From 7585813ebd1e1f5e87c20b472a45e05e74a9dfca Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Fri, 19 Feb 2021 19:41:33 +0100
Subject: [PATCH] fix PSMFeatureExtractor

---
 tools/openms/PSMFeatureExtractor.patch | 22 +++++++++++-----------
 tools/openms/PSMFeatureExtractor.xml   |  9 ++++-----
 2 files changed, 15 insertions(+), 16 deletions(-)

diff --git a/tools/openms/PSMFeatureExtractor.patch b/tools/openms/PSMFeatureExtractor.patch
index 4aca0a893..c66c5d52a 100644
--- a/tools/openms/PSMFeatureExtractor.patch
+++ b/tools/openms/PSMFeatureExtractor.patch
@@ -1,18 +1,19 @@
---- PSMFeatureExtractor.xml.orig	2021-02-16 16:30:38.919393993 +0100
-+++ PSMFeatureExtractor.xml	2021-02-16 16:32:34.862390198 +0100
-@@ -17,6 +17,11 @@
+--- PSMFeatureExtractor.xml.orig	2021-02-19 19:18:58.635157367 +0100
++++ PSMFeatureExtractor.xml	2021-02-19 19:23:28.943370062 +0100
+@@ -17,8 +17,12 @@
  
  ## Preprocessing
  mkdir in &&
 +#if $in
-+${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+ mkdir ${' '.join(["'in/%s'" % (i) for i, f in enumerate($in) if f])} && 
+ ${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in) if f])}
 +#else if $in_single
 +ln -s '$in_single' 'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)' &&  
 +#end if
- mkdir ${' '.join(["'in/%s'" % (i) for i, f in enumerate($in) if f])} && 
- ${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in) if f])}
  mkdir out &&
-@@ -28,7 +33,11 @@
+ 
+ ## Main program call
+@@ -28,6 +32,10 @@
  python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
  @EXECUTABLE@ -ini @EXECUTABLE@.ctd
  -in
@@ -23,14 +24,13 @@
 +#end if
  -out
  'out/output.${out_type}'
- 
-@@ -42,7 +51,8 @@
+@@ -42,7 +50,8 @@
      <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
    </configfiles>
    <inputs>
 -    <param name="in" argument="-in" type="data" format="idxml,mzid" multiple="true" optional="false" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
-+    <param name="in_single" argument="-in" type="data" format="idxml,mzid" multiple="false" optional="true" label="Input file for batch processing" help="(exactly one of -in or -in_list is required)"/>
-+    <param name="in" argument="-in" type="data" format="idxml,mzid" multiple="true" optional="true" label="Input file(s) for joint processing" help="(exactly one of -in or -in_list is required)"/>   
++    <param name="in_single" argument="-in" type="data" format="idxml,mzid" multiple="false" optional="true" label="Input file for batch processing" help="(exactly one of the two inputs required) select idxml,mzid data sets(s)"/>
++    <param name="in" argument="-in" type="data" format="idxml,mzid" multiple="true" optional="true" label="Input files for joint processing" help="(exactly one of the two inputs is required) select idxml,mzid data sets(s)"/>
      <param name="out_type" argument="-out_type" display="checkboxes" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
        <option value="idXML">idxml</option>
        <option value="mzid">mzid</option>
diff --git a/tools/openms/PSMFeatureExtractor.xml b/tools/openms/PSMFeatureExtractor.xml
index a6b1a9fd9..48a0a3cd8 100644
--- a/tools/openms/PSMFeatureExtractor.xml
+++ b/tools/openms/PSMFeatureExtractor.xml
@@ -18,12 +18,11 @@
 ## Preprocessing
 mkdir in &&
 #if $in
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'" % (i) for i, f in enumerate($in) if f])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in) if f])}
 #else if $in_single
 ln -s '$in_single' 'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)' &&  
 #end if
-mkdir ${' '.join(["'in/%s'" % (i) for i, f in enumerate($in) if f])} && 
-${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in) if f])}
 mkdir out &&
 
 ## Main program call
@@ -51,8 +50,8 @@ ${' '.join(["'in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="in_single" argument="-in" type="data" format="idxml,mzid" multiple="false" optional="true" label="Input file for batch processing" help="(exactly one of -in or -in_list is required)"/>
-    <param name="in" argument="-in" type="data" format="idxml,mzid" multiple="true" optional="true" label="Input file(s) for joint processing" help="(exactly one of -in or -in_list is required)"/>   
+    <param name="in_single" argument="-in" type="data" format="idxml,mzid" multiple="false" optional="true" label="Input file for batch processing" help="(exactly one of the two inputs required) select idxml,mzid data sets(s)"/>
+    <param name="in" argument="-in" type="data" format="idxml,mzid" multiple="true" optional="true" label="Input files for joint processing" help="(exactly one of the two inputs is required) select idxml,mzid data sets(s)"/>
     <param name="out_type" argument="-out_type" display="checkboxes" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
       <option value="idXML">idxml</option>
       <option value="mzid">mzid</option>