diff seqsero.xml @ 2:0d65b71ff8df draft

planemo upload commit 464b391afaa5819bc681452e85bea9d882730eb6

--- a/seqsero.xml	Fri Oct 27 17:47:00 2017 -0400
+++ b/seqsero.xml	Sun Nov 12 02:27:32 2017 -0500
@@ -1,18 +1,34 @@
 <tool id="seq_sero_reads_multiple" name="SeqSero Batch - Paired-End Reads" version="0.1.0">
-	<description>Salmonella Serotype Prediction from Paired-End Reads</description>
-        <command interpreter="python2.7">
+  <description>Salmonella Serotype Prediction from Paired-End Reads</description>  
+<requirements>
+	<requirement type="package" version="1.69">biopython</requirement>
+        <requirement type="package" version="0.5.9">bwa</requirement>
+        <requirement type="package" version="1.3.1">samtools</requirement>
+        <requirement type="package" version="2.5.0">blast</requirement>
+        <requirement type="package" version="2.6.2">sra_toolkit</requirement>
+  </requirements>
+       <stdio>
+                <exit_code range="0:" level="warning"/>
+                <regex match="Error:"/>
+        </stdio>  
+      <command interpreter="python2.7">
                 run_seqsero_batch_galaxy.py $input1 <!--$input2-->
                 <!--test_bioblend.py $input1 $input2-->
         </command>
         <inputs>
-                <param format="fastq,fastqsanger" name="input1" multiple="true" type="data" label="Source file"/>
+                <param format="fastq" name="input1" multiple="true" type="data" label="Source file"/>
                 <!--<param format="fastq" name="input2" multiple="true" type="data" label="Source file"/>-->
         </inputs>
         <outputs>
                 <data name="html_file" format="html" from_work_dir="Seqsero_result.html"/>
                 <data name="text_file" format="txt" from_work_dir="Seqsero_result.txt"/>
         </outputs>
-        <help>
+ 	<tests>
+        <test>
+            <output  name="text_file" file="Seqsero_result.txt" ftype="txt"/>
+ 	</test>
+    	</tests>
+	<help>
                This tool predicts Salmonella serotypes from shotgun WGS data.
 
           	Below is the link to the seqsero help
@@ -34,8 +50,4 @@
           }
           </citation>
      </citations>
-        <stdio>
-                <exit_code range="0:" level="warning"/>
-                <regex match="Error:"/>
-        </stdio>
 </tool>