diff rsem_calculate_expression.xml @ 2:f6b8155ab12a

Add test cases

--- a/rsem_calculate_expression.xml	Thu Dec 05 10:54:28 2013 -0600
+++ b/rsem_calculate_expression.xml	Thu Feb 06 11:46:40 2014 -0600
@@ -185,7 +185,7 @@
   <inputs>
     <param name="sample" type="text" value="rsem_sample" label="Sample name" />
     <conditional name="reference">
-      <param name="refSrc" type="select" label="RSEM Reference">
+      <param name="refSrc" type="select" label="RSEM Reference Source">
         <option value="cached">Locally cached</option>
         <option value="history">From your history</option>
       </param>
@@ -209,7 +209,7 @@
       </param>
       <when value="fastq">
         <param name="fastq_select" size="15" type="select" label="FASTQ type" >
-          <option value="--phred33-quals">phred33 qualities (default for sanger)</option>
+          <option value="--phred33-quals" selected="true">phred33 qualities (default for sanger)</option>
           <option value="--solexa-quals">solexa qualities</option>
           <option value="--phred64-quals">phred64 qualities</option>
         </param>
@@ -274,22 +274,48 @@
     <exit_code range="1:"  level="fatal" description="Error Running RSEM" />
   </stdio>
   <outputs>
-    <data format="tabular" name="output" label="${sample}.gene_abundances" from_work_dir="rsem_output.genes.results"/>
-    <data format="tabular" name="isoforms" label="${sample}.isoform_abundances" from_work_dir="rsem_output.isoforms.results"/>
+    <data format="tabular" name="gene_abundances" label="${sample}.gene_abundances" from_work_dir="rsem_output.genes.results"/>
+    <data format="tabular" name="isoform_abundances" label="${sample}.isoform_abundances" from_work_dir="rsem_output.isoforms.results"/>
     <data format="bam" name="transcript_bam" label="${sample}.transcript.bam" from_work_dir="rsem_output.transcript.bam" >
       <filter>rsem_outputs['result_bams'] != "none"</filter>
     </data>
-    <data format="bam" name="transcript__sorted_bam" label="${sample}.transcript.bam" from_work_dir="rsem_output.transcript.sorted.bam" >
+    <data format="bam" name="transcript_sorted_bam" label="${sample}.transcript.bam" from_work_dir="rsem_output.transcript.sorted.bam" >
       <filter>rsem_outputs['result_bams'] != "none"</filter>
     </data>
     <data format="bam" name="genome_bam" label="${sample}.genome.bam" from_work_dir="rsem_output.genome.bam">
       <filter>rsem_outputs['result_bams'] == "both"</filter>
     </data>
-    <data format="bam" name="genome_sorted_bam" label="${sample}.genome.bam" from_work_dir="rsem_output.genome.sorted.bam">
+    <data format="bam" name="genome_sorted_bam" label="${sample}.genome.sorted.bam" from_work_dir="rsem_output.genome.sorted.bam">
       <filter>rsem_outputs['result_bams'] == "both"</filter>
     </data>
     <data format="txt" name="log" label="${sample}.rsem_log"/>
   </outputs>
+  <tests>
+    <test>
+      <param name="sample" value="rsem_sample"/>
+      <param name="refSrc" value="history"/>
+      <param name="rsem_ref" value="RSEM_ref_reference.zip" ftype="rsem_ref"/>
+      <param name="format" value="fastq"/>
+      <param name="matepair" value="single"/>
+      <param name="singlefastq" value="test.fastq" ftype="fastqsanger"/>
+      <param name="result_bams" value="none"/>
+      <output name="gene_abundances"> 
+        <assert_contents>
+          <has_text text="ENST00000423562,ENST00000438504,ENST00000488147,ENST00000538476,ENST00000541675" />
+        </assert_contents>
+      </output>
+      <output name="isoform_abundances"> 
+        <assert_contents>
+          <has_text text="ENST00000332831" />
+        </assert_contents>
+      </output>
+      <output name="log"> 
+        <assert_contents>
+          <has_text text="Expression Results are written" />
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
   <help>