diff omssa.xml @ 7:51f6c6446e69 draft

Docker support and update for protk 1.4

--- a/omssa.xml	Sat Jun 14 18:01:42 2014 -0400
+++ b/omssa.xml	Thu Mar 26 20:04:12 2015 -0400
@@ -1,7 +1,8 @@
-<tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.0.1">
+<tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.1.0">
 
    <requirements>
-	    <requirement type="package" version="1.3">protk</requirement>
+        <container type="docker">iracooke/protk-1.4.1</container>
+	    <requirement type="package" version="1.4">protk</requirement>
     	<requirement type="package" version="2.1.9">omssa</requirement>
     	<requirement type="package" version="2.2.29">blast+</requirement>
    </requirements>
@@ -59,7 +60,7 @@
 		<conditional name="database">
 			<param name="source_select" type="select" label="Database source">
 				<option value="built_in">Built-In</option>
-				<option value="input_ref">Uploaded fasta file</option>
+				<option selected="true" value="input_ref">Uploaded fasta file</option>
 			</param>
 			<when value="built_in">
 				<param name="dbkey" type="select" format="text" >
@@ -98,7 +99,7 @@
 			<label>Missed Cleavages Allowed</label>
 		    <option value="0">0</option>		
 			<option value="1">1</option>
-			<option value="2">2</option>
+			<option selected="true" value="2">2</option>
 		</param>
 
 		<param name="enzyme" type="select" format="text">
@@ -130,12 +131,12 @@
 			<option value="24">Semi-Glu-C</option>
 		</param>
 
-		<param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/>
-		<param name="max_hit_expect" help="Expect values less than this are considered to be hits. Use a large value, eg 10000 when results will be processed downstream with Peptide Prophet" type="float" value="1.0" min="0" max="10000000" label="Maximum Expect value allowed in the hit list"/><!-- -he-->
+		<param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.5" min="0" max="10000" label="Fragment ion tolerance"/>
+		<param name="max_hit_expect" help="Expect values less than this are considered to be hits. Use a large value, eg 10000 when results will be processed downstream with Peptide Prophet" type="float" value="10000.0" min="0" max="10000000" label="Maximum Expect value allowed in the hit list"/><!-- -he-->
 		<param name="intensity_cut_off" help="Peak intensity cut-off as a fraction of maximum peak intensity" type="float" value="0.0005" min="0" max="1" label="Peak intensity cut-off"/><!-- -ci-->
 
 
-		<param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/>
+		<param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/>
 		<param name="precursor_tolu" type="select" format="text">
 		    <label>Precursor Ion Tolerance Units</label>
 		    <option value="ppm">ppm</option>		
@@ -155,10 +156,10 @@
 		</param>
 
 		<param name="searched_ions" display="checkboxes" type="select" multiple="true" format="text" label="Ions included in search" help="">
-		    <option selected="true" value="0">a</option>
+		    <option value="0">a</option>
 			<option selected="true" value="1">b</option>
 			<option value="2">c</option>
-			<option selected="true" value="3">x</option>
+			<option value="3">x</option>
 			<option selected="true" value="4">y</option>
 			<option value="5">zdot</option>
 			<option value="10">adot</option>
@@ -172,6 +173,27 @@
 		<data format="raw_pepxml" name="output" metadata_source="input_file" label="omssa_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.pepXML"/>
 	</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="AASequences.fasta" format="fasta"/>
+		    <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d.mgf" format="mgf"/>
+            <param name="max_hit_expect" value="1000"/>
+            <param name="precursor_ion_tol" value="1.2"/>
+            <param name="precursor_tolu" value="Da"/>
+            <param name="fix_mods" value="3"/>
+            <param name="variable_mods" value="1"/>
+
+
+		    <output name="output" format="raw_pepxml">
+		        <assert_contents>
+					<has_text text="VLFSQAQVYELERRFK" />
+		        </assert_contents>
+		    </output>
+		</test>
+	</tests>
+
 	<help>
 **What it does**