diff miRPlant.xml @ 44:0c4e11018934 draft

Uploaded

--- a/miRPlant.xml	Tue Oct 28 01:35:32 2014 -0400
+++ b/miRPlant.xml	Thu Oct 30 21:29:19 2014 -0400
@@ -4,9 +4,9 @@
   <requirements>
     <requirement type="set_environment">SCRIPT_PATH</requirement>
     <requirement type="package" version="0.12.7">bowtie</requirement>
-    <requirement type="package" version="2.11.0">R</requirement>
+    <requirement type="package" version="3.0.1">R</requirement>
 	<requirement type="package" version="0.0.13">fastx_toolkit </requirement>
-	<requirement type="package" version="1.5.0">X11</requirement>
+	<requirement type="package" version="1.5.0">libx11</requirement>
 	<requirement type="package" version="2.1.8">ViennaRNA</requirement>
   </requirements>
 
@@ -27,7 +27,7 @@
     -tag ${s.tag}
     #end for
 
-    -format $format -gfa $gfa -pre $pre -mat $mat -rfam $rfam  -a $a -M $mapnt -min $min -max $max -mis $mismatch -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe
+    -format $format -gfa $gfa -pre $pre -mat $mat -rfam $rfam  -a $a -M $mapnt -min $min -max $max -mis $mismatch -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe > run.log
   </command>
 
   <inputs>
@@ -72,16 +72,15 @@
   </inputs>
 
   <outputs>
-   <data format="txt" name="known microRNA express list" from_work_dir="miRPlant_out/known_microRNA_express.txt"/>
-   <data format="txt" name="known microRNA express alignment" from_work_dir="miRPlant_out/known_microRNA_express.aln"/>
-   <data format="txt" name="known microRNA moRs result" from_work_dir="miRPlant_out/known_microRNA_express.moRs"/>
-   <data format="txt" name="known microRNA precursor file" from_work_dir="miRPlant_out/known_microRNA_precursor.fa"/>
-   <data format="txt" name="known microRNA mature file" from_work_dir="miRPlant_out/known_microRNA_mature.fa"/>
-   <data format="txt" name="novel microRNA prediction file" from_work_dir="miRPlant_out/known_microRNA_mature.fa"/>
-   <data format="txt" name="novel microRNA express list" from_work_dir="miRPlant_out/novel_microRNA_express.txt"/>
-   <data format="txt" name="novel microRNA precursor file" from_work_dir="miRPlant_out/novel_microRNA_precursor.fa"/>
-   <data format="txt" name="novel microRNA mature sequence file" from_work_dir="miRPlant_out/novel_microRNA_mature.fa"/>
-   <data format="txt" name="analysis result" from_work_dir="miRPlant_out/result.html"/>
+   <data format="txt" name="known microRNA express list" from_work_dir="miRPlant_out/known_microRNA_express.txt" label="${tool.name} on ${on_string}: known microRNA express list"/>
+   <data format="txt" name="known microRNA express alignment" from_work_dir="miRPlant_out/known_microRNA_express.aln" label="${tool.name} on ${on_string}: known microRNA express alignment"/>
+   <data format="txt" name="known microRNA moRs result" from_work_dir="miRPlant_out/known_microRNA_express.moRs" label="${tool.name} on ${on_string}: known microRNA moRs result"/>
+   <data format="txt" name="known microRNA precursor file" from_work_dir="miRPlant_out/known_microRNA_precursor.fa" label="${tool.name} on ${on_string}: known microRNA precursor file"/>
+   <data format="txt" name="known microRNA mature file" from_work_dir="miRPlant_out/known_microRNA_mature.fa" label="${tool.name} on ${on_string}: known microRNA mature file"/>
+   <data format="txt" name="novel microRNA express list" from_work_dir="miRPlant_out/novel_microRNA_express.txt" label="${tool.name} on ${on_string}: novel microRNA express list"/>
+   <data format="txt" name="novel microRNA precursor file" from_work_dir="miRPlant_out/novel_microRNA_precursor.fa" label="${tool.name} on ${on_string}: novel microRNA precursor file"/>
+   <data format="txt" name="novel microRNA mature sequence file" from_work_dir="miRPlant_out/novel_microRNA_mature.fa" label="${tool.name} on ${on_string}: novel microRNA mature sequence file"/>
+   <data format="html" name="analysis result" from_work_dir="miRPlant_out/result.html" label="${tool.name} on ${on_string}: analysis result"/>
   </outputs>
 
  <help>