diff PeptideIndexer.xml @ 1:6b0add7e424d draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

--- a/PeptideIndexer.xml	Wed Mar 01 12:48:36 2017 -0500
+++ b/PeptideIndexer.xml	Wed Aug 09 09:44:22 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="PeptideIndexer" name="PeptideIndexer" version="2.1.0">
+<tool id="PeptideIndexer" name="PeptideIndexer" version="2.2.0">
   <description>Refreshes the protein references for all peptide hits.</description>
   <macros>
     <token name="@EXECUTABLE@">PeptideIndexer</token>
@@ -25,10 +25,20 @@
   -decoy_string     "$param_decoy_string"
 #end if
 #if $param_decoy_string_position:
-  -decoy_string_position $param_decoy_string_position
+  -decoy_string_position
+  #if " " in str($param_decoy_string_position):
+    "$param_decoy_string_position"
+  #else
+    $param_decoy_string_position
+  #end if
 #end if
 #if $param_missing_decoy_action:
-  -missing_decoy_action $param_missing_decoy_action
+  -missing_decoy_action
+  #if " " in str($param_missing_decoy_action):
+    "$param_missing_decoy_action"
+  #else
+    $param_missing_decoy_action
+  #end if
 #end if
 #if $param_write_protein_sequence:
   -write_protein_sequence
@@ -58,10 +68,20 @@
   -filter_aaa_proteins
 #end if
 #if $param_enzyme_name:
-  -enzyme:name $param_enzyme_name
+  -enzyme:name
+  #if " " in str($param_enzyme_name):
+    "$param_enzyme_name"
+  #else
+    $param_enzyme_name
+  #end if
 #end if
 #if $param_enzyme_specificity:
-  -enzyme:specificity $param_enzyme_specificity
+  -enzyme:specificity
+  #if " " in str($param_enzyme_specificity):
+    "$param_enzyme_specificity"
+  #else
+    $param_enzyme_specificity
+  #end if
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_force:
@@ -98,26 +118,26 @@
     <param name="param_IL_equivalent" display="radio" type="boolean" truevalue="-IL_equivalent" falsevalue="" checked="false" optional="True" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="(-IL_equivalent) "/>
     <param name="param_filter_aaa_proteins" display="radio" type="boolean" truevalue="-filter_aaa_proteins" falsevalue="" checked="false" optional="True" label="In the tolerant search for matches to proteins with ambiguous amino acids (AAAs), rebuild the search database to only consider proteins with AAAs" help="(-filter_aaa_proteins) This may save time if most proteins don't contain AAAs and if there is a significant number of peptides that enter the tolerant search"/>
     <param name="param_enzyme_name" type="select" optional="False" value="Trypsin" label="Enzyme which determines valid cleavage sites -" help="(-name) e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P)">
-      <option value="Lys-C/P">Lys-C/P</option>
-      <option value="unspecific cleavage">unspecific cleavage</option>
-      <option value="Lys-C">Lys-C</option>
-      <option value="Formic_acid">Formic_acid</option>
+      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+      <option value="CNBr">CNBr</option>
+      <option value="Asp-N_ambic">Asp-N_ambic</option>
       <option value="Trypsin" selected="true">Trypsin</option>
-      <option value="V8-DE">V8-DE</option>
+      <option value="Formic_acid">Formic_acid</option>
+      <option value="TrypChymo">TrypChymo</option>
+      <option value="proline endopeptidase">proline endopeptidase</option>
+      <option value="Lys-C/P">Lys-C/P</option>
+      <option value="Chymotrypsin">Chymotrypsin</option>
+      <option value="Arg-C">Arg-C</option>
+      <option value="PepsinA">PepsinA</option>
+      <option value="Asp-N">Asp-N</option>
+      <option value="Trypsin/P">Trypsin/P</option>
+      <option value="Lys-C">Lys-C</option>
+      <option value="no cleavage">no cleavage</option>
+      <option value="unspecific cleavage">unspecific cleavage</option>
       <option value="2-iodobenzoate">2-iodobenzoate</option>
-      <option value="Asp-N_ambic">Asp-N_ambic</option>
-      <option value="no cleavage">no cleavage</option>
       <option value="V8-E">V8-E</option>
       <option value="leukocyte elastase">leukocyte elastase</option>
-      <option value="CNBr">CNBr</option>
-      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-      <option value="TrypChymo">TrypChymo</option>
-      <option value="PepsinA">PepsinA</option>
-      <option value="Asp-N">Asp-N</option>
-      <option value="Arg-C">Arg-C</option>
-      <option value="proline endopeptidase">proline endopeptidase</option>
-      <option value="Chymotrypsin">Chymotrypsin</option>
-      <option value="Trypsin/P">Trypsin/P</option>
+      <option value="V8-DE">V8-DE</option>
     </param>
     <param name="param_enzyme_specificity" display="radio" type="select" optional="False" value="full" label="Specificity of the enzyme" help="(-specificity) &lt;br&gt;  'full': both internal cleavage sites must match. &lt;br&gt;  'semi': one of two internal cleavage sites must match. &lt;br&gt;  'none': allow all peptide hits no matter their context. Therefore, the enzyme chosen does not play a role here">
       <option value="full" selected="true">full</option>