Mercurial > repos > galaxyp > openms_msgfplusadapter

changeset 6:2244cc0ac5cd 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 13:05:04 -0500
parents a407b6790342
children f0761deada39
files MSGFPlusAdapter.xml SKIP_TOOLS_FILE.txt macros.xml readme.md tools_blacklist.txt
diffstat 5 files changed, 35 insertions(+), 35 deletions(-) [+]
line wrap: on
line diff
--- a/MSGFPlusAdapter.xml	Thu Jan 11 18:12:12 2018 -0500
+++ b/MSGFPlusAdapter.xml	Mon Feb 12 13:05:04 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: [Identification]-->
-<tool id="MSGFPlusAdapter" name="MSGFPlusAdapter" version="2.2.0">
+<tool id="MSGFPlusAdapter" name="MSGFPlusAdapter" version="2.3.0">
   <description>MS/MS database search using MS-GF+.</description>
   <macros>
     <token name="@EXECUTABLE@">MSGFPlusAdapter</token>
@@ -10,7 +10,7 @@
   <expand macro="references"/>
   <expand macro="stdio"/>
   <expand macro="requirements"/>
-  <command><![CDATA[
+<command><![CDATA[
 
  ## check input file type
  #set $in_type = $param_in.ext
@@ -143,13 +143,13 @@
   -force
 #end if
 #end if
-]]>
+ ]]>
 </command>
   <inputs>
     <param name="param_in" type="data" format="mzml,mzxml,mgf,ms2" optional="False" label="Input file (MS-GF+ parameter '-s')" help="(-in) "/>
     <param name="param_database" type="data" format="fasta" optional="False" label="Protein sequence database (FASTA file; MS-GF+ parameter '-d')" help="(-database) Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'"/>
     <param name="param_add_decoys" display="radio" type="boolean" truevalue="-add_decoys" falsevalue="" checked="false" optional="True" label="Create decoy proteins (reversed sequences) and append them to the database for the search (MS-GF+ parameter '-tda')" help="(-add_decoys) This allows the calculation of FDRs, but should only be used if the database does not already contain decoys"/>
-    <param name="param_precursor_mass_tolerance" type="float" value="20.0" label="Precursor monoisotopic mass tolerance (MS-GF+ parameter '-t')" help="(-precursor_mass_tolerance) "/>
+    <param name="param_precursor_mass_tolerance" type="float" value="10.0" label="Precursor monoisotopic mass tolerance (MS-GF+ parameter '-t')" help="(-precursor_mass_tolerance) "/>
     <param name="param_precursor_error_units" display="radio" type="select" optional="False" value="ppm" label="Unit of precursor mass tolerance (MS-GF+ parameter '-t')" help="(-precursor_error_units) ">
       <option value="Da">Da</option>
       <option value="ppm" selected="true">ppm</option>
@@ -174,17 +174,17 @@
       <option value="TOF">TOF</option>
       <option value="Q_Exactive">Q_Exactive</option>
     </param>
-    <param name="param_enzyme" type="select" optional="False" value="trypsin" label="Enzyme used for digestion, or type of cleavage (MS-GF+ parameter '-e')" help="(-enzyme) ">
-      <option value="unspecific">unspecific</option>
-      <option value="trypsin" selected="true">trypsin</option>
-      <option value="chymotrypsin">chymotrypsin</option>
-      <option value="LysC">LysC</option>
-      <option value="LysN">LysN</option>
-      <option value="GluC">GluC</option>
-      <option value="ArgC">ArgC</option>
-      <option value="AspN">AspN</option>
-      <option value="alphaLP">alphaLP</option>
-      <option value="no_cleavage">no_cleavage</option>
+    <param name="param_enzyme" type="select" optional="False" value="Trypsin/P" label="Enzyme used for digestion, or type of cleavage" help="(-enzyme) Note: MS-GF+ does not support blocking rules. (MS-GF+ parameter '-e')">
+      <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+      <option value="Arg-C/P">Arg-C/P</option>
+      <option value="Asp-N/B">Asp-N/B</option>
+      <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+      <option value="Lys-C/P">Lys-C/P</option>
+      <option value="Lys-N">Lys-N</option>
+      <option value="Trypsin/P" selected="true">Trypsin/P</option>
+      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+      <option value="no cleavage">no cleavage</option>
+      <option value="unspecific cleavage">unspecific cleavage</option>
     </param>
     <param name="param_protocol" type="select" optional="False" value="none" label="Labeling or enrichment protocol used, if any (MS-GF+ parameter '-p')" help="(-protocol) ">
       <option value="none" selected="true">none</option>
--- a/SKIP_TOOLS_FILE.txt	Thu Jan 11 18:12:12 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/macros.xml	Thu Jan 11 18:12:12 2018 -0500
+++ b/macros.xml	Mon Feb 12 13:05:04 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 18:12:12 2018 -0500
+++ b/readme.md	Mon Feb 12 13:05:04 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 13:05:04 2018 -0500
@@ -0,0 +1,9 @@
+OMSSAAdapter
+MyriMatchAdapter
+PepNovoAdapter
+SeedListGenerator
+SpecLibSearcher
+MapAlignerIdentification
+MapAlignerPoseClustering
+MapAlignerSpectrum
+MapAlignerRTTransformer