merge

templates/library/common/ldda_info.mako

@@ -117,14 +117,14 @@
         </div>
         %if ldda.creating_job_associations:
             <% job = ldda.creating_job_associations[0].job %>
-            %if job.stdout.strip() != '':
+            %if job.stdout and job.stdout.strip() != '':
                 <div class="form-row">
                     <label>Job Standard Output</label>
                     <pre>${job.stdout}</pre>
                     <div style="clear: both"></div>
                 </div>
             %endif
-            %if job.stderr.strip() != '':
+            %if job.stderr and job.stderr.strip() != '':
                 <div class="form-row">
                     <label>Job Standard Error</label>
                     <pre>${job.stderr}</pre>

tools/ngs_rna/cuffdiff_wrapper.xml

@@ -90,7 +90,7 @@
 
         <param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/>
         <param name="min_mapqual" type="integer" value="0" label="Min SAM Mapping Quality" help="Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number."/>
-        <param name="min_alignment_count" type="integer" value="0" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/>
+        <param name="min_alignment_count" type="integer" value="1000" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/>
         <param name="do_normalization" type="select" label="Perform quartile normalization" help="Removes top 25% of genes from FPKM denominator to improve accuracy of differential expression calls for low abundance transcripts.">
             <option value="No">No</option>
             <option value="Yes">Yes</option>