# HG changeset patch
# User galaxyp
# Date 1486000391 18000
# Node ID 7ba6c7b12b3070f29cf10b044228cfd1d3409a74
# Parent  caf7e9d77981fcc0486e40b2afe6425cfd035b97
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3

diff -r caf7e9d77981 -r 7ba6c7b12b30 macros.xml
--- a/macros.xml	Tue Dec 13 11:27:46 2016 -0500
+++ b/macros.xml	Wed Feb 01 20:53:11 2017 -0500
@@ -1,8 +1,8 @@
 <macros>
-    <token name="@VERSION@">3.0.10158</token>
+    <token name="@VERSION@">3.0.10246</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3_0_10158">bumbershoot</requirement>
+            <requirement type="package" version="3_0_10246">bumbershoot</requirement>
             <yield/>
         </requirements>
     </xml>
diff -r caf7e9d77981 -r 7ba6c7b12b30 myrimatch.xml
--- a/myrimatch.xml	Tue Dec 13 11:27:46 2016 -0500
+++ b/myrimatch.xml	Wed Feb 01 20:53:11 2017 -0500
@@ -13,7 +13,7 @@
     <command>
 <![CDATA[
         #set $db_name = $ProteinDatabase.display_name.replace(".fasta", "") + ".fasta"
-        #if $OutputFormat.value == "mzid"
+        #if $OutputFormat.value == "mzIdentML"
             #set $output_ext="mzid"
         #else
             #set $output_ext="pepXML"
@@ -75,7 +75,7 @@
           <param name="input" type="data" format="mzml,mzxml,mgf,ms2,mz5" label="Input Raw MS File(s)"/>
           <param argument="-OutputFormat" type="select" label="Output Type" help="The file format to use for results of the search.">
               <option value="pepXML">pepXML</option>
-              <option value="mzid">mzIdentML</option>
+              <option value="mzIdentML">mzIdentML</option>
           </param>
           <param argument="-ProteinDatabase" format="fasta" type="data" label="Protein Database" help="The FASTA protein database to search against. Only amino-acid type FASTA is supported." />
           <param argument="-DecoyPrefix" type="text" label="Decoy Prefix" value="rev_" help="If the protein database contains accessions prefixed with this string, those proteins will be considered decoys. If there are no decoy protein, this prefix will be used to generate an automatic decoy for each target protein. Set this to an empty string to disable automatic decoys." />
@@ -181,7 +181,7 @@
     <outputs>
         <data format="raw_pepxml" name="output" from_work_dir="output">
             <change_format>
-                <when input="OutputFormat" value="mzid" format="mzid" />
+                <when input="OutputFormat" value="mzIdentML" format="mzid" />
             </change_format>
         </data>
     </outputs>
@@ -207,7 +207,7 @@
             <param name="MaxResultRank" value="3" />
             <param name="MonoisotopeAdjustmentSet" value="[-1,2]" />
             <param name="UseSmartPlusThreeModel" value="false" />
-            <output name="output" file="201208-378803-mm.pepXML" lines_diff="12" />
+            <output name="output" file="201208-378803-mm.pepXML" lines_diff="14" />
         </test>
         <test>
             <param name="input" value="input/201208-378803.mzML" />
@@ -221,7 +221,7 @@
             <param name="NumChargeStates" value="3" />
             <param name="MaxResultRank" value="1" />
             <param name="MonoisotopeAdjustmentSet" value="0" />
-            <output name="output" file="201208-378803-mm-15ppm-fully-tryptic.pepXML" lines_diff="12" />
+            <output name="output" file="201208-378803-mm-15ppm-fully-tryptic.pepXML" lines_diff="14" />
         </test>
     </tests>
     <help>