# HG changeset patch
# User trinity_ctat
# Date 1516890331 18000
# Node ID 2e993ad06cf2d7996373b9a41d165c70f7a79bcc
# Parent  e4892a11c58daeb04f561c379f16727178209d7f
Removing mthod option from fusion_inspector tool. Only STAR is supported now.

diff -r e4892a11c58d -r 2e993ad06cf2 fusion_inspector.xml
--- a/fusion_inspector.xml	Wed Jan 24 12:54:45 2018 -0500
+++ b/fusion_inspector.xml	Thu Jan 25 09:25:31 2018 -0500
@@ -13,7 +13,7 @@
       --out_dir "subdir"
       --out_prefix "finspector" 
       --prep_for_IGV 
-      --align_utils $method
+      --align_utils STAR
       #if $trinity_status.trinity=="true"
       --include_Trinity
       #end if
@@ -30,12 +30,13 @@
       <param format="tabular" name="fusion_candidates_list" type="data" multiple="True" label="Choose candidate list:" help="Fusion predictions"/>
       <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
       <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
-      
+      <!-- The HISAT and GSNAP methods are not supported and are being removed, leaving only STAR.
       <param name="method" type="select" label="Choose method:">
              <option value="HISAT">HISAT</option>
              <option value="STAR">STAR</option>
              <option value="GSNAP">GSNAP</option>
       </param>
+      -->
       <conditional name="trinity_status">
            <param name="trinity" type="select" label="Use Trinity:">
              <option value="true">True</option>
@@ -50,8 +51,8 @@
       </param>
     </inputs>
     <outputs>
-      <data format="text" name="finspector_idx" label="fidx" from_work_dir="subdir/finspector.fa.fai"/>
-      <data format="text" name="cytoBand" label="cytoBand" from_work_dir="subdir/cytoBand.txt"/>
+      <data format="txt" name="finspector_idx" label="fidx" from_work_dir="subdir/finspector.fa.fai"/>
+      <data format="txt" name="cytoBand" label="cytoBand" from_work_dir="subdir/cytoBand.txt"/>
       <data format="fasta" name="finspector_fa" label="finspector_fasta" from_work_dir="subdir/finspector.fa"/>
       <data format="bed" name="finspector_bed" label="finspector_bed" from_work_dir="subdir/finspector.bed"/>
       <data format="tabular" name="FusionJuncSpan" label="FusionJuncSpan" from_work_dir="subdir/finspector.igv.FusionJuncSpan"/>
@@ -62,8 +63,8 @@
       <data format="bed" name="trinity_bed" label="trinity_bed" from_work_dir="subdir/finspector.gmap_trinity_GG.fusions.gff3.bed.sorted.bed">
             <filter>trinity_status['trinity'] == "true"</filter>
       </data>
-      <data format="text" name="fusionPredictions" label="fusion_predictions.final" from_work_dir="subdir/finspector.fusion_predictions.final"/>
-      <data format="text" name="fusionPredictionsAbridged" label="fusion_predictions_abridged" from_work_dir="subdir/finspector.fusion_predictions.final.abridged"/>
+      <data format="txt" name="fusionPredictions" label="fusion_predictions.final" from_work_dir="subdir/finspector.fusion_predictions.final"/>
+      <data format="txt" name="fusionPredictionsAbridged" label="fusion_predictions_abridged" from_work_dir="subdir/finspector.fusion_predictions.final.abridged"/>
       <data format="json" name="fusion_json" label="fusion_json" from_work_dir="subdir/finspector.fusion_inspector_web.json"/>
     </outputs>
     <tests>
@@ -71,7 +72,9 @@
         <param name="fusion_candidates_list" value="FusionInspector/fusion_targets.A.txt,FusionInspector/fusion_targets.B.txt,FusionInspector/fusion_targets.C.txt" />
         <param name="left_input" value="FusionInspector/test.reads_1.fastq.gz" />
         <param name="right_input" value="FusionInspector/test.reads_2.fastq.gz" />
+        <!-- The HISAT and GSNAP methods are not supported and are being removed, leaving only STAR.
         <param name="method" value="STAR" />
+        -->
         <param name="trinity" value="false" />
         <output name="finspector_idx" file="FusionInspector/test.reads_1_2.fa.fai" />
         <output name="cytoBand" file="FusionInspector/test.reads_1_2.cytoBand.tail.txt" compare="contains" />