# HG changeset patch
# User galaxyp
# Date 1625070684 0
# Node ID 529b61ba3d64dbdfc3b70ebde1175756973736be
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
diff -r 000000000000 -r 529b61ba3d64 proteomiqon_mzmltomzlite.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/proteomiqon_mzmltomzlite.xml Wed Jun 30 16:31:24 2021 +0000
@@ -0,0 +1,430 @@
+
+
+ converts mzML files to mzLite files.
+
+
+ 0.0.5
+
+
+ proteomiqon-mzmltomzlite
+
+ > '$out_paramfile' &&
+ #end if
+ ln -s $instrumentOutput '${basename}.mzML' &&
+ ln -s $out_mzlite '${basename}.mzlite' &&
+ proteomiqon-mzmltomzlite -i './${basename}.mzML' -p $paramfile -o ./
+ ]]>
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+ outputParamfile
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+ `_ to convert your raw data into .mzML.
+
+Further Reading
+---------------
+Additional information about the tool can be found in the `_documentation `_.
+ ]]>
+
+
diff -r 000000000000 -r 529b61ba3d64 test-data/result_1.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/result_1.json Wed Jun 30 16:31:24 2021 +0000
@@ -0,0 +1,15 @@
+
+
+ {
+ "Compress":0,
+ "StartRetentionTime":null,
+ "EndRetentionTime":null,
+ "MS1PeakPicking": {
+ "Case": "ProfilePeaks",
+ },
+ "MS2PeakPicking": {
+ "Case": "ProfilePeaks",
+ }
+ }
+
+
\ No newline at end of file
diff -r 000000000000 -r 529b61ba3d64 test-data/result_2.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/result_2.json Wed Jun 30 16:31:24 2021 +0000
@@ -0,0 +1,42 @@
+
+
+ {
+ "Compress":0,
+ "StartRetentionTime":null,
+ "EndRetentionTime":null,
+ "MS1PeakPicking": {
+ "Case": "Centroid",
+ "Fields" :
+ [
+ {
+ "Case" : "Wavelet",
+ "Fields" :
+ [
+ {
+ "NumberOfScales" : 3,
+ "YThreshold" :
+ {
+ "Case" : "Fixed",
+ "Fields":
+ [
+ 1.0,
+ ]
+ },
+ "Centroid_MzTolerance" : 0.1,
+ "SNRS_Percentile" : 95.0,
+ "MinSNR" : 1.0,
+ "RefineMZ" : false,
+ "SumIntensities" : false,
+ "PaddingParams" : null
+ }
+
+ ]
+ }
+ ]
+ },
+ "MS2PeakPicking": {
+ "Case": "ProfilePeaks",
+ }
+ }
+
+
\ No newline at end of file
diff -r 000000000000 -r 529b61ba3d64 test-data/result_3.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/result_3.json Wed Jun 30 16:31:24 2021 +0000
@@ -0,0 +1,56 @@
+
+
+ {
+ "Compress":0,
+ "StartRetentionTime":null,
+ "EndRetentionTime":null,
+ "MS1PeakPicking": {
+ "Case": "ProfilePeaks",
+ },
+ "MS2PeakPicking": {
+ "Case": "Centroid",
+ "Fields" :
+ [
+ {
+ "Case" : "Wavelet",
+ "Fields" :
+ [
+ {
+ "NumberOfScales" : 10,
+ "YThreshold" :
+ {
+ "Case" : "MinSpectrumIntensity",
+ },
+ "Centroid_MzTolerance" : 0.1,
+ "SNRS_Percentile" : 95.0,
+ "MinSNR" : 1.0,
+ "RefineMZ" : false,
+ "SumIntensities" : false,
+ "PaddingParams" :
+ {
+ "Case" : "Some",
+ "Fields" :
+ [
+ {
+ "MaximumPaddingPoints" : {
+ "Case" : "Some",
+ "Fields" : [
+ 7
+ ]
+ },
+ "Padding_MzTolerance" : 0.005,
+ "WindowSize" : 150,
+ "SpacingPerc" : 95.0
+ }
+ ]
+
+ }
+ }
+
+ ]
+ }
+ ]
+ }
+ }
+
+
\ No newline at end of file
diff -r 000000000000 -r 529b61ba3d64 test-data/result_4.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/result_4.json Wed Jun 30 16:31:24 2021 +0000
@@ -0,0 +1,28 @@
+
+
+ {
+ "Compress":0,
+ "StartRetentionTime":
+ {
+ "Case" : "Some",
+ "Fields" : [
+ 6.75
+ ],
+ },
+
+ "EndRetentionTime":
+ {
+ "Case" : "Some",
+ "Fields" : [
+ 6.75
+ ],
+ },
+ "MS1PeakPicking": {
+ "Case": "ProfilePeaks",
+ },
+ "MS2PeakPicking": {
+ "Case": "ProfilePeaks",
+ }
+ }
+
+
\ No newline at end of file
diff -r 000000000000 -r 529b61ba3d64 test-data/sample.mzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample.mzml Wed Jun 30 16:31:24 2021 +0000
@@ -0,0 +1,21 @@
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