diff snmf.xml @ 5:84becfc8c803 draft

Uploaded

--- a/snmf.xml	Tue Jun 21 19:42:42 2016 -0400
+++ b/snmf.xml	Fri Feb 09 01:30:26 2018 -0500
@@ -1,11 +1,17 @@
 <tool id="snmf" name="sNMF" version="1.2">
 	<description>a population structure from large SNP genotype datasets</description>
 	<requirements>
+                <requirement type="binary">perl</requirement>
+                <requirement type="package" version="1.6.924">perl-bioperl</requirement>
 		<requirement type="package" version="1.2">snmf</requirement>
 		<requirement type="package" version="1.90">plink</requirement>
 	</requirements>
+        <stdio>
+                <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
+                <exit_code range="1:" level="fatal" />
+        </stdio>
 	<command interpreter="bash">./snmf.sh $vcf $outputs $logs $best_k_output $best_k_logfile $kmin $kmax $best_k_groups $threshold_group
-    </command>
+        </command>
 	<inputs>
 		<param format="vcf" name="vcf" type="data" label="VCF file" help="VCF file"/>
 		<param type="text" name="kmin" label="K min" value="2"/>
@@ -19,19 +25,33 @@
 		<data format="txt" name="outputs" label="All Outputs"/>
 		<data format="txt" name="logs" label="All Logs"/>
 	</outputs>
-<!--
+
 	<tests>
 		<test>
 			<param name="vcf" value="input.vcf" />
-			<param name="kmax" value="3" />
-			<param name="threshold_group" value="60" />
-			<output name="best_k_output" file="output" />
-			<output name="outputs" file="outputs.Q" />
-			<output name="best_k_groups" file="groups" />
+			<param name="kmin" value="2" />
+			<param name="kmax" value="5" />
+			<param name="threshold_group" value="50" />
+			<output name="best_k_output" file="output"  compare="sim_size"  >
+			    <assert_contents>
+			   	<has_n_columns n="4" />
+                                <has_line_matching expression=".*\s\d\..*" />
+			    </assert_contents>
+                        </output>
+			<output name="best_k_groups" file="groups" compare="sim_size" >
+			    <assert_contents>
+                                <has_line_matching expression=".*;.*" />
+			    </assert_contents>
+                        </output>
+			<output name="outputs" file="outputs.Q" compare="sim_size" >
+			    <assert_contents>
+                                <has_line_matching expression=".*\s\d\..*" />
+			    </assert_contents>
+                       </output> 
+
 		</test>
+	</tests>
 
-	</tests>
--->
 	<help>