# HG changeset patch
# User yating-l
# Date 1486139442 18000
# Node ID da5fba0ed4fc79d5bb759085d9129d08a976a8ff
# Parent  e51fb8c5bb1ccae6673ebee7caddcfc2e091636e
planemo upload

diff -r e51fb8c5bb1c -r da5fba0ed4fc gbToFasta.xml
--- a/gbToFasta.xml	Thu Feb 02 18:30:34 2017 -0500
+++ b/gbToFasta.xml	Fri Feb 03 11:30:42 2017 -0500
@@ -5,19 +5,18 @@
       <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-      gbToFaRa
+    gbToFaRa
             /dev/null
-            '${output_fa}'
-            output_ra
-            output_ta
+            '${outputfa}'
+            outputra
+            outputta
             '${gbfile}'
       #if $cds == "yes"
             && raToTab
                   -cols=acc,cds
-                  output_ra
-                  '${output_cds}'
+                  outputra
+                  '${outputcds}'
       #end if
-
 ]]></command>
       <inputs>
             <param type="data" name="gbfile" format="genbank" />
@@ -28,8 +27,8 @@
                   
       </inputs>
       <outputs>
-            <data format="fasta" name="output_fa" label="${gbfile.name}:fasta"></data>
-            <data format="fasta" name="output_cds" label="${gbfile.name}:cds">
+            <data format="fasta" name="outputfa" label="${tool.name} on ${on_string}:fasta"></data>
+            <data format="fasta" name="outputcds" label="${tool.name} on ${on_string}:cds">
                   <filter>cds == "yes"</filter>
             </data>
       </outputs>
@@ -37,13 +36,13 @@
       <test>
             <param name="gbfile" value="Gallus_gallus_RefSeq.gb" />
             <param name="cds" value="yes" />
-            <output name="output_fa" value="Gallus_gallus_RefSeq.fa" />
-            <output name="output_cds" value="Gallus_gallus_RefSeq.cds" />
+            <output name="outputfa" value="Gallus_gallus_RefSeq.fa" />
+            <output name="outputcds" value="Gallus_gallus_RefSeq.cds" />
       </test>
       <test>
             <param name="gbfile" value="Gallus_gallus_RefSeq.gb" />
             <param name="cds" value="no" />
-            <output name="output_fa" value="Gallus_gallus_RefSeq.fa" />
+            <output name="outputfa" value="Gallus_gallus_RefSeq.fa" />
       </test>
   </tests> 
   <help>
@@ -62,32 +61,33 @@
 where filterFile is definition of which records and fields
 use /dev/null if you want no filtering.
 
-gbToFaRa /dev/null ${gbfile.fa} \
-  ${gbfile.ra} ${gbfile.ta} ${gbfile}
+gbToFaRa /dev/null gbfile.fa \
+  gbfile.ra gbfile.ta gbfile
 
 Create table with coding regions information for each mRNA record
 -----------------------------------------------------------------
 raToTab - Convert ra file to table.
-raToTab -cols=acc,cds ${gbfile.ra} ${gbfile.cds}
+raToTab -cols=acc,cds gbfile.ra gbfile.cds
 
 Source code:
 ============
 
 http://hgdownload.cse.ucsc.edu/admin/exe/
 
-]]></help>  
-<citations>
-      <citation type="bibtex">@article{kent2002blat,
-  title={BLAT—the BLAST-like alignment tool},
-  author={Kent, W James},
-  journal={Genome research},
-  volume={12},
-  number={4},
-  pages={656--664},
-  year={2002},
-  publisher={Cold Spring Harbor Lab}
-      }</citation>
-</citations> 
+]]></help> 
+ <citations>
+            <citation type="bibtex">@article{kent2002blat,
+                  title={BLAT—the BLAST-like alignment tool},
+                  author={Kent, W James},
+                  journal={Genome research},
+                  volume={12},
+                  number={4},
+                  pages={656--664},
+                  year={2002},
+                  publisher={Cold Spring Harbor Lab}
+            }</citation>
+      </citations> 
+      
 </tool>