| Next changeset 1:acb8aba959ed (2022-04-29) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475" |
|
added:
proteomiqon_mzmltomzlite.xml test-data/result_1.json test-data/result_2.json test-data/result_3.json test-data/result_4.json test-data/sample.mzml |
| b |
| 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 |
| [ |
| b'@@ -0,0 +1,430 @@\n+<tool id="proteomiqon_mzmltomzlite" name="ProteomIQon MzMLToMzLite" version="@VERSION@" python_template_version="20.05">\n+\t<description>\n+\t\tconverts mzML files to mzLite files.\n+\t</description>\n+\t<macros>\n+\t\t<token name="@VERSION@">0.0.5</token>\n+\t</macros>\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">proteomiqon-mzmltomzlite</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ #import re\n+ #set basename = $re.sub(r\'[^\\w ,.\\-+]\',\'_\',$instrumentOutput.element_identifier)\n+ #if $outputParamfile:\n+ cat \'$paramfile\' >> \'$out_paramfile\' &&\n+ #end if\n+ ln -s $instrumentOutput \'${basename}.mzML\' &&\n+ ln -s $out_mzlite \'${basename}.mzlite\' &&\n+ proteomiqon-mzmltomzlite -i \'./${basename}.mzML\' -p $paramfile -o ./\n+ ]]>\n+ </command>\n+ <configfiles>\n+ <configfile name="paramfile">\n+ <![CDATA[\n+ {\n+ "Compress":${BinaryDataCompressionType},\n+ #if $StartRetentionTime\n+ "StartRetentionTime":\n+ {\n+ "Case" : "Some",\n+ "Fields" : [\n+ ${StartRetentionTime}\n+ ],\n+ },\n+\n+ #else\n+ "StartRetentionTime":null,\n+ #end if\n+ #if $EndRetentionTime\n+ "EndRetentionTime":\n+ {\n+ "Case" : "Some",\n+ "Fields" : [\n+ ${EndRetentionTime}\n+ ],\n+ },\n+ #else\n+ "EndRetentionTime":null,\n+ #end if\n+ "MS1PeakPicking": {\n+ "Case": "${Ms1PeakPickingCond.Ms1PeakPicking}",\n+ #if $Ms1PeakPickingCond.Ms1PeakPicking == "Centroid"\n+ "Fields" : \n+ [ \n+ {\n+ "Case" : "${Ms1PeakPickingCond.CentroidModeCond.CentroidMode}",\n+ #if $Ms1PeakPickingCond.CentroidModeCond.CentroidMode == "Wavelet"\n+ "Fields" : \n+ [\n+ {\n+ "NumberOfScales" : ${Ms1PeakPickingCond.CentroidModeCond.NumberOfScales},\n+ "YThreshold" : \n+ {\n+ "Case" : "${Ms1PeakPickingCond.CentroidModeCond.YThresholdCond.YThreshold}",\n+ #if $Ms1PeakPickingCond.CentroidModeCond.YThresholdCond.YThreshold == "Fixed"\n+ "Fields": \n+ [\n+ ${Ms1PeakPickingCond.CentroidModeCond.YThresholdCond.Ms1YThreshold},\n+ ]\n+ #end if \n+ },\n+ "Centroid_MzTolerance" : ${Ms1PeakPickingCond.CentroidModeCond.Centroid_MzTolerance},\n+ "SNRS_Percentile" : ${Ms1PeakPickingCond.CentroidModeCond.SNRS_Percentile},\n+ "MinSNR" : ${Ms1PeakPickingCond.CentroidModeCond.MinSNR},\n+ "RefineMZ" : ${Ms1PeakPickingCond.CentroidModeCond.RefineMZ},\n+ "SumIntensities" : ${Ms1PeakPickingCond.CentroidModeCond.SumIntensities},\n+ #if $Ms1PeakPickingCond.CentroidModeCond.PaddingParamsCond.usePaddingparams == "yes"\n+ "PaddingParams" : \n+ {\n+ "Case" : "Some",\n+ "Fields" :\n+ [\n+ {\n+ '..b' <param name="MinSNR" value="1.0"/>\n+ <param name="RefineMZ" value="false"/>\n+ <param name="SumIntensities" value="false"/>\n+ <conditional name="PaddingParamsCond">\n+ <param name="usePaddingparams" value="yes"/>\n+ <conditional name="MaximumPaddingPointsCond">\n+ <param name="specifyMaximumPaddingPoints" value="yes" />\n+ <param name="MaximumPaddingPoints" value="7" />\n+ </conditional>\n+ <param name="Padding_MzTolerance" value="0.005" />\n+ <param name="WindowSize" value="150"/>\n+ <param name="SpacingPerc" value="95"/>\n+ </conditional>\n+ </conditional>\n+ </conditional>\n+ <param name="outputParamfile" value="true"/>\n+ <output name="out_paramfile" file="result_3.json"/>\n+ </test>\n+ <test expect_num_outputs="2">\n+ <param name="instrumentOutput" value="sample.mzml"/>\n+ <param name="BinaryDataCompressionType" value="0"/>\n+ <param name="StartRetentionTime" value="6.75"/>\n+ <param name="EndRetentionTime" value="6.75"/>\n+ <conditional name="Ms1PeakPickingCond">\n+ <param name="Ms1PeakPicking" value="ProfilePeaks"/>\n+ </conditional>\n+ <conditional name="Ms2PeakPickingCond">\n+ <param name="Ms2PeakPicking" value="ProfilePeaks"/>\n+ </conditional>\n+ <param name="outputParamfile" value="true"/>\n+ <output name="out_paramfile" file="result_4.json"/>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="instrumentOutput" value="sample.mzml"/>\n+ <param name="BinaryDataCompressionType" value="0"/>\n+ <param name="StartRetentionTime" value="6.75"/>\n+ <param name="EndRetentionTime" value="6.75"/>\n+ <conditional name="Ms1PeakPickingCond">\n+ <param name="Ms1PeakPicking" value="ProfilePeaks"/>\n+ </conditional>\n+ <conditional name="Ms2PeakPickingCond">\n+ <param name="Ms2PeakPicking" value="ProfilePeaks"/>\n+ </conditional>\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n+Introduction\n+------------\n+The success of modern proteomics was made possible by constant progression in the field of mass spectrometry. \n+Over the course of the past years quite a few manufacturers of mass spectrometers have managed to establish themselfes in the field of biological research. \n+Since aquisition and accession of mass spectra are performance critical processes, various performance optimized, but vendor specific and closed source formats have been developed to store raw MS data. \n+This comes to the disadvantage for toolchain developers which want to provide tools for every scientist regardless of the format of their raw data.\n+\n+In a effort to provide an open format for the storage of MS data the format mzML was developed. While this XML based format is straight forward to implement it falls behind in performance critical scenarios. \n+To be competitive in performance and to comply to the FAIR principles we chose to use mzLite, an open and SQLite based implementation of mzML, within our toolchain.\n+\n+What It Does\n+------------\n+The tool mzMLToMzLite allows to convert mzML files to mzLite files. Additionally, it allows the user to perform peak picking or filtering of mass spectra.\n+We recommend the use of `_msconvert <https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2>`_ to convert your raw data into .mzML. \n+\n+Further Reading\n+---------------\n+Additional information about the tool can be found in the `_documentation <https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html>`_.\n+ ]]>\n+ </help>\n+</tool>\n' |
| b |
| 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 |
| b |
| @@ -0,0 +1,15 @@ + + + { + "Compress":0, + "StartRetentionTime":null, + "EndRetentionTime":null, + "MS1PeakPicking": { + "Case": "ProfilePeaks", + }, + "MS2PeakPicking": { + "Case": "ProfilePeaks", + } + } + + \ No newline at end of file |
| b |
| 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 |
| b |
| 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 |
| b |
| 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 |
| b |
| 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 |
| b |
| @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="utf-8"?> +<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd"> + <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="20210611TEstTMcond002" version="1.1.0"> + <cvList count="0"> + </cvList> + <fileDescription> + </fileDescription> + <softwareList count="0"> + </softwareList> + <instrumentConfigurationList count="0"> + </instrumentConfigurationList> + <dataProcessingList count="0"> + </dataProcessingList> + <run id="_x0032_0210611TEstTMcond002" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2021-06-12T16:56:33Z" defaultSourceFileRef="WIFF"> + <spectrumList count="0" defaultDataProcessingRef="pwiz_Reader_ABI_conversion"> + </spectrumList> + <chromatogramList count="0" defaultDataProcessingRef="pwiz_Reader_ABI_conversion"> + </chromatogramList> + </run> + </mzML> +</indexedmzML> |