# HG changeset patch
# User galaxyp
# Date 1500072596 14400
# Node ID 94a245bf5e72c9c849cd9a9667707422b0646e4a
# Parent  77528cc89102b47ecd3fb6e476ab8cde387e56a2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit daf6dfc513ede9b890125d9fff2c2657d834eea9

diff -r 77528cc89102 -r 94a245bf5e72 IDFileConverter.xml
--- a/IDFileConverter.xml	Thu Apr 27 12:52:55 2017 -0400
+++ b/IDFileConverter.xml	Fri Jul 14 18:49:56 2017 -0400
@@ -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 CTD2Galaxy.-->
 <!--Proposed Tool Section: [ID Processing]-->
-<tool id="IDFileConverter" name="IDFileConverter" version="2.1.0">
+<tool id="IDFileConverter" name="IDFileConverter" version="2.2.0">
   <description>Converts identification engine file formats.</description>
   <macros>
     <token name="@EXECUTABLE@">IDFileConverter</token>
@@ -11,68 +11,71 @@
   <expand macro="stdio"/>
   <expand macro="requirements"/>
   <command><![CDATA[
-   
-  ## check input file type
-  #set $in_type = $param_in.ext
+
+## check input file type
+#set $in_type = $param_in.ext
 
-  ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files
-  ln -s '$param_in' 'param_in.${in_type}' &&
-  
-  IDFileConverter
+## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files
+ln -s '$param_in' 'param_in.${in_type}' &&
+
+IDFileConverter
 
-  #if $param_in:
-    -in 'param_in.${in_type}'
-  #end if
-  #if $param_out:
-    -out $param_out
-  #end if
-  #if $param_out_type:
-    -out_type
-    #if " " in str($param_out_type):
-      "$param_out_type"
-    #else
-      $param_out_type
-    #end if
-  #end if
-  #if $param_mz_file:
-    -mz_file $param_mz_file
+#if $param_in:
+  -in 'param_in.${in_type}'
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_out_type:
+  -out_type
+  #if " " in str($param_out_type):
+    "$param_out_type"
+  #else
+    $param_out_type
   #end if
-  #if $param_mz_name:
-    -mz_name     "$param_mz_name"
-  #end if
-  #if $param_peptideprophet_analyzed:
-    -peptideprophet_analyzed
+#end if
+#if $param_mz_file:
+  -mz_file $param_mz_file
+#end if
+#if $param_mz_name:
+  -mz_name     "$param_mz_name"
+#end if
+#if $param_peptideprophet_analyzed:
+  -peptideprophet_analyzed
+#end if
+#if $param_score_type:
+  -score_type
+  #if " " in str($param_score_type):
+    "$param_score_type"
+  #else
+    $param_score_type
   #end if
-  #if $param_score_type:
-    -score_type
-    #if " " in str($param_score_type):
-      "$param_score_type"
-    #else
-      $param_score_type
-    #end if
-  #end if
-  #if $adv_opts.adv_opts_selector=='advanced':
-      #if $adv_opts.param_ignore_proteins_per_peptide:
-    -ignore_proteins_per_peptide
-  #end if
-      #if $adv_opts.param_scan_regex:
-    -scan_regex     "$adv_opts.param_scan_regex"
-  #end if
-      #if $adv_opts.param_force:
-    -force
-  #end if
-  #end if
- ]]>
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_ignore_proteins_per_peptide:
+  -ignore_proteins_per_peptide
+#end if
+    #if $adv_opts.param_scan_regex:
+  -scan_regex     "$adv_opts.param_scan_regex"
+#end if
+    #if $adv_opts.param_no_spectra_data_override:
+  -no_spectra_data_override
+#end if
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+]]>
 </command>
   <inputs>
-    <param name="param_in" type="data" format="tabular,mzid,pepxml,idxml" optional="False" label="Input file or directory containing the data to convert" help="(-in) This may be: &lt;br&gt;- a single file in a multi-purpose XML format (pepXML, protXML, idXML, mzid), &lt;br&gt;- a single file in a search engine-specific format (Mascot: mascotXML, OMSSA: omssaXML, X! Tandem: xml, Percolator: psms), &lt;br&gt;- a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits), &lt;br&gt;- for Sequest results, a directory containing .out files. &lt;br&gt;"/>
+    <param name="param_in" type="data" format="pepxml,protXML,mascotXML,omssaXML,xml,psms,tabular,idxml,mzid" optional="False" label="Input file or directory containing the data to convert" help="(-in) This may be: &lt;br&gt;- a single file in a multi-purpose XML format (pepXML, protXML, idXML, mzid), &lt;br&gt;- a single file in a search engine-specific format (Mascot: mascotXML, OMSSA: omssaXML, X! Tandem: xml, Percolator: psms), &lt;br&gt;- a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits), &lt;br&gt;- for Sequest results, a directory containing .out files. &lt;br&gt;"/>
     <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type (default: determined from file extension)" help="(-out_type) ">
       <option value="idXML">idXML</option>
       <option value="mzid">mzid</option>
       <option value="pepXML">pepXML</option>
       <option value="FASTA">FASTA</option>
     </param>
-    <param name="param_mz_file" type="data" format="mzxml,mzml" optional="True" label="[pepXML, Sequest, Mascot, X! Tandem, Percolator only] Retention times will be looked up in this file" help="(-mz_file) "/>
+    <param name="param_mz_file" type="data" format="mzml,mzxml,mzData" optional="True" label="[pepXML, Sequest, Mascot, X! Tandem, mzid, Percolator only] Retention times and native spectrum ids (spectrum_references) will be looked up in this file" help="(-mz_file) "/>
     <param name="param_mz_name" type="text" size="30" label="[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute)" help="(-mz_name) Only necessary if different from 'mz_file'">
       <sanitizer>
         <valid initial="string.printable">
@@ -97,6 +100,7 @@
           </valid>
         </sanitizer>
       </param>
+      <param name="param_no_spectra_data_override" display="radio" type="boolean" truevalue="-no_spectra_data_override" falsevalue="" checked="false" optional="True" label="[+mz_file only] Setting this flag will avoid overriding 'spectra_data' in ProteinIdentifications if mz_file is given and 'spectrum_reference's are added/updated" help="(-no_spectra_data_override) Use only if you are sure it is absolutely the same mz_file as used for identification"/>
       <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
     </expand>
   </inputs>
diff -r 77528cc89102 -r 94a245bf5e72 macros.xml
--- a/macros.xml	Thu Apr 27 12:52:55 2017 -0400
+++ b/macros.xml	Fri Jul 14 18:49:56 2017 -0400
@@ -2,7 +2,7 @@
 <macros>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="2.1">openms</requirement>
+      <requirement type="package" version="2.2">openms</requirement>
       <requirement type="package" version="15.12.15.2">xtandem</requirement>
       <requirement type="package" version="1.0">fido</requirement>
       <requirement type="package" version="2016.10.26">msgf_plus</requirement>
diff -r 77528cc89102 -r 94a245bf5e72 readme.md
--- a/readme.md	Thu Apr 27 12:52:55 2017 -0400
+++ b/readme.md	Fri Jul 14 18:49:56 2017 -0400
@@ -14,15 +14,29 @@
 Generating OpenMS wrappers
 ==========================
 
- * install OpenMS (you can do this automatically through the Tool Shed)
+ * install OpenMS (you can do this automatically through Conda)
  * create a folder called CTD
- * inside of your new installed openms/bin folder, execute the following command:
+ * if you installed openms as a binary in a specific directory, execute the following command in the `openms/bin` directory:
     
     ```bash
     for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done;
     ```
     
- * `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`).
+ * if there is no binary release (e.g. as with version 2.2), download and unpack the Conda package, find the `bin` folder and create a list of the tools as follow:
+ 
+    ```bash
+    ls >> tools.txt
+    ```
+    
+ * search for the `bin` folder of your conda environment containing OpenMS and do:
+ 
+    ```bash
+    while read p; do
+        ./PATH/TO/BIN/$p -write_ctd /PATH/TO/YOUR/CTD;
+    done <tools.txt
+    ```
+    
+ * You should have all CTD files now. `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`).
 
  * clone or install CTDopts
 
@@ -42,7 +56,7 @@
     git clone https://github.com/WorkflowConversion/CTD2Galaxy.git
     ```
     
- * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository.
+ * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository. You might have to install `libxslt` and `lxml` to run it.
 
     ```bash
     python generator.py \ 
diff -r 77528cc89102 -r 94a245bf5e72 tool.conf
--- a/tool.conf	Thu Apr 27 12:52:55 2017 -0400
+++ b/tool.conf	Fri Jul 14 18:49:56 2017 -0400
@@ -6,13 +6,7 @@
     <tool file="openms/RTModel.xml"/>
     <tool file="openms/RTPredict.xml"/>
   </section>
-  <section id="section-id-DEFAULT" name="DEFAULT">
-    <tool file="openms/OpenSwathFileSplitter.xml"/>
-    <tool file="openms/OpenSwathMzMLFileCacher.xml"/>
-  </section>
   <section id="section-id-TargetedExperiments" name="Targeted Experiments">
-    <tool file="openms/ConvertTraMLToTSV.xml"/>
-    <tool file="openms/ConvertTSVToTraML.xml"/>
     <tool file="openms/InclusionExclusionListCreator.xml"/>
     <tool file="openms/MRMMapper.xml"/>
     <tool file="openms/OpenSwathAnalyzer.xml"/>
@@ -22,13 +16,17 @@
     <tool file="openms/OpenSwathDecoyGenerator.xml"/>
     <tool file="openms/OpenSwathDIAPreScoring.xml"/>
     <tool file="openms/OpenSwathFeatureXMLToTSV.xml"/>
+    <tool file="openms/OpenSwathFileSplitter.xml"/>
+    <tool file="openms/OpenSwathMzMLFileCacher.xml"/>
     <tool file="openms/OpenSwathRewriteToFeatureXML.xml"/>
     <tool file="openms/OpenSwathRTNormalizer.xml"/>
     <tool file="openms/PrecursorIonSelector.xml"/>
+    <tool file="openms/TargetedFileConverter.xml"/>
   </section>
   <section id="section-id-Utilities" name="Utilities">
     <tool file="openms/AccurateMassSearch.xml"/>
     <tool file="openms/CVInspector.xml"/>
+    <tool file="openms/DatabaseFilter.xml"/>
     <tool file="openms/DecoyDatabase.xml"/>
     <tool file="openms/DeMeanderize.xml"/>
     <tool file="openms/Digestor.xml"/>
@@ -44,7 +42,6 @@
     <tool file="openms/LabeledEval.xml"/>
     <tool file="openms/LowMemPeakPickerHiRes.xml"/>
     <tool file="openms/LowMemPeakPickerHiRes_RandomAccess.xml"/>
-    <tool file="openms/MapAlignmentEvaluation.xml"/>
     <tool file="openms/MassCalculator.xml"/>
     <tool file="openms/MetaboliteSpectralMatcher.xml"/>
     <tool file="openms/MetaProSIP.xml"/>
@@ -62,12 +59,14 @@
     <tool file="openms/QCMerger.xml"/>
     <tool file="openms/QCShrinker.xml"/>
     <tool file="openms/RNPxl.xml"/>
+    <tool file="openms/RNPxlSearch.xml"/>
     <tool file="openms/RNPxlXICFilter.xml"/>
     <tool file="openms/RTEvaluation.xml"/>
     <tool file="openms/SemanticValidator.xml"/>
     <tool file="openms/SequenceCoverageCalculator.xml"/>
     <tool file="openms/SimpleSearchEngine.xml"/>
     <tool file="openms/SpecLibCreator.xml"/>
+    <tool file="openms/SpectraSTSearchAdapter.xml"/>
     <tool file="openms/SvmTheoreticalSpectrumGeneratorTrainer.xml"/>
     <tool file="openms/TICCalculator.xml"/>
     <tool file="openms/TopPerc.xml"/>
@@ -78,6 +77,7 @@
     <tool file="openms/ConsensusMapNormalizer.xml"/>
     <tool file="openms/FeatureLinkerLabeled.xml"/>
     <tool file="openms/FeatureLinkerUnlabeled.xml"/>
+    <tool file="openms/FeatureLinkerUnlabeledKD.xml"/>
     <tool file="openms/FeatureLinkerUnlabeledQT.xml"/>
     <tool file="openms/MapRTTransformer.xml"/>
   </section>
@@ -154,9 +154,7 @@
     <tool file="openms/FeatureFinderMultiplex.xml"/>
     <tool file="openms/FeatureFinderSuperHirn.xml"/>
     <tool file="openms/IsobaricAnalyzer.xml"/>
-    <tool file="openms/ITRAQAnalyzer.xml"/>
     <tool file="openms/ProteinQuantifier.xml"/>
     <tool file="openms/ProteinResolver.xml"/>
-    <tool file="openms/TMTAnalyzer.xml"/>
   </section>
 </toolbox>