# HG changeset patch
# User jjohnson
# Date 1593702614 14400
# Node ID e37e3c4a87a985abc31421b1e4729b53ff68cb05
# Parent  114b44e35d3047d7b581d78385fd6d7c3c9cc50f
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit e3a6bfbf90e9ee3efeb6ff6517074bcc69f8d424"

diff -r 114b44e35d30 -r e37e3c4a87a9 encyclopedia_searchtolib.xml.bak
--- a/encyclopedia_searchtolib.xml.bak	Wed Jul 01 11:24:59 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,138 +0,0 @@
-<tool id="encyclopedia_searchtolib" name="SearchToLib" version="@VERSION@.0">
-    <description>Build a Chromatogram Library or quantify samples from Data-Independent Acquisition (DIA) MS/MS Data</description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
-    <command detect_errors="exit_code"><![CDATA[
-        @CMD_IMPORTS@
-        @LINK_SCAN_INPUTS@
-        @LINK_FASTA_INPUT@
-        @LINK_TARGET_FASTA@
-        @LINK_LIB_INPUT@
-        for SCAN_FILE in `ls -1 inputs/*`; do 
-        echo "\$SCAN_FILE" &&
-        EncyclopeDIA -Djava.awt.headless=true -Xmx20g 
-        #if not $l
-            -walnut
-        #end if
-        -i \$SCAN_FILE
-        @FASTA_INPUT@
-        @TARGET_FASTA@
-        @LIB_INPUT@
-        @COMMON_OPTIONS@
-        @MASS_LIBRARY_TOLERANCE@
-        @PERCOLATOR_OPTIONS@
-        @PEAK_OPTIONS@
-        @WINDOW_OPTIONS@
-        @MODIFICATION_OPTIONS@
-        @SEARCH_OPTIONS@ | tee -a search2lib.log
-        ; done && 
-        EncyclopeDIA -Djava.awt.headless=true -Xmx12g -libexport
-        #if not $l
-            -pecan
-        #end if
-        @SCAN_INPUTS@
-        @FASTA_INPUT@
-        @TARGET_FASTA@
-        @LIB_INPUT@
-        -a $a
-        -o chromatogram_library.elib
-        | tee -a search2lib.log
-    ]]></command>
-    <inputs>
-        <expand macro="scan_inputs"/>
-        <expand macro="lib_input" optional="true" libhelp="Use a Chromatogram elib for quantification, or a Prosit dlib spectral library to make a chromatogram elib using EncyclopeDIA, or else leave blank to make a Chromatogram library from just the fasta using Walnut"/>
-        <expand macro="fasta_input"/>
-        <expand macro="target_fasta"/>
-        <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files" help="retention-time alignment of peptides should be enabled when quantifying samples"/>
-        <expand macro="common_options"/>
-        <expand macro="mass_library_tolerance"/>
-        <expand macro="percolator_options"/>
-        <expand macro="peak_options"/>
-        <expand macro="window_options"/>
-        <expand macro="modification_options"/>
-        <expand macro="search_options"/>
-        <param name="select_outputs" type="select" label="Select outputs" multiple="true">
-            <option value="log" selected="true">log</option>
-            <option value="elib" selected="true">elib</option>
-            <option value="features" selected="true">concatenated_features.txt</option>
-            <option value="results" selected="true">concatenated_results.txt</option>
-            <option value="decoy" selected="false">concatenated_decoy.txt</option>
-            <option value="peptides" selected="true">peptides.txt (requires match between runs)</option>
-            <option value="proteins" selected="true">proteins.txt (requires match between runs)</option>
-        </param>
-    </inputs>
-    <outputs>
-        <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="search2lib.log">
-            <filter>'log' in select_outputs</filter>
-        </data>
-        <data name="elib" format="elib" label="${tool.name} ${on_string} elib" from_work_dir="chromatogram_library.elib">
-            <filter>'elib' in select_outputs</filter>
-        </data>
-        <data name="features" format="tabular" label="${tool.name} ${on_string} concatenated_features.txt" from_work_dir="inputs/chromatogram_library_concatenated_features.txt">
-            <filter>'features' in select_outputs</filter>
-            <actions>
-                <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,rank,peakZScore,peakCalibratedScore,deltaSn,avgIdotp,midIdotp,peakScore,peakWeightedScore,NCI,CIMassErrMean,CIMassErrVar,precursorMassErrMean,precursorMassErrVar,peakSimilarity,sampledTimes,midTime,spectraNorm,pepLength,charge2,charge3,precursorMz,sequence,protein" />
-            </actions>
-        </data>
-        <data name="results" format="tabular" label="${tool.name} ${on_string} concatenated_results.txt" from_work_dir="inputs/chromatogram_library_concatenated_results.txt">
-            <filter>'results' in select_outputs</filter>
-            <actions>
-                <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
-            </actions>
-        </data>
-        <data name="decoy" format="tabular" label="${tool.name} ${on_string} concatenated_decoy.txt" from_work_dir="inputs/chromatogram_library_concatenated_decoy.txt">
-            <filter>'decoy' in select_outputs</filter>
-            <actions>
-                <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
-            </actions>
-        </data>
-        <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.peptides.txt">
-            <filter>a and 'peptides' in select_outputs</filter>
-            <actions>
-                <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" />
-            </actions>
-        </data>
-        <data name="proteins" format="tabular" label="${tool.name} ${on_string} proteins.txt" from_work_dir="chromatogram_library.proteins.txt">
-            <filter>a and 'proteins' in select_outputs</filter>
-            <actions>
-                <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" />
-            </actions>
-        </data>
-    </outputs>
-    <help><![CDATA[
-
-**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. 
-
-SearchToLIB can also quantify peptides from the chromatogram library. 
-
-@MSCONVERT_HELP@
-
-**Typical DIA SearchToLib 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.
-
-  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. SearchToLib is then run on the wide-window quantitative replicate mzML files using that chromatogram library, with the *align between files* option, to produce quantification results.
-
-.. image:: SearchToLib_Workflow.png
-  :height: 439
-  :width: 768
-
-.. _Prosit: https://www.proteomicsdb.org/prosit
-
-    ]]></help>
-    <expand macro="citations" />
-</tool>
diff -r 114b44e35d30 -r e37e3c4a87a9 macros.xml
--- a/macros.xml	Wed Jul 01 11:24:59 2020 -0400
+++ b/macros.xml	Thu Jul 02 11:10:14 2020 -0400
@@ -479,6 +479,7 @@
             <expand macro="peak_options"/>
             <expand macro="window_options"/>
             <expand macro="modification_options"/>
+            <expand macro="search_options"/>
         </section>
     </xml>