# HG changeset patch
# User galaxyp
# Date 1518458341 18000
# Node ID 54be6743323c0c80f7e7db9ca7b1c1300456cf29
# Parent  382cde407f81edabf557dac0e68314891dff1074
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b

diff -r 382cde407f81 -r 54be6743323c IDFilter.xml
--- a/IDFilter.xml	Thu Jan 11 17:51:39 2018 -0500
+++ b/IDFilter.xml	Mon Feb 12 12:59:01 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: [ID Processing]-->
-<tool id="IDFilter" name="IDFilter" version="2.2.0">
+<tool id="IDFilter" name="IDFilter" version="2.3.0">
   <description>Filters results from protein or peptide identification engines based on different criteria.</description>
   <macros>
     <token name="@EXECUTABLE@">IDFilter</token>
@@ -225,7 +225,7 @@
     <param name="param_score_pep" type="float" value="0.0" label="The score which should be reached by a peptide hit to be kept" help="(-pep) "/>
     <param name="param_score_prot" type="float" value="0.0" label="The score which should be reached by a protein hit to be kept" help="(-prot) Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides"/>
     <param name="param_whitelist_proteins" type="data" format="fasta" optional="True" label="Filename of a FASTA file containing protein sequences" help="(-proteins) &lt;br&gt;All peptides that are not referencing a protein in this file are removed. &lt;br&gt;All proteins whose accessions are not present in this file are removed"/>
-    <repeat name="rep_param_whitelist_protein_accessions" min="0" max="1" title="param_whitelist_protein_accessions">
+    <repeat name="rep_param_whitelist_protein_accessions" min="0" title="param_whitelist_protein_accessions">
       <param name="param_whitelist_protein_accessions" type="text" size="30" label="All peptides that do not reference at least one of the provided protein accession are removed" help="(-protein_accessions) &lt;br&gt;Only proteins of the provided list are retained">
         <sanitizer>
           <valid initial="string.printable">
@@ -237,7 +237,7 @@
     </repeat>
     <param name="param_whitelist_peptides" type="data" format="idxml" optional="True" label="Only peptides with the same sequence and modification assignment as any peptide in this file are kept" help="(-peptides) Use with 'whitelist:ignore_modifications' to only compare by sequence. &lt;br&gt;"/>
     <param name="param_whitelist_ignore_modifications" display="radio" type="boolean" truevalue="-whitelist:ignore_modifications" falsevalue="" checked="false" optional="True" label="Compare whitelisted peptides by sequence only" help="(-ignore_modifications) "/>
-    <repeat name="rep_param_whitelist_modifications" min="0" max="1" title="param_whitelist_modifications">
+    <repeat name="rep_param_whitelist_modifications" min="0" title="param_whitelist_modifications">
       <param name="param_whitelist_modifications" type="select" optional="True" label="Keep only peptides with sequences that contain (any of) the selected modification(s)" help="(-modifications) ">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
@@ -2771,7 +2771,7 @@
       </param>
     </repeat>
     <param name="param_blacklist_proteins" type="data" format="fasta" optional="True" label="Filename of a FASTA file containing protein sequences" help="(-proteins) &lt;br&gt;All peptides that are referencing a protein in this file are removed. &lt;br&gt;All proteins whose accessions are present in this file are removed"/>
-    <repeat name="rep_param_blacklist_protein_accessions" min="0" max="1" title="param_blacklist_protein_accessions">
+    <repeat name="rep_param_blacklist_protein_accessions" min="0" title="param_blacklist_protein_accessions">
       <param name="param_blacklist_protein_accessions" type="text" size="30" label="All peptides that reference at least one of the provided protein accession are removed" help="(-protein_accessions) &lt;br&gt;Only proteins not in the provided list are retained">
         <sanitizer>
           <valid initial="string.printable">
@@ -2783,7 +2783,7 @@
     </repeat>
     <param name="param_blacklist_peptides" type="data" format="idxml" optional="True" label="Peptides with the same sequence and modification assignment as any peptide in this file are filtered out" help="(-peptides) Use with 'blacklist:ignore_modifications' to only compare by sequence. &lt;br&gt;"/>
     <param name="param_blacklist_ignore_modifications" display="radio" type="boolean" truevalue="-blacklist:ignore_modifications" falsevalue="" checked="false" optional="True" label="Compare blacklisted peptides by sequence only" help="(-ignore_modifications) "/>
-    <repeat name="rep_param_blacklist_modifications" min="0" max="1" title="param_blacklist_modifications">
+    <repeat name="rep_param_blacklist_modifications" min="0" title="param_blacklist_modifications">
       <param name="param_blacklist_modifications" type="select" optional="True" label="Remove all peptides with sequences that contain (any of) the selected modification(s)" help="(-modifications) ">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
@@ -5318,26 +5318,31 @@
     </repeat>
     <param name="param_digest_fasta" type="data" format="fasta" optional="True" label="Input sequence database in FASTA format" help="(-fasta) "/>
     <param name="param_digest_enzyme" type="select" optional="False" value="Trypsin" label="Specify the digestion enzyme" help="(-enzyme) ">
+      <option value="V8-DE">V8-DE</option>
+      <option value="Asp-N_ambic">Asp-N_ambic</option>
+      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+      <option value="Lys-N">Lys-N</option>
+      <option value="TrypChymo">TrypChymo</option>
+      <option value="leukocyte elastase">leukocyte elastase</option>
       <option value="Formic_acid">Formic_acid</option>
+      <option value="Arg-C">Arg-C</option>
+      <option value="Trypsin/P">Trypsin/P</option>
+      <option value="Trypsin" selected="true">Trypsin</option>
+      <option value="proline endopeptidase">proline endopeptidase</option>
+      <option value="PepsinA">PepsinA</option>
+      <option value="V8-E">V8-E</option>
+      <option value="CNBr">CNBr</option>
+      <option value="no cleavage">no cleavage</option>
+      <option value="Alpha-lytic protease">Alpha-lytic protease</option>
       <option value="unspecific cleavage">unspecific cleavage</option>
-      <option value="V8-DE">V8-DE</option>
-      <option value="PepsinA">PepsinA</option>
+      <option value="Chymotrypsin/P">Chymotrypsin/P</option>
       <option value="Asp-N">Asp-N</option>
-      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-      <option value="Trypsin/P">Trypsin/P</option>
       <option value="2-iodobenzoate">2-iodobenzoate</option>
-      <option value="TrypChymo">TrypChymo</option>
       <option value="Lys-C/P">Lys-C/P</option>
+      <option value="Asp-N/B">Asp-N/B</option>
       <option value="Lys-C">Lys-C</option>
-      <option value="CNBr">CNBr</option>
-      <option value="V8-E">V8-E</option>
-      <option value="proline endopeptidase">proline endopeptidase</option>
       <option value="Chymotrypsin">Chymotrypsin</option>
-      <option value="leukocyte elastase">leukocyte elastase</option>
-      <option value="Asp-N_ambic">Asp-N_ambic</option>
-      <option value="no cleavage">no cleavage</option>
-      <option value="Trypsin" selected="true">Trypsin</option>
-      <option value="Arg-C">Arg-C</option>
+      <option value="Arg-C/P">Arg-C/P</option>
     </param>
     <param name="param_digest_specificity" display="radio" type="select" optional="False" value="full" label="Specificity of the filte" help="(-specificity) ">
       <option value="full" selected="true">full</option>
diff -r 382cde407f81 -r 54be6743323c SKIP_TOOLS_FILE.txt
--- a/SKIP_TOOLS_FILE.txt	Thu Jan 11 17:51:39 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
diff -r 382cde407f81 -r 54be6743323c macros.xml
--- a/macros.xml	Thu Jan 11 17:51:39 2018 -0500
+++ b/macros.xml	Mon Feb 12 12:59:01 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>
diff -r 382cde407f81 -r 54be6743323c readme.md
--- a/readme.md	Thu Jan 11 17:51:39 2018 -0500
+++ b/readme.md	Mon Feb 12 12:59:01 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
diff -r 382cde407f81 -r 54be6743323c tools_blacklist.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools_blacklist.txt	Mon Feb 12 12:59:01 2018 -0500
@@ -0,0 +1,9 @@
+OMSSAAdapter
+MyriMatchAdapter
+PepNovoAdapter
+SeedListGenerator
+SpecLibSearcher
+MapAlignerIdentification
+MapAlignerPoseClustering
+MapAlignerSpectrum
+MapAlignerRTTransformer