diff msgfplus_search.xml @ 9:827f19088303 draft default tip

planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty

--- a/msgfplus_search.xml	Mon Jan 05 17:17:45 2015 -0500
+++ b/msgfplus_search.xml	Tue Oct 20 20:01:22 2015 -0400
@@ -1,8 +1,8 @@
-<tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.3">
+<tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.1.0">
     <description>Run an MSGF+ Search</description>
     <requirements>
-        <container type="docker">simonalpha/protk:1.4.0</container>
-        <requirement type="package" version="1.3">protk</requirement>
+        <container type="docker">iracooke/protk-1.4.3</container>
+        <requirement type="package" version="1.4.3">protk</requirement>
         <requirement type="package" version="20140210">msgfplus</requirement>
         <requirement type="package" version="3_0_4388">proteowizard</requirement>
     </requirements>
@@ -47,8 +47,7 @@
         --num-reported-matches=$num_reported_matches
         --java-mem=$java_mem
 
-        --threads $threads
-
+        --threads "\${GALAXY_SLOTS:-12}"
         #if $pepxml_output_use:
         --pepxml
         #end if
@@ -75,7 +74,7 @@
         </conditional>
         <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/>
         <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple Selection Allowed">
-            <options from_file="msgfplus_mods.loc">
+            <options from_file="msgfplus_mods_var.loc">
                 <column name="name" index="0" />
                 <column name="value" index="2" />
             </options>
@@ -85,7 +84,7 @@
             <param name="custom_mod" type="text" />
         </repeat>
         <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple Selection Allowed">
-            <options from_file="msgfplus_mods.loc">
+            <options from_file="msgfplus_mods_fix.loc">
                 <column name="name" index="0" />
                 <column name="value" index="2" />
             </options>
@@ -155,7 +154,6 @@
         <param name="max_pep_charge" help="" type="integer" value="3" label="Maximum Peptide Charge"/>
         <param name="num_reported_matches" help="Number of matches per spectrum to be reported" type="integer" value="1" label="Num reported matches"/>
         <param name="java_mem" help="Increase this value if you get out of memory errors" type="text" size="80" value="3500M" label="Java Memory Limit"/>
-        <param name="threads" type="integer" value="1" label="Threads" help="Number of threads to use for search."/>        
         <param name="pepxml_output_use" checked="true" type="boolean" label="Convert results to pepXML" help="" truevalue="true" falsevalue="false" />
     </inputs>
     <outputs>
@@ -165,14 +163,23 @@
             </change_format>
         </data>
     </outputs>
+
     <tests>
+        <!-- Just test that the tool runs and produces vaguely correct output -->
         <test>
             <param name="source_select" value="input_ref"/>
-              <param name="fasta_file" value="bsa.fasta"/>
-                  <param name="input_file" value="bsa.mzML"/>
-              <output name="output" file="bsa.mzid" compare="sim_size" delta="600" /> 
+            <param name="fasta_file" value="testdb.fasta" format="fasta"/>
+            <param name="input_file" value="tiny.mzML" format="mzml"/>
+            <param name="precursor_ion_tol" value="200"/>
+            <param name="pepxml_output_use" value="true"/>
+            <output name="output" format="raw_pepxml">
+                <assert_contents>
+                    <has_text text="FALPQYLKTVYQHQKAMKPWIQPKTKVIPYVRYL" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
+
     <help>
 
 **What it does**