diff macros.xml @ 43:7963340ab569 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad

--- a/macros.xml	Tue Jan 23 08:48:07 2018 -0500
+++ b/macros.xml	Mon Mar 05 10:09:34 2018 -0500
@@ -2,7 +2,7 @@
     <xml name="stdio">
         <stdio>
             <exit_code range="1:" level="fatal" description="Job Failed" />
-            <regex match="java.*Exception" level="fatal" description="Java Exception"/> 
+            <regex match="java.*Exception" level="fatal" description="Java Exception"/>
             <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
             <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
         </stdio>
@@ -17,8 +17,8 @@
             -max_charge $precursor_options.max_charge
             -fi $precursor_options.forward_ion
             -ri $precursor_options.reverse_ion
-            -min_isotope ${precursor_options.min_isotope} 
-            -max_isotope ${precursor_options.max_isotope} 
+            -min_isotope ${precursor_options.min_isotope}
+            -max_isotope ${precursor_options.max_isotope}
             #if $protein_digest_options.digestion.cleavage == 'default':
               ## -enzyme "Trysin"
               -mc $protein_digest_options.digestion.missed_cleavages
@@ -30,7 +30,7 @@
                   #silent $enzymes.append(str($digest.enzyme))
                   #silent $missed_cleavages.append(str($digest.missed_cleavages))
                   ## #silent $specificities.append(str($digest.specificity))
-              #end for    
+              #end for
               -enzyme "#echo ','.join($enzymes)#"
               -mc "#echo ','.join($missed_cleavages)#"
               ## -specificity "#echo ','.join($specificities)#"
@@ -41,7 +41,7 @@
             #set $fixed_mods_str = $protein_modification_options.fixed_modifications or ''
             #set $variable_mods_str = $protein_modification_options.variable_modifications or ''
             #if $fixed_mods_str
-                -fixed_mods "$fixed_mods_str" 
+                -fixed_mods "$fixed_mods_str"
             #end if
             #if $variable_mods_str
                 -variable_mods "$variable_mods_str"
@@ -79,7 +79,7 @@
                             <option value="Trypsin + CNBr">Trypsin + CNBr</option>
                             <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
                             <option value="Trypsin, no P rule">Trypsin, no P rule</option>
-                            <option value="Whole Protein">Whole Protein</option> 
+                            <option value="Whole Protein">Whole Protein</option>
                             <option value="Asp-N">Asp-N</option>
                             <option value="Glu-C">Glu-C</option>
                             <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
@@ -129,7 +129,7 @@
             <param name="fragment_tol_units" type="select" label="Fragment Tolerance Units"
                 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
                 <option value="1">Parts per million (ppm)</option>
-                <option value="0">Daltons</option>
+                <option value="0" selected="true">Daltons</option>
             </param>
             <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance"
                 help="Provide error value for fragment ions, based on instrument used"/>
@@ -157,7 +157,7 @@
                     <column name="value" index="0" />
                 </options>
             </param>
-            <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" 
+            <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true"
                 help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
                 <options from_file="searchgui_mods.loc">
                     <column name="name" index="0" />