Mercurial > repos > galaxyp > openms_idposteriorerrorprobability
view test-data/examples/TOPPAS/GenericWrapper_Rscript-generic.toppas @ 18:6daaa75ccb99 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
| author | galaxyp |
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| date | Sun, 13 Dec 2020 15:03:50 +0000 |
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<?xml version="1.0" encoding="ISO-8859-1"?> <PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> <NODE name="info" description=""> <ITEM name="version" value="2.0.1" type="string" description="" required="false" advanced="false" /> <ITEM name="num_vertices" value="7" type="int" description="" required="false" advanced="false" /> <ITEM name="num_edges" value="6" type="int" description="" required="false" advanced="false" /> <ITEM name="description" value="<![CDATA[<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'Arial'; font-size:12pt; font-weight:400; font-style:normal;"> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> </p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">Example workflow for downstream R analysis.</span></p> <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; color:#000000;"><br /></p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">The R script used here is very minimal, but should get you started.</span></p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">Make a copy and modify to your needs.</span></p> <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; color:#000000;"><br /></p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">The GenericWrapper node can deal with up to four input and six output nodes. </span></p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">The inputs are designed as lists, but by definition can also be single files (lists of length 1).</span></p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">Outputs are up to four single files (out1 to out4) or lists (outlist1 and outlist2).</span></p> <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; color:#000000;"><br /></p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">This is useful in TOPPAS since for output lists the number of files is deduced by TOPPAS from the length of the input list(s).</span></p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">If your R script writes single files no matter how long the input lists are, then use out1 to out4.</span></p> <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; color:#000000;"><br /></p></body></html>]]>" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="vertices" description=""> <NODE name="0" description=""> <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> <ITEM name="toppas_type" value="input file list" type="string" description="" required="false" advanced="false" /> <ITEMLIST name="file_names" type="string" description="" required="false" advanced="false"> <LISTITEM value="../BSA/BSA1_OMSSA.idXML"/> <LISTITEM value="../BSA/BSA2_OMSSA.idXML"/> </ITEMLIST> <ITEM name="x_pos" value="-160" type="double" description="" required="false" advanced="false" /> <ITEM name="y_pos" value="80" type="double" description="" required="false" advanced="false" /> </NODE> <NODE name="6" description=""> <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> <ITEM name="toppas_type" value="output file list" type="string" description="" required="false" advanced="false" /> <ITEM name="x_pos" value="440" type="double" description="" required="false" advanced="false" /> <ITEM name="y_pos" value="-60" type="double" description="" required="false" advanced="false" /> <ITEM name="output_folder_name" value="" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="1" description=""> <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> <ITEM name="toppas_type" value="input file list" type="string" description="" required="false" advanced="false" /> <ITEMLIST name="file_names" type="string" description="" required="false" advanced="false"> <LISTITEM value="../../SCRIPTS/Rscript_generic_example.R"/> </ITEMLIST> <ITEM name="x_pos" value="-60" type="double" description="" required="false" advanced="false" /> <ITEM name="y_pos" value="-260" type="double" description="" required="false" advanced="false" /> </NODE> <NODE name="2" description=""> <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> <ITEM name="toppas_type" value="input file list" type="string" description="" required="false" advanced="false" /> <ITEMLIST name="file_names" type="string" description="" required="false" advanced="false"> <LISTITEM value="data/BSA_Identification/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta"/> </ITEMLIST> <ITEM name="x_pos" value="-160" type="double" description="" required="false" advanced="false" /> <ITEM name="y_pos" value="-60" type="double" description="" required="false" advanced="false" /> </NODE> <NODE name="3" description=""> <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> <ITEM name="toppas_type" value="merger" type="string" description="" required="false" advanced="false" /> <ITEM name="x_pos" value="0" type="double" description="" required="false" advanced="false" /> <ITEM name="y_pos" value="20" type="double" description="" required="false" advanced="false" /> <ITEM name="round_based" value="false" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="4" description=""> <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> <ITEM name="tool_name" value="GenericWrapper" type="string" description="" required="false" advanced="false" /> <ITEM name="tool_type" value="Rscript_generic" type="string" description="" required="false" advanced="false" /> <ITEM name="x_pos" value="200" type="double" description="" required="false" advanced="false" /> <ITEM name="y_pos" value="-60" type="double" description="" required="false" advanced="false" /> <NODE name="parameters" description=""> <ITEM name="type" value="Rscript_generic" type="string" description="Which external tool configuration to load?! See 'C:/dev/oms/share/OpenMS/TOOLS/EXTERNAL'." required="false" advanced="false" restrictions="hardklor,RAWFileConvert,QCMLExport,RAWDirConvert,Rscript_generic,Rscript_qcfigures_acc,Rscript_qcfigures_idmap,Rscript_qcfigures_setid,Rscript_qcfigures_tic,TPP_RefreshParser,TPP_ProteinProphet" /> <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" /> <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> <NODE name="ETool" description="tool specific parameters"> <ITEM name="file_script" value="" type="input-file" description="input R script; an example is provided in share/OpenMS/SCRIPTS/Rscript_generic_example.R" required="false" advanced="false" /> <ITEMLIST name="in1" type="input-file" description="Input file(s) separated by blanks" required="false" advanced="false"> </ITEMLIST> <ITEMLIST name="in2" type="input-file" description="Input file(s) separated by blanks" required="false" advanced="false"> </ITEMLIST> <ITEMLIST name="in3" type="input-file" description="Input file(s) separated by blanks" required="false" advanced="false"> </ITEMLIST> <ITEMLIST name="in4" type="input-file" description="Input file(s) separated by blanks" required="false" advanced="false"> </ITEMLIST> <ITEM name="out1" value="" type="output-file" description="Output file which your R script writes to" required="false" advanced="false" /> <ITEM name="out2" value="" type="output-file" description="Output file which your R script writes to" required="false" advanced="false" /> <ITEM name="out3" value="" type="output-file" description="Output file which your R script writes to" required="false" advanced="false" /> <ITEM name="out4" value="" type="output-file" description="Output file which your R script writes to" required="false" advanced="false" /> <ITEMLIST name="outlist1" type="output-file" description="Output file(s) separated by blanks" required="false" advanced="false"> </ITEMLIST> <ITEMLIST name="outlist2" type="output-file" description="Output file(s) separated by blanks" required="false" advanced="false"> </ITEMLIST> </NODE> </NODE> </NODE> <NODE name="5" description=""> <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> <ITEM name="toppas_type" value="output file list" type="string" description="" required="false" advanced="false" /> <ITEM name="x_pos" value="440" type="double" description="" required="false" advanced="false" /> <ITEM name="y_pos" value="80" type="double" description="" required="false" advanced="false" /> <ITEM name="output_folder_name" value="" type="string" description="" required="false" advanced="false" /> </NODE> </NODE> <NODE name="edges" description=""> <NODE name="0" description=""> <NODE name="source/target" description=""> <ITEM name="" value="0/3" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="source_out_param" description=""> <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="target_in_param" description=""> <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> </NODE> </NODE> <NODE name="1" description=""> <NODE name="source/target" description=""> <ITEM name="" value="4/6" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="source_out_param" description=""> <ITEM name="" value="ETool:out1" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="target_in_param" description=""> <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> </NODE> </NODE> <NODE name="2" description=""> <NODE name="source/target" description=""> <ITEM name="" value="1/4" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="source_out_param" description=""> <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="target_in_param" description=""> <ITEM name="" value="ETool:file_script" type="string" description="" required="false" advanced="false" /> </NODE> </NODE> <NODE name="3" description=""> <NODE name="source/target" description=""> <ITEM name="" value="4/5" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="source_out_param" description=""> <ITEM name="" value="ETool:outlist1" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="target_in_param" description=""> <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> </NODE> </NODE> <NODE name="4" description=""> <NODE name="source/target" description=""> <ITEM name="" value="3/4" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="source_out_param" description=""> <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="target_in_param" description=""> <ITEM name="" value="ETool:in2" type="string" description="" required="false" advanced="false" /> </NODE> </NODE> <NODE name="5" description=""> <NODE name="source/target" description=""> <ITEM name="" value="2/4" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="source_out_param" description=""> <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> </NODE> <NODE name="target_in_param" description=""> <ITEM name="" value="ETool:in1" type="string" description="" required="false" advanced="false" /> </NODE> </NODE> </NODE> </PARAMETERS>