Mercurial > repos > galaxyp > dia_umpire
diff dia_umpire_se.xml @ 1:2b785516abfc draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
| author | galaxyp |
|---|---|
| date | Mon, 04 Mar 2019 11:50:31 -0500 |
| parents | 22a1fa7d9d6a |
| children |
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--- a/dia_umpire_se.xml Mon Mar 04 11:50:10 2019 -0500 +++ b/dia_umpire_se.xml Mon Mar 04 11:50:31 2019 -0500 @@ -7,27 +7,16 @@ <expand macro="stdio" /> <command> <![CDATA[ +#set $output_dir = 'gx_path' #import re -## want to save all outputs in a directory output.extra_files_path to be used by dia_umpire_quant -## Is file naming going to be a problem? May need to have a name param -#if $se_extraction_data: -#set se_params = $se_ser -#set $ser_dir = $se_ser.extra_files_path -mkdir $ser_dir -&& ln -s '$ser_dir' '$output_dir' -&& cat $se_config > $se_ser -#else: -#set se_params = $params mkdir '$output_dir' && cat $se_config > $se_params -#end if -## && echo " " >> $se_params && echo "Thread = \$GALAXY_SLOTS" >> $se_params #if $input_prefix and len($input_prefix.strip()) > 0: #set $input_path = str($output_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 $input_path = str($output_dir) + '/' + $re.sub('\.[mM]\w+$','',$re.sub('[^-a-zA-Z0-9_.]','_',$input.element_identifier)) + '.mzXML' #end if && ln -s '${input}' '$input_path' && dia_umpire_se '$input_path' '$se_params' @@ -201,8 +190,6 @@ <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"> <validator type="regex" message="">[a-zA-Z][a-zA-Z0-9_-]*</validator> </param> - <param name="output_dir" type="hidden" value="gx_path"/> - <conditional name="instrument"> <param name="model" type="select" label="instrument used" help="Sets default parameters"> <option value="Thermo_Orbitrap">Thermo Orbitrap</option> @@ -210,7 +197,6 @@ <option value="other">other</option> </param> <when value="Thermo_Orbitrap"> - <param name="SE_MS1PPM" type="float" value="5" min="1" max="20" optional="true" label="Maximum mass error for two MS1 peaks"> <help> SE.MS1PPM: (Unit: ppm) Maximum mass error for two MS1 peaks in consecutive spectra to be considered signal of the same ion. Used in MS1 signal detection and precursor alignment between samples/runs. @@ -224,7 +210,6 @@ </help> </param> <expand macro="common_se_params" /> - </when> <when value="AB_SCIEX_Triple_TOF_5600"> <param name="SE_MS1PPM" type="float" value="30" min="1" max="50" optional="true" label="Maximum mass error for two MS1 peaks"> @@ -287,7 +272,6 @@ RTOverlap: Retention time overlap. (Default: 0.3) </help> </param> - <param name="DeltaApex" type="float" value=".6" min="0" optional="true" label="DeltaApex" > <help> DeltaApex: (Unit: minute) Maximum retention time difference of LC profile apexes between precursor and fragment (the lower, the more stringent). (Default: 0.6) @@ -313,7 +297,6 @@ </param> <when value="no"/> <when value="yes"> - <param name="SE_MinMSIntensity" type="float" value="" optional="true" label="MinMSIntensity" > <help> SE.MinMSIntensity: Minimum signal intensity for a peak in an MS1 spectrum to be considered as a valid signal. Any MS1 peak having intensity lower than this threshold will be ignored. It is the main parameter controlling how many peaks and isotopic envelopes will be detected. @@ -378,7 +361,6 @@ <param name="SE_MinRTRange" type="float" value="" optional="true" label="MinRTRange" > <help> - </help> </param> <param name="SE_MaxNoPeakCluster" type="integer" value="" optional="true" label="MaxNoPeakCluster" > @@ -394,7 +376,6 @@ <param name="SE_MinMS2NoPeakCluster" type="integer" value="" optional="true" label="MinMS2NoPeakCluster" > <help> SE.MinMS2NoPeakCluster (new parameter in v1.4): Minimum number of isotope peaks for a MS2 feature. When it is set as 1, the algorithm will group fragments even for peaks without any isotope signal being found. For these cases, the assumed charged states will be from the parameter SE.StartCharge to SE.EndCharge. - </help> </param> <param name="SE_RTtol" type="float" value="" optional="true" label="RTtol" > @@ -437,8 +418,6 @@ <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" /> @@ -446,12 +425,7 @@ <outputs> <data format="txt" name="logfile" label="${tool.name} ${on_string} log"/> - <data format="dia_umpire.ser" name="se_ser" label="${tool.name} ${input.name} ${se_extraction_data}"> - <filter>se_extraction_data</filter> - </data> - <data format="txt" name="params" label="${tool.name} ${input.name} ${se_extraction_data}"> - <filter>not se_extraction_data</filter> - </data> + <data format="txt" name="se_params" label="${tool.name} ${input.name} diaumpire_se.params"/> <data format="csv" name="PrecursorPeak" label="${tool.name} ${input.name} PeakCluster.csv" from_work_dir="gx_path/swath_PeakCurve.csv"> <filter>ExportPrecursorPeak</filter> </data> @@ -489,7 +463,7 @@ <output name="q2_mgf"> <assert_contents> <has_text text="BEGIN IONS" /> - <has_text_matching expression="^PEPMASS=740.\d+$" /> + <has_text text="PEPMASS=740" /> </assert_contents> </output> </test> @@ -561,9 +535,7 @@ Note: Each file corresponds to a different "quality level" of precursor ions (Q1= More than two isotopic peaks detected in MS1, Q2 = only two isotopic peak detected, Q3 = detected unfragmented precursor in MS2). These spectra are written to separate files, because they must be searched separately against a protein database as a consequence of differences in FDR estimates for these varying quality data. - 2. *DIA_Umpire_SE Signal Extraction data* - includes the binary files (.ser) containing contain all necessary information for quantitation procedures (parameter settings, all detected precursor and fragment peaks, precursor-fragment grouping information). - - 3. If ExportPrecursorPeak and/or ExportFragmentPeak options were set to true, text files with detailed information about detected MS1 and/or MS2 features will be generated. + 2. If ExportPrecursorPeak and/or ExportFragmentPeak options were set to true, text files with detailed information about detected MS1 and/or MS2 features will be generated. ]]>