a593dded1 test-data/MM14_IPO_parameters4xcmsSet_ppm.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/MM14_IPO_parameters4xcmsSet_ppm.tsv Wed Apr 12 08:53:04 2017 -0400
@@ -0,0 +1,11 @@
+ppm 60
+prefilter 3
+min_peakwidth 3.325
+max_peakwidth 11
+mzdiff -0.001
+snthresh 10
+integrate 1
+noise 0
+value_of_prefilter 100
+mzCenterFun wMean
+fitgauss FALSE
diff -r 03fdfbd914ab -r dd0a593dded1 test-data/faahKO_IPO_parameters4retgroup_bw.tsv
--- a/test-data/faahKO_IPO_parameters4retgroup_bw.tsv Thu Mar 30 11:27:09 2017 -0400
+++ b/test-data/faahKO_IPO_parameters4retgroup_bw.tsv Wed Apr 12 08:53:04 2017 -0400
@@ -1,13 +1,13 @@
bw 4.168192
-span 0.22
+mzwid 0.25
minfrac 1
-mzwid 0.25
+max 50
retcorMethod loess
smooth loess
extra 1
missing 1
+span 0.2
family gaussian
plottype none
minsamp 1
-max 50
center 2