diff segmentation-fold.xml @ 3:59ab674be4b5 draft

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 4b12ac5efae0802d2614747a639475d8778a68b4-dirty

--- a/segmentation-fold.xml	Wed Dec 02 04:34:50 2015 -0500
+++ b/segmentation-fold.xml	Mon Feb 29 10:43:37 2016 -0500
@@ -1,8 +1,8 @@
-<tool id="segmentation_fold" name="segmentation-fold" version="1.1.0_1">
+<tool id="segmentation_fold" name="segmentation-fold" version="1.6.0_0">
     <description>RNA-Folding including predefined segments including K-turns</description>
     
     <requirements>
-        <requirement type="package" version="1.1.0">segmentation-fold</requirement>
+        <requirement type="package" version="1.6.0">segmentation-fold</requirement>
     </requirements>
     
     <stdio></stdio>
@@ -15,16 +15,16 @@
             #if $input.method == "fasta"
                 -f $input.input_fasta
             #else
-                -s ${input.input_sequence}
+                -s $input.input_sequence
             #end if
             
             -p $predict_segments
             -h $min_hairpin_size
             
             #if $parameters.settings == "default"
-                -x "${SEGMENTATION_FOLD_DEFAULT_XML}"
+                -x "\$SEGMENTATION_FOLD_DEFAULT_XML"
             #else
-                -x $parameters.input_xml
+                -x "${parameters.input_xml}"
             #end if
             
             -t \${GALAXY_SLOTS:-4}
@@ -32,7 +32,6 @@
     ]]></command>
     
     <inputs>
-        
         <conditional name="input">
             <param name="method" type="select" label="Energy parameters">
                 <option value="fasta" selected="true">As FASTA-file</option>
@@ -62,7 +61,8 @@
     </inputs>
     
     <outputs>
-        <data format="dot-bracket" name="output_dbn" label="${tool.name} on ${input.input_fasta.hid + ': ' + input.input_fasta.name if $input.method == 'fasta' else $input.input_sequence.upper() }" />
+        <data format="dot-bracket" name="output_dbn" label="asdasdasd" />
+        <!--<data format="dot-bracket" name="output_dbn" label="${tool.name} on ${str(input.input_fasta.hid) + ': ' + input.input_fasta.name if $input.method == 'fasta' else $input.input_sequence.upper() }" />-->
     </outputs>
     
     <tests>