diff sRbowtieCascade.xml @ 1:0dfcb397699e draft

Uploaded
author drosofff
date Mon, 13 Apr 2015 12:31:00 -0400
parents ecb041b49cd7
children 0052d1dd31df
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--- a/sRbowtieCascade.xml	Mon Nov 03 10:26:15 2014 -0500
+++ b/sRbowtieCascade.xml	Mon Apr 13 12:31:00 2015 -0400
@@ -1,9 +1,8 @@
-<tool id="sRbowtie_cascade" name="Annotate smRNA datasets" version="1.0.0">
+<tool id="sRbowtie_cascade" name="Annotate smRNA datasets" version="1.0.1">
   <description>Using iterative sRbowtie Alignments</description>
   <requirements>
         <requirement type="package" version="0.12.7">bowtie</requirement>
   </requirements>
-  <parallelism method="basic"></parallelism>
   <command interpreter="python"> sRbowtieCascade.py --output $output
                                                     --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie
                                                     --mismatch $mismatches
@@ -94,9 +93,19 @@
    <data format="tabular" name="output" label="Cascade Annotation Analysis"/>
    </outputs>
 
-    <test>
-    </test>
 
+    <tests>
+        <test>
+      <param name="input" value ="sample1.fa,sample2.fa,sample3.fa" ftype="fasta" />
+      <param name="genomeSource" value="history" />
+      <param name="ownFile" value ="dmel-2L-r6.04.fasta" ftype="fasta" />
+      <param name="AdditionalQueries_0|refGenomeSource|genomeSource" value="history"/>
+      <param name="AdditionalQueries_0|refGenomeSource|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
+      <param name="AdditionalQueries_1|refGenomeSource|genomeSource" value="history"/>
+      <param name="AdditionalQueries_1|refGenomeSource|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
+      <output name="output" ftype="tabular" file="Cascade_Annotation_Analysis.tab" />
+        </test>
+    </tests>
   <help>
 
 **Intro**