Mercurial > repos > galaxyp > openms_simplesearchengine

changeset 5:242ba7640825 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author galaxyp
date Mon, 12 Feb 2018 12:54:18 -0500
parents a62e8d76a463
children a3b09a079597
files SKIP_TOOLS_FILE.txt SimpleSearchEngine.xml macros.xml readme.md tools_blacklist.txt
diffstat 5 files changed, 65 insertions(+), 39 deletions(-) [+]
line wrap: on
line diff
--- a/SKIP_TOOLS_FILE.txt	Thu Jan 11 18:00:11 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-OMSSAAdapter
-MyriMatchAdapter
-PepNovoAdapter
-SeedListGenerator
-SpecLibSearcher
-MapAlignerIdentification
-MapAlignerPoseClustering
-MapAlignerSpectrum
-MapAlignerRTTransformer
--- a/SimpleSearchEngine.xml	Thu Jan 11 18:00:11 2018 -0500
+++ b/SimpleSearchEngine.xml	Mon Feb 12 12:54:18 2018 -0500
@@ -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.-->
+<!--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: [Utilities]-->
-<tool id="SimpleSearchEngine" name="SimpleSearchEngine" version="2.2.0">
+<tool id="SimpleSearchEngine" name="SimpleSearchEngine" version="2.3.0">
   <description>Annotates MS/MS spectra using SimpleSearchEngine.</description>
   <macros>
     <token name="@EXECUTABLE@">SimpleSearchEngine</token>
@@ -40,6 +40,17 @@
     $param_precursor_mass_tolerance_unit
   #end if
 #end if
+
+#if $rep_param_precursor_isotopes:
+-precursor:isotopes
+  #for token in $rep_param_precursor_isotopes:
+    #if " " in str(token):
+      "$token.param_precursor_isotopes"
+    #else
+      $token.param_precursor_isotopes
+    #end if
+  #end for
+#end if
 #if $param_fragment_mass_tolerance:
   -fragment:mass_tolerance $param_fragment_mass_tolerance
 #end if
@@ -104,38 +115,53 @@
     <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/>
     <param name="param_database" type="data" format="fasta" optional="False" label="input file" help="(-database) "/>
     <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The enzyme used for peptide digestion" help="(-enzyme) ">
-      <option value="unspecific cleavage">unspecific cleavage</option>
+      <option value="leukocyte elastase">leukocyte elastase</option>
+      <option value="Arg-C/P">Arg-C/P</option>
+      <option value="V8-E">V8-E</option>
+      <option value="2-iodobenzoate">2-iodobenzoate</option>
+      <option value="Asp-N/B">Asp-N/B</option>
+      <option value="PepsinA">PepsinA</option>
       <option value="Trypsin" selected="true">Trypsin</option>
-      <option value="leukocyte elastase">leukocyte elastase</option>
       <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-      <option value="Asp-N_ambic">Asp-N_ambic</option>
-      <option value="2-iodobenzoate">2-iodobenzoate</option>
-      <option value="PepsinA">PepsinA</option>
-      <option value="CNBr">CNBr</option>
-      <option value="Chymotrypsin">Chymotrypsin</option>
+      <option value="no cleavage">no cleavage</option>
       <option value="Arg-C">Arg-C</option>
-      <option value="Formic_acid">Formic_acid</option>
-      <option value="Asp-N">Asp-N</option>
-      <option value="Lys-C">Lys-C</option>
-      <option value="TrypChymo">TrypChymo</option>
+      <option value="CNBr">CNBr</option>
       <option value="V8-DE">V8-DE</option>
-      <option value="no cleavage">no cleavage</option>
-      <option value="V8-E">V8-E</option>
+      <option value="Chymotrypsin">Chymotrypsin</option>
+      <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+      <option value="Lys-C/P">Lys-C/P</option>
+      <option value="unspecific cleavage">unspecific cleavage</option>
+      <option value="Asp-N">Asp-N</option>
+      <option value="Trypsin/P">Trypsin/P</option>
+      <option value="Lys-N">Lys-N</option>
+      <option value="TrypChymo">TrypChymo</option>
+      <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+      <option value="Asp-N_ambic">Asp-N_ambic</option>
       <option value="proline endopeptidase">proline endopeptidase</option>
-      <option value="Trypsin/P">Trypsin/P</option>
-      <option value="Lys-C/P">Lys-C/P</option>
+      <option value="Formic_acid">Formic_acid</option>
+      <option value="Lys-C">Lys-C</option>
     </param>
     <param name="param_precursor_mass_tolerance" type="float" value="10.0" label="Width of precursor mass tolerance window" help="(-mass_tolerance) "/>
     <param name="param_precursor_mass_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of precursor mass tolerance" help="(-mass_tolerance_unit) ">
       <option value="ppm" selected="true">ppm</option>
       <option value="Da">Da</option>
     </param>
+    <repeat name="rep_param_precursor_isotopes" min="0" max="1" title="param_precursor_isotopes">
+      <param name="param_precursor_isotopes" type="text" size="30" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(-isotopes) (E.g.: 1 = prec. may be misassigned to first isotopic peak)">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
     <param name="param_fragment_mass_tolerance" type="float" value="10.0" label="Fragment mass tolerance" help="(-mass_tolerance) "/>
     <param name="param_fragment_mass_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of fragment m" help="(-mass_tolerance_unit) ">
       <option value="ppm" selected="true">ppm</option>
       <option value="Da">Da</option>
     </param>
-    <repeat name="rep_param_modifications_fixed" min="0" max="1" title="param_modifications_fixed">
+    <repeat name="rep_param_modifications_fixed" min="0" title="param_modifications_fixed">
       <param name="param_modifications_fixed" type="select" optional="True" label="Fixed modifications, specified using UniMod (www.unimod.org) terms," help="(-fixed) e.g. 'Carbamidomethyl (C)'">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
@@ -2668,7 +2694,7 @@
         <option value="trifluoro (L)">trifluoro (L)</option>
       </param>
     </repeat>
-    <repeat name="rep_param_modifications_variable" min="0" max="1" title="param_modifications_variable">
+    <repeat name="rep_param_modifications_variable" min="0" title="param_modifications_variable">
       <param name="param_modifications_variable" type="select" optional="True" label="Variable modifications, specified using UniMod (www.unimod.org) terms," help="(-variable) e.g. 'Oxidation (M)'">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
@@ -5218,5 +5244,5 @@
   <help>Annotates MS/MS spectra using SimpleSearchEngine.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/classSimpleSearchEngine.html</help>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SimpleSearchEngine.html</help>
 </tool>
--- a/macros.xml	Thu Jan 11 18:00:11 2018 -0500
+++ b/macros.xml	Mon Feb 12 12:54:18 2018 -0500
@@ -2,10 +2,10 @@
 <macros>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="2.2">openms</requirement>
+      <requirement type="package" version="2.3">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>
+      <requirement type="package" version="2017.07.21">msgf_plus</requirement>
       <yield/>
     </requirements>
   </xml>
--- a/readme.md	Thu Jan 11 18:00:11 2018 -0500
+++ b/readme.md	Mon Feb 12 12:54:18 2018 -0500
@@ -53,29 +53,29 @@
  * clone or install CTD2Galaxy
 
     ```bash
-    git clone https://github.com/WorkflowConversion/CTD2Galaxy.git
+    git clone https://github.com/WorkflowConversion/CTDConverter.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. You might have to install `libxslt` and `lxml` to run it.
+ * If you have CTDopts and CTDConverter 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. Further information can be found on the CTDConverter page.
 
     ```bash
-    python generator.py \ 
+    python convert.py galaxy \ 
     -i /PATH/TO/YOUR/CTD/*.ctd \
     -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \
     -d datatypes_conf.xml -g openms \
     -b version log debug test no_progress threads \
      in_type executable myrimatch_executable \
      fido_executable fidocp_executable \
-     omssa_executable pepnovo_executable \
+     omssa_executable pepnovo_e xecutable \
      xtandem_executable param_model_directory \
      java_executable java_memory java_permgen \
      r_executable rt_concat_trafo_out param_id_pool \
     -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \
-    -s PATH/TO/SKIP_TOOLS_FILES.txt
+    -s PATH/TO/tools_blacklist.txt
     ```
 
 
- * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example:
+ * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. Some of these tools might already be deprecated and the files might not exist:
 
     ```
     sed -i '13 a\-fido_executable Fido' wrappers/FidoAdapter.xml
@@ -171,8 +171,8 @@
     ```
     
 
- * These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in
-   by the automatic conversion step and are therefore in `SKIP_TOOLS_FILES.txt`:
+ * `This section might not be up to date. It might be worth trying if these tools will run now.` These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in
+   by the automatic conversion step and are therefore in `tools_blacklist.txt`:
     * SeedListGenerator
     * SpecLibSearcher
     * MapAlignerIdentification
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools_blacklist.txt	Mon Feb 12 12:54:18 2018 -0500
@@ -0,0 +1,9 @@
+OMSSAAdapter
+MyriMatchAdapter
+PepNovoAdapter
+SeedListGenerator
+SpecLibSearcher
+MapAlignerIdentification
+MapAlignerPoseClustering
+MapAlignerSpectrum
+MapAlignerRTTransformer