--- a/ConsensusID.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/ConsensusID.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,64 +1,101 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="ConsensusID" name="ConsensusID" version="1.12.0">
-  <description>Computes a consensus identification from peptide identifications of several identification engines.</description>
-  <macros>
-    <token name="@EXECUTABLE@">ConsensusID</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>ConsensusID
+<?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 CTD2Galaxy.-->
+  <!--Proposed Tool Section: [ID Processing]-->
+  <tool id="ConsensusID" name="ConsensusID" version="2.0.0">
+    <description>Computes a consensus of peptide identifications of several identification engines.</description>
+    <macros>
+      <token name="@EXECUTABLE@">ConsensusID</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>ConsensusID
 
--in ${param_in}
--out ${param_out}
--rt_delta ${param_rt_delta}
--mz_delta ${param_mz_delta}
--min_length ${param_min_length}
-${param_use_all_hits}
--threads \${GALAXY_SLOTS:-24} 
--algorithm:algorithm ${param_algorithm}
--algorithm:considered_hits ${param_considered_hits}
--algorithm:number_of_runs ${param_number_of_runs}
--algorithm:PEPIons:MinNumberOfFragments ${param_MinNumberOfFragments}
--algorithm:PEPIons:common ${param_common}
--algorithm:PEPMatrix:common ${param_common}
--algorithm:PEPMatrix:penalty ${param_penalty}
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_rt_delta:
+  -rt_delta $param_rt_delta
+#end if
+#if $param_mz_delta:
+  -mz_delta $param_mz_delta
+#end if
+#if $param_algorithm:
+  -algorithm
+  #if &quot; &quot; in str($param_algorithm):
+    &quot;$param_algorithm&quot;
+  #else
+    $param_algorithm
+  #end if
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $param_filter_considered_hits:
+  -filter:considered_hits $param_filter_considered_hits
+#end if
+#if $param_filter_min_support:
+  -filter:min_support $param_filter_min_support
+#end if
+#if $param_filter_count_empty:
+  -filter:count_empty
+#end if
+#if $param_PEPIons_mass_tolerance:
+  -PEPIons:mass_tolerance $param_PEPIons_mass_tolerance
+#end if
+#if $param_PEPIons_min_shared:
+  -PEPIons:min_shared $param_PEPIons_min_shared
+#end if
+#if $param_PEPMatrix_matrix:
+  -PEPMatrix:matrix
+  #if &quot; &quot; in str($param_PEPMatrix_matrix):
+    &quot;$param_PEPMatrix_matrix&quot;
+  #else
+    $param_PEPMatrix_matrix
+  #end if
+#end if
+#if $param_PEPMatrix_penalty:
+  -PEPMatrix:penalty $param_PEPMatrix_penalty
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
 </command>
-  <inputs>
-    <param name="param_in" type="data" format="idXML,featureXML,consensusXML" optional="False" label="input file" help="(-in)"/>
-    <param name="param_rt_delta" type="float" min="0.0" optional="True" value="0.1" label="Maximum allowed precursor RT deviation between identifications." help="(-rt_delta)"/>
-    <param name="param_mz_delta" type="float" min="0.0" optional="True" value="0.1" label="Maximum allowed precursor m/z deviation between identifications." help="(-mz_delta)"/>
-    <param name="param_min_length" type="integer" min="1" optional="True" value="6" label="Minimum of length of peptides for final consensus list" help="(-min_length)"/>
-    <param name="param_use_all_hits" type="boolean" truevalue="-use_all_hits true" falsevalue="-use_all_hits false" checked="false" optional="True" label="If 'true' not only the first hit, but all are used (peptides only)" help="(-use_all_hits)"/>
-    <param name="param_algorithm" type="select" optional="True" value="PEPMatrix" label="Algorithm used for the consensus scoring.#br#ranked -- reorders the hits according to a consensus score computed from the ranks in the input runs. The score is normalized to the interval (0,100). The PeptideIdentifications do not need to have the same score type.#br#average -- reorders the hits according to the average score of the input runs. Make sure to use PeptideIdentifications with the same score type only!#br#PEPMatrix -- calculates a consensus score based on posterior error probabilities and scoring matrices for siimilarity. This algorithm uses the PAM30MS matrix to score sequences not listed by all engines. Make sure to use PeptideIdentifications with score types converted to PEPs only!#br#PEPIons -- calculates a consensus score based on posterior error probabilities and fragment ion siimilarity. Make sure to use PeptideIdentifications with score types converted to PEPs only!#br#Minimum -- calculates a consensus score based on the minimal score. Make sure to use PeptideIdentifications with score types converted to PEPs only!#br#" help="(-algorithm)">
-      <option value="ranked">ranked</option>
-      <option value="average">average</option>
-      <option value="PEPMatrix">PEPMatrix</option>
-      <option value="PEPIons">PEPIons</option>
-      <option value="Minimum">Minimum</option>
-    </param>
-    <param name="param_considered_hits" type="integer" min="1" optional="True" value="10" label="The number of top hits that are used for the consensus scoring." help="(-considered_hits)"/>
-    <param name="param_number_of_runs" type="integer" min="0" optional="True" value="0" label="The number of runs used as input. This information is used in 'Ranked' and 'Average' to compute the new scores. If not given, the number of input identifications is taken." help="(-number_of_runs)"/>
-    <param name="param_MinNumberOfFragments" type="integer" min="0" optional="True" value="2" label="The minimal number of similar (between two suggested sequences) fragment ion masses that is necessary to evaluate the shared peak count similarity (SPC)." help="(-MinNumberOfFragments)"/>
-    <param name="param_common" type="float" min="0.0" max="1.1" optional="True" value="1.1" label="Similarity threshold to accept the best score. E.g. for a given spectrum: engine 1 -&gt; pep 1 with score x1 and engine2 -&gt; pep2 with score x2. The better score from {x1,x2} will be used if the degree of similarity between pep1 and pep2 &gt;= common, Note that 0 &lt;= degree of similarity &lt;= 1. Values &gt; 1 will disable this option." help="(-common)"/>
-    <param name="param_common" type="float" min="0.0" max="1.1" optional="True" value="1.1" label="Similarity threshold to accept the best score. E.g. for a given spectrum: engine 1 -&gt; pep 1 with score x1 and engine2 -&gt; pep2 with score x2. The better score from {x1,x2} will be used if the degree of similarity between pep1 and pep2 &gt;= common, Note that 0 &lt;= degree of similarity &lt;= 1. Values &gt; 1 will disable this option." help="(-common)"/>
-    <param name="param_penalty" type="integer" value="5" label="Give the gap penalty (the same penalty will be used for opening and extension) as a positive integer" help="(-penalty)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="output file" format="consensusXML">
-      <change_format>
-        <when input="param_out_type" value="idXML" format="idXML"/>
-        <when input="param_out_type" value="featureXML" format="featureXML"/>
-      </change_format>
-    </data>
-  </outputs>
-  <help>**What it does**
-
-Computes a consensus identification from peptide identifications of several identification engines.
+    <inputs>
+      <param format="xml,consensusxml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
+      <param help="(-rt_delta) " label="[idXML input only] Maximum allowed retention time deviation between identifications belonging to the same spectrum" min="0.0" name="param_rt_delta" optional="True" type="float" value="0.1"/>
+      <param help="(-mz_delta) " label="[idXML input only] Maximum allowed precursor m/z deviation between identifications belonging to the same spectrum" min="0.0" name="param_mz_delta" optional="True" type="float" value="0.1"/>
+      <param help="(-algorithm) &lt;br&gt;* PEPMatrix: Scoring based on posterior error probabilities (PEPs) and peptide sequence similarities (scored by a substitution matrix). Requires PEPs as scores. &lt;br&gt;* PEPIons: Scoring based on posterior error probabilities (PEPs) and fragment ion similarities ('shared peak count'). Requires PEPs as scores. &lt;br&gt;* 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. &lt;br&gt;* 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. &lt;br&gt;* 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. &lt;br&gt;* 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" label="Algorithm used for consensus scoring" name="param_algorithm" optional="True" type="select" value="PEPMatrix">
+        <option value="PEPMatrix">PEPMatrix</option>
+        <option value="PEPIons">PEPIons</option>
+        <option value="best">best</option>
+        <option value="worst">worst</option>
+        <option value="average">average</option>
+        <option value="ranks">ranks</option>
+      </param>
+      <param help="(-considered_hits) " label="The number of top hits in each ID run that are considered for consensus scoring ('0' for all hits)" min="0" name="param_filter_considered_hits" optional="True" type="integer" value="0"/>
+      <param help="(-min_support) " label="For each peptide hit from an ID run, the fraction of other ID runs that must support that hit (otherwise it is removed)" max="1.0" min="0.0" name="param_filter_min_support" optional="True" type="float" value="0.0"/>
+      <param checked="false" falsevalue="" help="(-count_empty) those containing no peptide hit for the current spectrum) when calculating 'min_support'?" label="Count empty ID runs (i.e" name="param_filter_count_empty" optional="True" truevalue="-filter:count_empty" type="boolean"/>
+      <param help="(-mass_tolerance) " label="Maximum difference between fragment masses (in Da) for fragments to be considered 'shared' between peptides" min="0.0" name="param_PEPIons_mass_tolerance" optional="True" type="float" value="0.5"/>
+      <param help="(-min_shared) " label="The minimal number of 'shared' fragments (between two suggested peptides) that is necessary to evaluate the similarity based on shared peak count (SPC)" min="1" name="param_PEPIons_min_shared" optional="True" type="integer" value="2"/>
+      <param help="(-matrix) " label="Substitution matrix to use for alignment-based similarity scoring" name="param_PEPMatrix_matrix" optional="True" type="select" value="identity">
+        <option value="identity">identity</option>
+        <option value="PAM30MS">PAM30MS</option>
+      </param>
+      <param help="(-penalty) " label="Alignment gap penalty (the same value is used for gap opening and extension)" min="1" name="param_PEPMatrix_penalty" optional="True" type="integer" value="5"/>
+      <expand macro="advanced_options">
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="input" metadata_source="param_in" name="param_out"/>
+    </outputs>
+    <help>Computes a consensus of peptide identifications of several identification engines.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConsensusID.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConsensusID.html</help>
+  </tool>