diff macros.xml @ 4:e969a182e3cb draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43

--- a/macros.xml	Thu Sep 12 08:06:44 2024 +0000
+++ b/macros.xml	Fri Dec 13 15:17:28 2024 +0000
@@ -1,7 +1,7 @@
 <macros>
     <import>msfragger_macros.xml</import>
     <token name="@TOOL_VERSION@">20.0</token>
-    <token name="@VERSION_SUFFIX@">3</token>
+    <token name="@VERSION_SUFFIX@">4</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">fragpipe</requirement>
@@ -350,13 +350,27 @@
     <!-- Set Percolator workflow options -->
     <token name="@PERCOLATOR@"><![CDATA[
         #set $prc = $wf.validation.validation_tab.psm_validation.percolator
-        #set $wfdict['run-validation-tab'] = $wf.validation.validation_tab.run_validation
-        #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false'
         #set $wfdict['percolator.run-percolator'] = 'true'
         #set $wfdict['percolator.keep-tsv-files'] = str($prc.keep_tsv_files)
         #set $wfdict['percolator.min-prob'] = str($prc.min_prob)
     ]]></token>
 
+    <xml name="msbooster">
+        <section name="msbooster" expanded="true" title="MSBooster">
+            <param name="predict_rt" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict RT"/>
+            <param name="predict_spectra" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict spectra"/>
+            <param name="use_correlated_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use correlated features"/>
+        </section>
+    </xml>
+    <token name="@MSBOOSTER@"><![CDATA[
+        #set $prfx = $wf.validation.validation_tab.psm_validation.msbooster
+        #set $wfdict['msbooster.run-msbooster'] = 'true'
+        #set $wfdict['msbooster.predict-rt'] = str($prfx.predict_rt)
+        #set $wfdict['msbooster.predict-spectra'] = str($prfx.predict_spectra)
+        #set $wfdict['msbooster.use-correlated-features'] = str($prfx.use_correlated_features)
+    ]]></token>
+
+
     <!-- Philosopher Report (phi-report) options -->
     <xml name="phi_report">
         <conditional name="phi_report">
@@ -424,16 +438,6 @@
         <param name="run_crystalc" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Run Crystal-C" help="Recommend for open searches for additional resuts cleanup"/>
     </xml>
 
-    <!-- MSBooster options. Disabled until DIA-NN integrated.
-    <xml name="msbooster">
-        <section name="msbooster" expanded="false" title="MSBooster">
-            <param name="predict_rt" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict RT"/>
-            <param name="predict_spectra" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict spectra"/>
-            <param name="use_correlated_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use correlated features"/>
-        </section>
-    </xml>
-     -->
-
     <!-- Protein Prophet options -->
     <xml name="protein_prophet" token_minprob="0.05">
         <conditional name="protein_prophet">
@@ -484,9 +488,7 @@
                         <param name="run_psm_validation" type="select" label="PSM Validation">
                             <option value="peptide_prophet" selected="@PEP@">Run PeptideProphet</option>
                             <option value="percolator" selected="@PERC@">Run Percolator</option>
-                            <!-- MSBooster disabled until DIA-NN integrated
                             <option value="msbooster_percolator" selected="@BOOST@">Run MSBooster and Percolator</option>
-                            -->
                             <option value="no" selected="@NO@">Use workflow values</option>
                         </param>
                         <when value="peptide_prophet">
@@ -495,12 +497,10 @@
                         <when value="percolator">
                             <expand macro="percolator"/>
                         </when>
-                        <!-- MSBooster disabled until DIA-NN integrated
                         <when value="msbooster_percolator">
                             <expand macro="msbooster"/>
                             <expand macro="percolator"/>
                         </when>
-                        -->
                         <when value="no">
                         </when>
                     </conditional>
@@ -524,9 +524,13 @@
         #elif $prfx.run_psm_validation == 'percolator'
             #set $wfdict['run-psm-validation'] = 'true'
             #set $wfdict['msbooster.run-msbooster'] = 'false'
+            #set $wfdict['peptide-prophet.run-peptide-prophet=false'] = 'false'
             @PERCOLATOR@
-        ##elif $prfx.run_psm_validation == 'msbooster_percolator'
-        # MSBooster disabled until DIA-NN integrated.
+        #elif $prfx.run_psm_validation == 'msbooster_percolator'
+            #set $wfdict['run-psm-validation'] = 'true'
+            #set $wfdict['peptide-prophet.run-peptide-prophet=false'] = 'false'
+            @MSBOOSTER@
+            @PERCOLATOR@
         #end if
         @PROTEINPROPHET@
         @PHIREPORT@