--- a/ConsensusID.xml	Fri Nov 06 19:49:28 2020 +0000
+++ b/ConsensusID.xml	Mon Feb 22 10:46:10 2021 +0000
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [ID Processing]-->
-<tool id="ConsensusID" name="ConsensusID" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="ConsensusID" name="ConsensusID" version="@TOOL_VERSION@+galaxy1" profile="20.05">
   <description>Computes a consensus of peptide identifications of several identification engines.</description>
   <macros>
     <token name="@EXECUTABLE@">ConsensusID</token>
@@ -17,7 +17,8 @@
 
 ## Preprocessing
 mkdir 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])}
 mkdir out &&
 
 ## Main program call
@@ -27,7 +28,7 @@
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in) if f])}
 -out
 'out/output.${in[0].ext}'
 
@@ -42,8 +43,8 @@
   </configfiles>
   <inputs>
     <param name="in" argument="-in" type="data" format="consensusxml,featurexml,idxml" multiple="true" optional="false" label="input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
-    <param name="rt_delta" argument="-rt_delta" type="float" optional="true" min="0.0" value="0.1" label="[idXML input only] Maximum allowed retention time deviation between identifications belonging to the same spectrum" help=""/>
-    <param name="mz_delta" argument="-mz_delta" type="float" optional="true" min="0.0" value="0.1" label="[idXML input only] Maximum allowed precursor m/z deviation between identifications belonging to the same spectrum" help=""/>
+    <param name="rt_delta" argument="-rt_delta" type="float" optional="false" min="0.0" value="0.1" label="[idXML input only] Maximum allowed retention time deviation between identifications belonging to the same spectrum" help=""/>
+    <param name="mz_delta" argument="-mz_delta" type="float" optional="false" min="0.0" value="0.1" label="[idXML input only] Maximum allowed precursor m/z deviation between identifications belonging to the same spectrum" help=""/>
     <param name="per_spectrum" argument="-per_spectrum" type="boolean" truevalue="true" falsevalue="false" checked="false" label="(only idXML) if set, mapping will be done based on exact matching of originating mzml file and spectrum_ref" help=""/>
     <param name="algorithm" argument="-algorithm" type="select" optional="false" label="Algorithm used for consensus scoring" help="* PEPMatrix: Scoring based on posterior error probabilities (PEPs) and peptide sequence similarities (scored by a substitution matrix). Requires PEPs as scores.. * PEPIons: Scoring based on posterior error probabilities (PEPs) and fragment ion similarities ('shared peak count'). Requires PEPs as scores.. * best: For each peptide ID, use the best score of any search engine as the consensus score. Requires the same score type in all ID runs.. * worst: For each peptide ID, use the worst score of any search engine as the consensus score. Requires the same score type in all ID runs.. * average:  For each peptide ID, use the average score of all search engines as the consensus. Requires the same score type in all ID runs.. * ranks: Calculates a consensus score based on the ranks of peptide IDs in the results of different search engines. The final score is in the range (0, 1], with 1 being the best score. No requirements about score types">
       <option value="PEPMatrix" selected="true">PEPMatrix</option>
@@ -52,30 +53,30 @@
       <option value="worst">worst</option>
       <option value="average">average</option>
       <option value="ranks">ranks</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="algorithm"/>
     </param>
     <section name="filter" title="Options for filtering peptide hits" help="" expanded="false">
-      <param name="considered_hits" argument="-filter:considered_hits" type="integer" optional="true" min="0" value="0" label="The number of top hits in each ID run that are considered for consensus scoring ('0' for all hits)" help=""/>
-      <param name="min_support" argument="-filter:min_support" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="For each peptide hit from an ID run, the fraction of other ID runs that must support that hit (otherwise it is removed)" help=""/>
+      <param name="considered_hits" argument="-filter:considered_hits" type="integer" optional="false" min="0" value="0" label="The number of top hits in each ID run that are considered for consensus scoring ('0' for all hits)" help=""/>
+      <param name="min_support" argument="-filter:min_support" type="float" optional="false" min="0.0" max="1.0" value="0.0" label="For each peptide hit from an ID run, the fraction of other ID runs that must support that hit (otherwise it is removed)" help=""/>
       <param name="count_empty" argument="-filter:count_empty" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Count empty ID runs" help="(i.e. those containing no peptide hit for the current spectrum) when calculating 'min_support'?"/>
       <param name="keep_old_scores" argument="-filter:keep_old_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if set, keeps the original scores as user params" help=""/>
     </section>
     <section name="PEPIons" title="PEPIons algorithm parameters" help="" expanded="false">
-      <param name="mass_tolerance" argument="-PEPIons:mass_tolerance" type="float" optional="true" min="0.0" value="0.5" label="Maximum difference between fragment masses (in Da) for fragments to be considered 'shared' between peptides" help=""/>
-      <param name="min_shared" argument="-PEPIons:min_shared" type="integer" optional="true" min="1" value="2" label="The minimal number of 'shared' fragments (between two suggested peptides) that is necessary to evaluate the similarity based on shared peak count (SPC)" help=""/>
+      <param name="mass_tolerance" argument="-PEPIons:mass_tolerance" type="float" optional="false" min="0.0" value="0.5" label="Maximum difference between fragment masses (in Da) for fragments to be considered 'shared' between peptides" help=""/>
+      <param name="min_shared" argument="-PEPIons:min_shared" type="integer" optional="false" min="1" value="2" label="The minimal number of 'shared' fragments (between two suggested peptides) that is necessary to evaluate the similarity based on shared peak count (SPC)" help=""/>
     </section>
     <section name="PEPMatrix" title="PEPMatrix algorithm parameters" help="" expanded="false">
-      <param name="matrix" argument="-PEPMatrix:matrix" display="radio" type="select" optional="false" label="Substitution matrix to use for alignment-based similarity scoring" help="">
+      <param name="matrix" argument="-PEPMatrix:matrix" display="checkboxes" type="select" optional="false" label="Substitution matrix to use for alignment-based similarity scoring" help="">
         <option value="identity" selected="true">identity</option>
         <option value="PAM30MS">PAM30MS</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="matrix"/>
       </param>
-      <param name="penalty" argument="-PEPMatrix:penalty" type="integer" optional="true" min="1" value="5" label="Alignment gap penalty (the same value is used for gap opening and extension)" help=""/>
+      <param name="penalty" argument="-PEPMatrix:penalty" type="integer" optional="false" min="1" value="5" label="Alignment gap penalty (the same value is used for gap opening and extension)" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san"/>
+      <param name="test" argument="-test" type="hidden" optional="false" value="False" label="Enables the test mode (needed for internal use only)" help="">
+        <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
     <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">