Repository 'openms_xtandemadapter'
hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter

Changeset 1:cd0746ee4796 (2017-08-09)
Previous changeset 0:f9bc00c0ebed (2017-03-01) Next changeset 2:22e9bb7d151a (2017-10-18)
Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
modified:
XTandemAdapter.xml
filetypes.txt
macros.xml
readme.md
tool.conf
removed:
datatypes_conf.xml
b
diff -r f9bc00c0ebed -r cd0746ee4796 XTandemAdapter.xml
--- a/XTandemAdapter.xml Wed Mar 01 12:31:29 2017 -0500
+++ b/XTandemAdapter.xml Wed Aug 09 09:18:43 2017 -0400
[
b'@@ -1,7 +1,7 @@\n <?xml version=\'1.0\' encoding=\'UTF-8\'?>\n <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->\n <!--Proposed Tool Section: [Identification]-->\n-<tool id="XTandemAdapter" name="XTandemAdapter" version="2.1.0">\n+<tool id="XTandemAdapter" name="XTandemAdapter" version="2.2.0">\n   <description>Annotates MS/MS spectra using X! Tandem.</description>\n   <macros>\n     <token name="@EXECUTABLE@">XTandemAdapter</token>\n@@ -19,6 +19,9 @@\n #if $param_out:\n   -out $param_out\n #end if\n+#if $param_xml_out:\n+  -xml_out $param_xml_out\n+#end if\n #if $param_database:\n   -database $param_database\n #end if\n@@ -35,19 +38,26 @@\n   -fragment_mass_tolerance $param_fragment_mass_tolerance\n #end if\n #if $param_precursor_error_units:\n-  -precursor_error_units $param_precursor_error_units\n+  -precursor_error_units\n+  #if " " in str($param_precursor_error_units):\n+    "$param_precursor_error_units"\n+  #else\n+    $param_precursor_error_units\n+  #end if\n #end if\n #if $param_fragment_error_units:\n-  -fragment_error_units $param_fragment_error_units\n-#end if\n-#if $param_min_precursor_charge:\n-  -min_precursor_charge $param_min_precursor_charge\n+  -fragment_error_units\n+  #if " " in str($param_fragment_error_units):\n+    "$param_fragment_error_units"\n+  #else\n+    $param_fragment_error_units\n+  #end if\n #end if\n #if $param_max_precursor_charge:\n   -max_precursor_charge $param_max_precursor_charge\n #end if\n-#if $param_allow_isotope_error:\n-  -allow_isotope_error $param_allow_isotope_error\n+#if $param_no_isotope_error:\n+  -no_isotope_error\n #end if\n \n #if $rep_param_fixed_modifications:\n@@ -71,30 +81,34 @@\n     #end if\n   #end for\n #end if\n-#if $param_missed_cleavages:\n-  -missed_cleavages $param_missed_cleavages\n-#end if\n #if $param_minimum_fragment_mz:\n   -minimum_fragment_mz $param_minimum_fragment_mz\n #end if\n-#if $param_cleavage_site:\n-  -cleavage_site $param_cleavage_site\n+#if $param_enzyme:\n+  -enzyme\n+  #if " " in str($param_enzyme):\n+    "$param_enzyme"\n+  #else\n+    $param_enzyme\n+  #end if\n+#end if\n+#if $param_missed_cleavages:\n+  -missed_cleavages $param_missed_cleavages\n+#end if\n+#if $param_semi_cleavage:\n+  -semi_cleavage\n #end if\n #if $param_output_results:\n-  -output_results $param_output_results\n+  -output_results\n+  #if " " in str($param_output_results):\n+    "$param_output_results"\n+  #else\n+    $param_output_results\n+  #end if\n #end if\n #if $param_max_valid_expect:\n   -max_valid_expect $param_max_valid_expect\n #end if\n-#if $param_refinement:\n-  -refinement\n-#end if\n-#if $param_use_noise_suppression:\n-  -use_noise_suppression\n-#end if\n-#if $param_semi_cleavage:\n-  -semi_cleavage\n-#end if\n #if $adv_opts.adv_opts_selector==\'advanced\':\n     #if $adv_opts.param_force:\n   -force\n@@ -102,10 +116,10 @@\n #end if\n </command>\n   <inputs>\n-    <param name="param_in" type="data" format="mzml" optional="False" label="Input file" help="(-in) "/>\n+    <param name="param_in" type="data" format="mzml" optional="False" label="Input file containing MS2 spectra" help="(-in) "/>\n     <param name="param_database" type="data" format="fasta" optional="False" label="FASTA file or pro file" help="(-database) Non-existing relative file-names are looked up via\'OpenMS.ini:id_db_dir\'"/>\n-    <param name="param_default_config_file" type="data" format="" optional="True" value="CHEMISTRY/XTandem_default_input.xml" label="Default parameters input file, defaulting to the ones in the OpenMS/share folder.All parameters of this adapter take precedence over this file! Use it for parameters not available here!" help="(-default_config_file) "/>\n-    <param name="param_ignore_adapter_param" display="radio" type="boolean" truevalue="-ignore_adapter_param" falsevalue="" checked="false" optional="True" label="The config given in \'default_config_file\' is used exclusively! No matter what other parameters (apart from -in,-out,-database,-xtandem_executable) are sayin'..b'benzoate</option>\n+      <option value="Asp-N">Asp-N</option>\n+      <option value="Arg-C">Arg-C</option>\n+      <option value="V8-E">V8-E</option>\n+      <option value="Lys-C">Lys-C</option>\n       <option value="V8-DE">V8-DE</option>\n-      <option value="Trypsin" selected="true">Trypsin</option>\n-      <option value="Lys-C">Lys-C</option>\n-      <option value="TrypChymo">TrypChymo</option>\n-      <option value="Lys-C/P">Lys-C/P</option>\n+      <option value="leukocyte elastase">leukocyte elastase</option>\n       <option value="Asp-N_ambic">Asp-N_ambic</option>\n+      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>\n+      <option value="Chymotrypsin">Chymotrypsin</option>\n       <option value="Trypsin/P">Trypsin/P</option>\n-      <option value="Formic_acid">Formic_acid</option>\n-      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>\n-      <option value="V8-E">V8-E</option>\n-      <option value="leukocyte elastase">leukocyte elastase</option>\n-      <option value="Arg-C">Arg-C</option>\n-      <option value="Chymotrypsin">Chymotrypsin</option>\n-      <option value="CNBr">CNBr</option>\n-      <option value="Asp-N">Asp-N</option>\n-      <option value="2-iodobenzoate">2-iodobenzoate</option>\n-      <option value="PepsinA">PepsinA</option>\n+      <option value="Trypsin" selected="true">Trypsin</option>\n+      <option value="unspecific cleavage">unspecific cleavage</option>\n+      <option value="Lys-C/P">Lys-C/P</option>\n     </param>\n+    <param name="param_missed_cleavages" type="integer" value="1" label="Number of possible cleavage sites missed by the enzyme" help="(-missed_cleavages) "/>\n+    <param name="param_semi_cleavage" display="radio" type="boolean" truevalue="-semi_cleavage" falsevalue="" checked="false" optional="True" label="Require only peptide end to have a valid cleavage site, not both" help="(-semi_cleavage) "/>\n     <param name="param_output_results" display="radio" type="select" optional="False" value="all" label="Which hits should be reported" help="(-output_results) All, valid ones (passing the E-Value threshold), or stochastic (failing the threshold)">\n       <option value="all" selected="true">all</option>\n       <option value="valid">valid</option>\n       <option value="stochastic">stochastic</option>\n     </param>\n-    <param name="param_max_valid_expect" type="float" value="0.1" label="Maximal E-Value of a hit to be reported (only evaluated if \'output_result\' is \'valid\' or \'stochastic\'" help="(-max_valid_expect) "/>\n-    <param name="param_refinement" display="radio" type="boolean" truevalue="-refinement" falsevalue="" checked="false" optional="True" label="Enable the refinement" help="(-refinement) For most applications (especially when using FDR, PEP approaches) it is NOT recommended to set this flag"/>\n-    <param name="param_use_noise_suppression" display="radio" type="boolean" truevalue="-use_noise_suppression" falsevalue="" checked="false" optional="True" label="Enable the use of the noise suppression routines" help="(-use_noise_suppression) "/>\n-    <param name="param_semi_cleavage" display="radio" type="boolean" truevalue="-semi_cleavage" falsevalue="" checked="false" optional="True" label="If set, both termini must NOT follow the cutting rule" help="(-semi_cleavage) For most applications it is NOT recommended to set this flag"/>\n+    <param name="param_max_valid_expect" type="float" value="0.1" label="Maximal E-Value of a hit to be reported (only evaluated if \'output_result\' is \'valid\' or \'stochastic\')" help="(-max_valid_expect) "/>\n     <expand macro="advanced_options">\n       <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>\n     </expand>\n   </inputs>\n   <outputs>\n     <data name="param_out" format="idxml"/>\n+    <data name="param_xml_out" format="xml"/>\n   </outputs>\n   <help>Annotates MS/MS spectra using X! Tandem.\n \n'
b
diff -r f9bc00c0ebed -r cd0746ee4796 datatypes_conf.xml
--- a/datatypes_conf.xml Wed Mar 01 12:31:29 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,33 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<datatypes>
-  <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications">
-    <datatype extension="mzxml" type="galaxy.datatypes.proteomics:MzXML" mimetype="application/xml"/>
-    <datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml"/>
-    <datatype extension="idxml" type="galaxy.datatypes.proteomics:IdXM" mimetype="application/xml"/>
-    <datatype extension="txt" type="galaxy.datatypes.data:Text"/>
-    <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/>
-    <datatype extension="txt" type="galaxy.datatypes.data:Text"/>
-    <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta"/>
-    <datatype extension="mgf" type="galaxy.datatypes.proteomics:Mgf"/>
-    <datatype extension="mzml" type="galaxy.datatypes.proteomics:MzML" mimetype="application/xml"/>
-    <datatype extension="trafoxml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/>
-    <datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml"/>
-    <datatype extension="msp" type="galaxy.datatypes.proteomics:Msp"/>
-    <datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/>
-    <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/>
-    <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta"/>
-    <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/>
-    <datatype extension="consensusxml" type="galaxy.datatypes.proteomics:ConsensusXML" mimetype="application/xml"/>
-    <datatype extension="xml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/>
-    <datatype extension="mzq" type="galaxy.datatypes.proteomics:MzQuantML" mimetype="application/xml"/>
-    <datatype extension="grid" type="galaxy.datatypes.data:Grid"/>
-    <datatype extension="pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml"/>
-    <datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/>
-    <datatype extension="qcml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/>
-    <datatype extension="featurexml" type="galaxy.datatypes.proteomics:FeatureXML" mimetype="application/xml"/>
-    <datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/>
-    <datatype extension="txt" type="galaxy.datatypes.data:Text"/>
-    <datatype extension="mzid" type="galaxy.datatypes.proteomics:MzIdentML" mimetype="application/xml"/>
-    <datatype extension="txt" type="galaxy.datatypes.data:Text"/>
-  </registration>
-</datatypes>
b
diff -r f9bc00c0ebed -r cd0746ee4796 filetypes.txt
--- a/filetypes.txt Wed Mar 01 12:31:29 2017 -0500
+++ b/filetypes.txt Wed Aug 09 09:18:43 2017 -0400
b
@@ -14,7 +14,7 @@
 consensusXML  consensusxml      galaxy.datatypes.proteomics:ConsensusXML    application/xml
 edta          tabular           galaxy.datatypes.tabular:Tabular 
 featureXML    featurexml        galaxy.datatypes.proteomics:FeatureXML      application/xml
-idXML         idxml             galaxy.datatypes.proteomics:IdXM            application/xml
+idXML         idxml             galaxy.datatypes.proteomics:IdXML           application/xml
 mzML          mzml              galaxy.datatypes.proteomics:MzML            application/xml
 mzXML         mzxml             galaxy.datatypes.proteomics:MzXML           application/xml
 pepXML        pepxml            galaxy.datatypes.proteomics:PepXml          application/xml
@@ -26,4 +26,4 @@
 msp           msp               galaxy.datatypes.proteomics:Msp
 mzid          mzid              galaxy.datatypes.proteomics:MzIdentML       application/xml
 png           png               galaxy.datatypes.images:Png                 image/png
-mgf           mgf               galaxy.datatypes.proteomics:Mgf
\ No newline at end of file
+mgf           mgf               galaxy.datatypes.proteomics:Mgf
b
diff -r f9bc00c0ebed -r cd0746ee4796 macros.xml
--- a/macros.xml Wed Mar 01 12:31:29 2017 -0500
+++ b/macros.xml Wed Aug 09 09:18:43 2017 -0400
b
@@ -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>
b
diff -r f9bc00c0ebed -r cd0746ee4796 readme.md
--- a/readme.md Wed Mar 01 12:31:29 2017 -0500
+++ b/readme.md Wed Aug 09 09:18:43 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
 
@@ -39,10 +53,10 @@
  * clone or install CTD2Galaxy
 
     ```bash
-    git clone https://github.com/blankclemens/CTD2Galaxy.git
+    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. 
+ * 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 \ 
@@ -102,17 +116,32 @@
     [...]
     ]]>
     ```
- * In `PeakPickerHiRes.xml`, the parameter `report_FWHM_unit` has to be put in quotation marks. Look for the following line
+    
+ * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where):
  
-        -algorithm:report_FWHM_unit $param_algorithm_report_FWHM_unit
-     
-   and change it to
+   ```
+    <command><![CDATA[
    
-        -algorithm:report_FWHM_unit "$param_algorithm_report_FWHM_unit"
+      ## 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
 
- * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.:
+      #if $param_in:
+        -in 'param_in.${in_type}'
+      #end if
+
+        [...]
+        ]]>
+    ```
+
+ * In `IDFileConverter.xml` and `FileConverter.xml` add `auto_format="true"` to the output, e.g.:
  
-        <data name="param_out" metadata_source="param_in" auto_format="true"/>
+   - `<data name="param_out" auto_format="true"/>`
+   - `<data name="param_out" metadata_source="param_in" auto_format="true"/>`
         
  * To add an example test case to `DecoyDatabase.xml` add the following after the output section. If standard settings change you might have to adjust the options and/or the test files.
  
b
diff -r f9bc00c0ebed -r cd0746ee4796 tool.conf
--- a/tool.conf Wed Mar 01 12:31:29 2017 -0500
+++ b/tool.conf Wed Aug 09 09:18:43 2017 -0400
b
@@ -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>