Mercurial > repos > yating-l > ucsc_blat

diff blat.xml @ 9:c4f0808a68ad draft

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planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf
author yating-l
date Thu, 02 Feb 2017 12:55:12 -0500
parents 5e4e16939d3b
children 3511cb739854
line wrap: on
line diff
--- a/blat.xml	Wed Feb 01 18:09:22 2017 -0500
+++ b/blat.xml	Thu Feb 02 12:55:12 2017 -0500
@@ -16,9 +16,9 @@
         '${query}'
         output
     && sort -k 10,10 -k 12,12n output > '${output_sorted}'
-    && pslReps -minAli=0.25 '${output_sorted}' output.reps.psl output.reps.psr
-    && faPolyASizes '${query}' query.polyA
     #if $filter_param.filter =="yes"
+      && pslReps -minAli=0.25 '${output_sorted}' output.reps.psl output.reps.psr
+      && faPolyASizes '${query}' query.polyA
       && pslCDnaFilter
             #if $filter_param.assembly_type == "native"
                   -localNearBest=0.001
@@ -106,8 +106,8 @@
       </outputs>
   <tests>
       <test>
-            <param name="database" value="amaVit1.fa" />
-            <param name="query" value="Gallus_gallus_RefSeq.fa" />
+            <param name="database" value="amaVit1_Gallus/amaVit1.fa" />
+            <param name="query" value="amaVit1_Gallus/Gallus_gallus_RefSeq.fa" />
             <param name="database_type" value="dnax" />    
             <param name="query_type" value="rnax" />     
             <param name="noHead" value="true" />
@@ -115,9 +115,23 @@
             <param name="filter" value="yes" />
             <param name="assembly_type" value="xeno" />
             <param name="assembly_category" value="well-ordered" />
-            <output name="output_sorted" value="amaVit1_Gallus_gallus.psl" />
-            <output name="output_filtered" value="amaVit1_Gallus_gallus_filtered.psl" />
+            <output name="output_sorted" value="amaVit1_Gallus/amaVit1_Gallus_gallus.psl" />
+            <output name="output_filtered" value="amaVit1_Gallus/amaVit1_Gallus_gallus_filtered.psl" />
       </test>
+      <test>
+            <param name="database" value="dbia3/dbia3.fa" />
+            <param name="query" value="dbia3/dmel-all-translation-r6.11.fasta" />
+            <param name="database_type" value="dnax" />    
+            <param name="query_type" value="prot" />     
+            <param name="noHead" value="true" />
+            <param name="mask" value="lower" />
+            <param name="filter" value="yes" />
+            <param name="assembly_type" value="xeno" />
+            <param name="assembly_category" value="well-ordered" />
+            <output name="output_sorted" value="dbia3/dbia3.sorted.psl" />
+            <output name="output_filtered" value="dbia3/dbia3_dmel_filtered.psl" />
+      </test>
+
   </tests> 
   <help>
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