diff macros.xml @ 32:ff592231f118 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d

--- a/macros.xml	Wed Jan 18 16:43:44 2017 -0500
+++ b/macros.xml	Wed Jan 25 15:37:43 2017 -0500
@@ -16,6 +16,8 @@
             ### multiple enzymes?
             -enzyme "${enzyme}"
             ### -specificity
+            ### value per enzyme
+            -mc $missed_cleavages
             #set $fixed_mods_str = $fixed_modifications or ''
             #set $variable_mods_str = $variable_modifications or ''
             #if $fixed_mods_str
@@ -26,10 +28,11 @@
             #end if
             -min_charge $min_charge
             -max_charge $max_charge
-            ### value per enzyme
-            -mc $missed_cleavages
             -fi $forward_ion
             -ri $reverse_ion
+            -min_isotope ${min_isotope} 
+            -max_isotope ${max_isotope} 
+
     </token>
     <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>
     <token name="@SEARCHGUI_VERSION@">3.1.4</token>
@@ -106,6 +109,8 @@
             <option value="y" selected="true">y</option>
             <option value="z">z</option>
         </param>
+        <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" />
+        <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" />
     </xml>
 
     <xml name="citations">