diff encyclopedia_searchtolib.xml @ 1:a7d52df6763f draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"

--- a/encyclopedia_searchtolib.xml	Fri Jun 19 10:21:31 2020 -0400
+++ b/encyclopedia_searchtolib.xml	Tue Jun 30 11:43:03 2020 -0400
@@ -1,5 +1,5 @@
 <tool id="encyclopedia_searchtolib" name="SearchToLib" version="@VERSION@.0">
-    <description>PeCAn-based Peptide Detection Directly from Data-Independent Acquisition (DIA) MS/MS Data</description>
+    <description>Build a Chromatogram Library from Data-Independent Acquisition (DIA) MS/MS Data</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -36,23 +36,16 @@
         @FASTA_INPUT@
         @TARGET_FASTA@
         @LIB_INPUT@
-        ## @COMMON_OPTIONS@
-        ## @MASS_LIBRARY_TOLERANCE@
-        ## @PERCOLATOR_OPTIONS@
-        ## @PEAK_OPTIONS@
-        ## @WINDOW_OPTIONS@
-        ## @MODIFICATION_OPTIONS@
-        ## @SEARCH_OPTIONS@
         -a $a
         -o chromatogram_library.elib
         | tee -a search2lib.log
     ]]></command>
     <inputs>
         <expand macro="scan_inputs"/>
-        <expand macro="lib_input" token_optional="true" token_help="If a prosit dlib is supplied, use EncycopeDIA, else use walnut"/>
+        <expand macro="lib_input" optional="true" libhelp="Use a Prosit dlib spectral library to make a chromatogram elib using EncyclopeDIA, or else leave blank to make a Chromatogram library from just the fasta using Walnut"/>
         <expand macro="fasta_input"/>
         <expand macro="target_fasta"/>
-        <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="match between runs"/>
+        <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files" help="retention-time alignment of peptides is generally not needed when using narrow-window spectrums"/>
         <expand macro="common_options"/>
         <expand macro="mass_library_tolerance"/>
         <expand macro="percolator_options"/>
@@ -63,11 +56,13 @@
         <param name="select_outputs" type="select" label="Select outputs" multiple="true">
             <option value="log" selected="true">log</option>
             <option value="elib" selected="true">elib</option>
-            <option value="features" selected="true">concatenated_features.txt</option>
-            <option value="results" selected="true">concatenated_results.txt</option>
+            <option value="features" selected="false">concatenated_features.txt</option>
+            <option value="results" selected="false">concatenated_results.txt</option>
             <option value="decoy" selected="false">concatenated_decoy.txt</option>
-            <option value="peptides" selected="true">peptides.txt (requires match between runs)</option>
-            <option value="proteins" selected="true">proteins.txt (requires match between runs)</option>
+            <!--
+            <option value="peptides" selected="false">peptides.txt (requires align between files)</option>
+            <option value="proteins" selected="false">proteins.txt (requires align between files)</option>
+            -->
         </param>
     </inputs>
     <outputs>
@@ -95,8 +90,9 @@
                 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
             </actions>
         </data>
+        <!--
         <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.peptides.txt">
-            <filter>a and peptides' in select_outputs</filter>
+            <filter>a and 'peptides' in select_outputs</filter>
             <actions>
                 <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" />
             </actions>
@@ -107,56 +103,39 @@
                 <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" />
             </actions>
         </data>
-<!--
--->
+        -->
     </outputs>
     <help><![CDATA[
-SearchToLIB uses EncyclopeDIA, Walnut (Pecan), or XCorDIA to create an DIA Elib for EncyclopeDIA DIA search
-Walnut is a FASTA database search engine for DIA data that uses PECAN-style scoring.
-You should prefix your arguments with a high memory setting, e.g. "-Xmx8g" for 8gb
+
+**SearchToLIB**
+
+@ENCYCLOPEDIA_WIKI@
+
+SearchToLIB uses the EncyclopeDIA algorithm, or the Walnut (Pecan) algorithm to search Data-Independent Acquisition (DIA) MS/MS spectrum files and creates a DIA elib chromatogram library for EncyclopeDIA DIA quantitation search. 
 
-Required Parameters: 
-	-i	input .DIA or .MZML file
-	-f	background FASTA file
+SearchToLIB can also quantify peptides from the chromatogram library. 
+
+@MSCONVERT_HELP@
+
+**Typical DIA Workflow**
+
+Two sets of Mass Spec MS/MS DIA data are collected for the experiment.  In addition to collecting wide-window DIA experiments on each quantitative replicate, a pool containing peptides from every condition is measured using several staggered narrow-window DIA experiments.
 
-Other Parameters: 
-	-t	target FASTA file (default: background FASTA file)
-	-tp	true/false target FASTA file contains peptides (default: false)
-	-o	output report file (default: [input file].pecan.txt)
-	-acquisition                          (default: overlapping dia)
-	-addDecoysToBackground                (default: false)
-	-alpha                                (default: 1.8)
-	-beta                                 (default: 0.4)
-	-dontRunDecoys                        (default: false)
-	-enzyme                               (default: trypsin)
-	-filterPeaklists                      (default: false)
-	-fixed                                (default: C=57.0214635)
-	-foffset                              (default: 0)
-	-frag                                 (default: YONLY)
-	-ftol                                 (default: 10)
-	-ftolunits                            (default: ppm)
-	-maxCharge                            (default: 3)
-	-maxLength                            (default: 100)
-	-maxMissedCleavage                    (default: 1)
-	-minCharge                            (default: 2)
-	-minEluteTime                         (default: 12)
-	-minIntensity                         (default: -1.0)
-	-minLength                            (default: 5)
-	-minNumOfQuantitativePeaks            (default: 3)
-	-minQuantitativeIonNumber             (default: 3)
-	-numberOfQuantitativePeaks            (default: 5)
-	-numberOfReportedPeaks                (default: 1)
-	-numberOfThreadsUsed                  (default: 12)
-	-percolatorProteinThreshold           (default: 0.01)
-	-percolatorThreshold                  (default: 0.01)
-	-percolatorVersionNumber              (default: 3)
-	-poffset                              (default: 0)
-	-precursorIsolationMargin             (default: 0)
-	-precursorWindowSize                  (default: -1)
-	-ptol                                 (default: 10)
-	-ptolunits                            (default: ppm)
-	-requireVariableMods                  (default: false)
-	-variable                             (default: -)
+  1. SearchToLib is first run with the pooled narrow-window mzML files to create a combined DIA elib chromatogram library.   
+     If a Spectral library argument is provided, for example from **Prosit**, SearchToLIB uses EncyclopeDIA to search each input spectrum mzML file.  
+     Otherwise, SearchToLIB uses Walnut, a FASTA database search engine for DIA data that uses PECAN-style scoring.
+
+
+       * Prosit_ generates a predicted spectrum library of fragmentation patterns and retention times for every +2H and +3H tryptic peptide in a FASTA database, with up to one missed cleavage.
+
+
+  2. EncyclopeDIA Quantify is then run on the wide-window quantitative replicate mzML files using that chromatogram library to produce quantification results.
+
+.. image:: SearchToLib_Workflow.png
+  :height: 439
+  :width: 768
+
+.. _Prosit: https://www.proteomicsdb.org/prosit
 
     ]]></help>
     <expand macro="citations" />