Mercurial > repos > galaxyp > fragpipe

diff macros.xml @ 6:2e667f0ec33c draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 3fe4cafecf2b25f602915c638b0d6993d957e1e6
author galaxyp
date Sun, 30 Mar 2025 23:01:00 +0000
parents 048390db1932
children
line wrap: on
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--- a/macros.xml	Sat Feb 01 18:12:08 2025 +0000
+++ b/macros.xml	Sun Mar 30 23:01:00 2025 +0000
@@ -1,7 +1,7 @@
 <macros>
     <import>msfragger_macros.xml</import>
     <token name="@TOOL_VERSION@">20.0</token>
-    <token name="@VERSION_SUFFIX@">5</token>
+    <token name="@VERSION_SUFFIX@">6</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">fragpipe</requirement>
@@ -84,7 +84,7 @@
         #if str($database_options) != 'none'
             philosopher workspace --init &&
             philosopher database --custom genericized_db.fas --prefix rev_
-            #if str($database_options) != 'decoy_and_contam'
+            #if str($database_options) == 'decoy_and_contam'
                 --contam
             #end if
             --contamprefix &&
@@ -166,8 +166,8 @@
                 </section>
                 <expand macro="validation"
                   pep="false"
-                  perc="true"
-                  boost="false"
+                  perc="false"
+                  boost="true"
                   no="false"
                   masswidth="5"
                   clevel="0"
@@ -212,8 +212,8 @@
                 </section>
                 <expand macro="validation"
                   pep="false"
-                  perc="true"
-                  boost="false"
+                  perc="false"
+                  boost="true"
                   no="true"
                   masswidth="5"
                   clevel="0"
@@ -232,11 +232,10 @@
                 <section name="msfragger" expanded="false" title="MSFragger Options">
                     <expand macro="msfragger_LFQ_MBR"/>
                 </section>
-                <!-- MSBooster should be enabled once included in FragPipe Galaxy tool -->
                 <expand macro="validation"
                   pep="false"
-                  perc="true"
-                  boost="false"
+                  perc="false"
+                  boost="true"
                   no="true"
                   masswidth="5"
                   clevel="0"
@@ -270,8 +269,8 @@
         </section>
         <expand macro="validation"
           pep="false"
-          perc="true"
-          boost="false"
+          perc="false"
+          boost="true"
           no="false"
           masswidth="5"
           clevel="0"
@@ -524,11 +523,11 @@
         #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'
+            #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false'
             @PERCOLATOR@
         #elif $prfx.run_psm_validation == 'msbooster_percolator'
             #set $wfdict['run-psm-validation'] = 'true'
-            #set $wfdict['peptide-prophet.run-peptide-prophet=false'] = 'false'
+            #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false'
             @MSBOOSTER@
             @PERCOLATOR@
         #end if