# HG changeset patch
# User jjohnson
# Date 1503685521 14400
# Node ID 69274b068a488f75bcb0f2a7985d09d9fb58820f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pecan commit 21855dec2949420d3bccfd6c9912578e9aacecf0
diff -r 000000000000 -r 69274b068a48 pecan.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/pecan.xml Fri Aug 25 14:25:21 2017 -0400
@@ -0,0 +1,286 @@
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+ detect peptides directly from DIA Mass Spec
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+ pecan
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+ pecan --VERSION
+ 1 && $1 ~ /^[0-9]+(\.[0-9]*)?$/{print \$1; print \$2; print "$outputRoot"}' $isolationfile |
+ xargs -n3 -P\${GALAXY_SLOTS}
+ pecan
+ #if $backgroundProteome:
+ --backgroundProteome='$backgroundProteome'
+ #end if
+ --bgDecoyNumber=$bgDecoyNumber
+ #if $decoyTag and str($decoyTag):
+ --decoyTag=$decoyTag
+ #end if
+ --ionTypes=$--ionTypes
+ --minElution=$minElution
+ --maxElution=$maxElution
+ --overlap=$advanced_options.overlap
+ #if $advanced_options.ms1.ms1Unit == 'ppm':
+ --ms1Unit=ppm
+ --ms1Tolerance=$advanced_options.ms1.ms1Tolerance
+ #elif $advanced_options.ms1.ms1Unit == 'mz':
+ --ms1Unit=mz
+ --ms1Tolerance=$advanced_options.ms1.ms1Tolerance
+ #end if
+ #if $advanced_options.ms2.ms2Unit == 'ppm':
+ --ms2Unit=ppm
+ --ms2Tolerance=$advanced_options.ms2.ms2Tolerance
+ #elif $advanced_options.ms2.ms2Unit == 'mz':
+ --ms2Unit=mz
+ --ms2Tolerance=$advanced_options.ms2.ms2Tolerance
+ #end if
+ --minCharge=$advanced_options.minCharge
+ --maxCharge=$advanced_options.maxCharge
+ #if $advanced_options.ms2Boundaries.specify == 'specify':
+ --ms2Boundaries="$advanced_options.ms2Boundaries.ms2BoundariesMin,$advanced_options.ms2Boundaries.ms2BoundariesMax"
+ #end if
+ --alpha=$advanced_options.alpha
+ --beta=$advanced_options.beta
+ --idotp=$advanced_options.idotp
+ --topX=$advanced_options.topX
+ #if $advanced_options.fixedMod and str($advanced_options.fixedMod):
+ --fixedMod='$advanced_options.fixedMod'
+ #end if
+ $input $peptides 2>1 > run.log
+ && cat "$outputRoot"*.log > '$log_file'
+ && cat "$outputRoot"*.td.feature | awk 'NR==1{print $0};!/peakCalibratedScore/{print $0}' > '$feature_file'
+ ]]>
+
+
+ #slurp
+#import re
+#if $isolation.isolationsrc == 'entered':
+#echo $re.sub(r'(\d+[.]\d+)\s+(\d+[.]\d)\s*',r'\1\t\2\n',$isolation.isolation_windows.strip())
+#end if
+ #slurp
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+ ^(?ms)(\d+[.]\d+\s\d+[.]\d)(\s\d+[.]\d+\s\d+[.]\d)*$
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+ ^([A-Z]\[[+-]\d+[.]\d+\](,[A-Z]\[[+-]\d+[.]\d+\])*)*$
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diff -r 000000000000 -r 69274b068a48 pecan2blib.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/pecan2blib.xml Fri Aug 25 14:25:21 2017 -0400
@@ -0,0 +1,38 @@
+
+ Convert PECAN results after percolator (.peptides) into spectral library (.blib)
+
+ pecan
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+ '$spectral_lib'
+ ]]>
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