Mercurial > repos > galaxyp > dia_umpire
diff dia_umpire_se.xml @ 2:b4f82d15cac0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty
| author | galaxyp |
|---|---|
| date | Mon, 19 Mar 2018 16:40:29 -0400 |
| parents | acd0df26c1e9 |
| children | 6caa9011f245 |
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--- a/dia_umpire_se.xml Wed Jan 24 08:08:58 2018 -0500 +++ b/dia_umpire_se.xml Mon Mar 19 16:40:29 2018 -0400 @@ -8,35 +8,25 @@ <command> <![CDATA[ #import re -## want to save all outputs in a directory output.extra_files_path to be used by dia_umpire_quant +## want to save all outputs in a directory output.extra_files_path to be used by ## Is file naming going to be a problem? May need to have a name param -#if $se_extraction_data: #set $ser_dir = $se_params.extra_files_path mkdir $ser_dir -&& ln -s '$ser_dir' '$output_dir' -#else: -mkdir '$output_dir' -#end if +&& ln -s $ser_dir $output_dir && cat $se_config > $se_params ## && echo " " >> $se_params && echo "Thread = \$GALAXY_SLOTS" >> $se_params +#for $i, $input_file in enumerate( $inputs ): #if $input_prefix and len($input_prefix.strip()) > 0: -#set $input_path = str($output_dir) + '/' + $input_prefix.__str__ + '_rep' + str($i + 1) + '.mzXML' +#set $input_path = $ser_dir + "/" + $input_prefix.__str__ + "_rep" + str($i + 1) + ".mzXML" #else: -#set $input_path = str($output_dir) + '/' + $re.sub('\.[mM]\w+$','',$re.sub('[^-a-zA-Z0-9_.]','_',$input.name)) + '.mzXML' +#set $input_path = $ser_dir + "/" + $re.sub('\.[mM]\w+$','',$re.sub('[^-a-zA-Z0-9_.]','_',$input_file.name)) + ".mzXML" #end if -&& ln -s '${input}' '$input_path' -&& dia_umpire_se '$input_path' '$se_params' +&& ln -s "${input_file}" "$input_path" +&& java -jar \$DIA_UMPIRE_SE_JAR $input_path $se_params && cat $output_dir/*.log >> "$logfile" -#if not $mgfs_as_collection: -&& cp "$output_dir/"*_Q1.mgf '$q1_mgf' -&& cp "$output_dir/"*_Q2.mgf '$q2_mgf' -&& cp "$output_dir/"*_Q3.mgf '$q3_mgf' -#end if -#if $ExportPrecursorPeak: -&& cp "$output_dir/"*PeakCluster.csv '$PrecursorPeak' -#end if +#end for ]]> </command> <configfiles> @@ -45,12 +35,14 @@ #Data Independent Acquisition data processing and analysis package (Signal extraction module) #import re +#for $i, $input_file in enumerate( $inputs ): #if $input_prefix: #set $input_path = $input_prefix.__str__ + "_rep" + str($i + 1) + ".mzXML" #else: -#set $input_path = $re.sub('\.[mM]\w+$','',$re.sub('[^-a-zA-Z0-9_.]','_',$input.name)) + ".mzXML" +#set $input_path = $re.sub('\.[mM]\w+$','',$re.sub('[^-a-zA-Z0-9_.]','_',$input_file.name)) + ".mzXML" #end if -# $input.name $input_path $input +# $input_file.name $input_path $input_file +#end for #No of threads Thread = 6 @@ -92,7 +84,7 @@ RFmax = #if $frag_settings.RFmax then $frag_settings.RFmax else 300# CorrThreshold = #if $frag_settings.CorrThreshold then $frag_settings.CorrThreshold else 0.2# DeltaApex = #if $frag_settings.DeltaApex then $frag_settings.DeltaApex else 0.6# -RTOverlap = 0.3 +RTOverlap = #if $frag_settings.RTOverlap then $frag_settings.RTOverlap else 0.3# AdjustFragIntensity = #if $frag_settings.AdjustFragIntensity then $frag_settings.AdjustFragIntensity else true# BoostComplementaryIon = #if $frag_settings.BoostComplementaryIon then $frag_settings.BoostComplementaryIon else true# #else: @@ -101,6 +93,7 @@ RFmax = 300 CorrThreshold = 0.2 DeltaApex = 0.6 +RTOverlap = 0.3 AdjustFragIntensity = true BoostComplementaryIon = true #end if @@ -117,14 +110,14 @@ SE.EstimateBG = #if $se_settings.SE_EstimateBG then $se_settings.SE_EstimateBG else true# SE.MinNoPeakCluster = #if $se_settings.SE_MinNoPeakCluster then $se_settings.SE_MinNoPeakCluster else 2# SE.MaxNoPeakCluster = #if $se_settings.SE_MaxNoPeakCluster then $se_settings.SE_MaxNoPeakCluster else 4# -SE.StartRT = 0 -SE.EndRT = 9999 -SE.MinMZ = 200 -SE.MinPrecursorMass = 700 -SE.MaxPrecursorMass = 5000 -SE.IsoPattern = 0.3 -SE.MassDefectFilter = true -SE.MassDefectOffset = 0.1 +SE.StartRT = #if $se_settings.SE_StartRT then $se_settings.SE_MaxNoPeakCluster else 0# +SE.EndRT = #if $se_settings.SE_EndRT then $se_settings.SE_EndRT else 9999# +SE.MinMZ = #if $se_settings.SE_MinMZ then $se_settings.SE_MinMZ else 200# +SE.MinPrecursorMass = #if $se_settings.SE_MinPrecursorMass then $se_settings.SE_MinPrecursorMass else 700# +SE.MaxPrecursorMass = #if $se_settings.SE_MaxPrecursorMass then $se_settings.SE_MaxPrecursorMass else 5000# +SE.IsoPattern = #if $se_settings.SE_IsoPattern then $se_settings.SE_IsoPattern else 0.3# +SE.MassDefectFilter = #if $se_settings.SE_MassDefectFilter then $se_settings.SE_MassDefectFilter else true# +SE.MassDefectOffset = #if $se_settings.SE_MassDefectOffset then $se_settings.SE_MassDefectOffset else 0.1# #if $se_settings.SE_MinMS2NoPeakCluster: SE.MinMS2NoPeakCluster = $se_settings.SE_MinMS2NoPeakCluster #end if @@ -157,10 +150,6 @@ SE.MaxNoPeakCluster = 3#slurp #end if -## SE.RemoveGroupedPeaksRTOverlap -## SE.RemoveGroupedPeaksCorr -## SE.IsoCorrThreshold - #if $instrument.model != 'Thermo_Orbitrap': WindowType = $instrument.window.WindowType #if $instrument.window.WindowType == 'SWATH': @@ -193,8 +182,8 @@ </configfiles> <inputs> - <param name="input" type="data" format="mzxml" label="Proteomics Spectrum files in mzXML format"/> - <param name="input_prefix" type="text" value="" optional="true" label="File name prefix" help="Names inputs: prefix_rep#.mzXML Leave blank to use History names of input"> + <param name="inputs" type="data" format="mzxml" multiple="true" label="Proteomics Spectrum files in mzXML format"/> + <param name="input_prefix" type="text" value="" optional="true" label="File name prefix" help="Names inputs: prefix_rep#.mzXML Leave blank to use History names of inputs"> <validator type="regex" message="">[a-zA-Z][a-zA-Z0-9_-]*</validator> </param> <param name="output_dir" type="hidden" value="gx_path"/> @@ -278,6 +267,11 @@ CorrThreshold: (0.0~1.0) Minimum Pearson correlation between a precursor and a fragment to be considered, the higher, the more stringent. (Default: 0.2) </help> </param> + <param name="RTOverlap" type="float" value=".3" min="0" optional="true" label="RTOverlap" > + <help> +RTOverlap: Retention time overlap. (Default: 0.3) + </help> + </param> <param name="DeltaApex" type="float" value=".6" min="0" optional="true" label="DeltaApex" > <help> @@ -334,6 +328,39 @@ Same as para.SN, but for possible unfragmented precursors in MS2 data (i.e. for selecting precursors to generate Q3 tier pseudo spectra). </help> </param> + <param name="SE_StartRT" type="float" value="0" optional="true" label="StartRT" > + <help> + </help> + </param> + <param name="SE_EndRT" type="float" value="9999" optional="true" label="EndRT" > + <help> + </help> + </param> + <param name="SE_MinMZ" type="float" value="200" optional="true" label="MinMZ" > + <help> + </help> + </param> + <param name="SE_MinPrecursorMass" type="float" value="700" optional="true" label="MinPrecursorMass" > + <help> + </help> + </param> + <param name="SE_MaxPrecursorMass" type="float" value="5000" optional="true" label="MaxPrecursorMass" > + <help> + </help> + </param> + <param name="SE_IsoPattern" type="float" value="0.3" optional="true" label="IsoPattern" > + <help> + </help> + </param> + <param name="SE_MassDefectFilter" type="boolean" truevalue="true" falsevalue="false" checked="true" label="MassDefectFilter" > + <help> + </help> + </param> + <param name="SE_MassDefectOffset" type="float" value="0.1" optional="true" label="MassDefectOffset" > + <help> + </help> + </param> + <param name="SE_MinRTRange" type="float" value="" optional="true" label="MinRTRange" > <help> @@ -389,49 +416,30 @@ </when> </conditional> - <param name="ExportPrecursorPeak" type="boolean" truevalue="true" falsevalue="false" checked="false" - label="ExportPrecursorPeak" + <param name="ExportPrecursorPeak" type="boolean" truevalue="true" falsevalue="false" checked="false" label="ExportPrecursorPeak" help="Output detailed information about detected MS1 precursor and MS2 unfragmented precursor signals"/> - <param name="ExportFragmentPeak" type="boolean" truevalue="true" falsevalue="false" checked="false" - label="ExportFragmentPeak" + <param name="ExportFragmentPeak" type="boolean" truevalue="true" falsevalue="false" checked="false" label="ExportFragmentPeak" help="Output detailed information about detected MS2 signals"/> - <param name="se_extraction_data" type="boolean" truevalue="Signal Extraction data" falsevalue="diaumpire_se.params" checked="false" - label="Output Signal Extraction data for DIA_Umpire_Quant" /> - <param name="mgfs_as_collection" type="boolean" truevalue="true" falsevalue="false" checked="false" - label="Output MGFs as a collection" /> </inputs> <outputs> - <data format="txt" name="logfile" label="${tool.name} ${on_string} log"/> - <data format="dia_umpire.ser" name="se_params" label="${tool.name} ${input.name} ${se_extraction_data}"> + <data format="txt" name="logfile" label="${tool.name} log"/> + <data format="dia_umpire.ser" name="se_params" label="${tool.name} Signal Extraction data"> </data> - <data format="csv" name="PrecursorPeak" label="${tool.name} ${input.name} PeakCluster.csv" from_work_dir="gx_path/swath_PeakCurve.csv"> + <data format="csv" name="PrecursorPeak" label="" from_work_dir="gx_path/swath_PeakCurve.csv"> <filter>ExportPrecursorPeak</filter> </data> - <!-- <data format="csv" name="FragmentPeak" label="" from_work_dir="gx_path/swath_PeakCurve.csv"> <filter>ExportFragmentPeak</filter> </data> - --> <collection name="dia_umpire_se_mgfs" type="list" label="${tool.name} MGFs"> - <filter>mgfs_as_collection</filter> <discover_datasets pattern="(?P<name>.*Q[1-3]\.mgf)" ext="mgf" visible="false" directory="gx_path" /> </collection> - <data format="mgf" name="q1_mgf" label="${tool.name} ${input.name}_Q1.mgf" > - <filter>not mgfs_as_collection</filter> - </data> - <data format="mgf" name="q2_mgf" label="${tool.name} ${input.name}_Q2.mgf" > - <filter>not mgfs_as_collection</filter> - </data> - <data format="mgf" name="q3_mgf" label="${tool.name} ${input.name}_Q3.mgf" > - <filter>not mgfs_as_collection</filter> - </data> + </outputs> <tests> <test> - <param name="input" value="LongSwath_UPS1_1ug_rep1_xs.mzXML" ftype="mzxml"/> - <output name="q2_mgf" file="LongSwath_UPS1_1ug_rep1_xs_Q2.mgf"/> </test> </tests> <help>