changeset 1:133fc317a812 draft

planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 746497a64b955f6b9afc1944d1c1d8d877e53267

--- a/structure_to_gspan.xml	Mon May 22 12:44:17 2017 -0400
+++ b/structure_to_gspan.xml	Tue Jul 18 01:44:04 2017 -0400
@@ -1,13 +1,15 @@
-<tool id="structure_to_gspan" name="Structure to GSPAN" version="0.1">
+<tool id="structure_to_gspan" name="Structure to GSPAN" version="0.2">
     <requirements>
-        <requirement type="package" version="0.2.0">graphclust-wrappers</requirement>
+        <requirement type="package" version="0.3.1">graphclust-wrappers</requirement>
     </requirements>
     <command detect_errors="exit_code">
     <![CDATA[
         mkdir ./temp/ ./GSPAN_Outputs/ &&
+        which structure_2_gspan.pl && 
         structure_2_gspan.pl
             --input-file '$dataFile'
-            --input-format 'rnafold'
+            --input-format '$inputFormat'
+            --input-structure-type '$structureType'
             $abstr
             $stack
             $seq_graph_t
@@ -18,8 +20,10 @@
     </command>
     <inputs>
         <param type="data" name="dataFile" format="dbn" label="Sequence and Structure input file in the prediction tool format" />
-        <param name="inputFormat" type="text" value="rnafold"
-            label="  Sequence Structure format of the input. Allowed format: rnafold" help="-input-format"/>
+        <param name="inputFormat" type="text" value="vrna-simple"
+            label="  Sequence Structure format of the input. Allowed formats: vrna-simple, vrna-mea" help="-input-format"/>
+        <param name="structureType" type="text" value="MFE"
+            label="  Sequence Structure type from the input to use. Allowed types: MFE, MEA" help="-input-structure-type"/>
         <param argument="-stack" truevalue="-stack" falsevalue="" checked="true"  type="boolean"
             label="Add stacking information to graphs"/>
         <param argument="abstr" truevalue="-abstr" falsevalue="" type="boolean"
@@ -58,8 +62,8 @@
 
 + **input** : The sequence and structure data, the output of structure prediction tool.
 
-+ **input-format** : Sequence Structure format of the input. Allowed format: "rnafold"
-                        example of input-file for rnafold format:
++ **input-format** : Sequence Structure format of the input. Allowed format: "vrna-simple" "vrna-mea"
+                        example of input-file for vrna-simple format:
                         >seq1
                         CCGGGCGUGCUG
                         .(((.....))) ( -0.30)
@@ -67,6 +71,22 @@
                         GCGGUUGCCG
                         .(((...))) ( -0.50)
 
+                        example of input-file for vrna-simple format:
+                        >seq1
+                        CCGGGCGUGCUG
+                        .(((.....))) ( -0.30)
+                        .{{{.....}}} [ -0.67]
+                        .(((.....))) { -0.30 d=1.29}
+                        .(((.....))) { -0.30 MEA=9.52}
+                         frequency of mfe structure in ensemble 0.550454; ensemble diversity 1.58  
+                        >seq2
+                        GCGGUUGCCG
+                        .(((...))) ( -0.50)
+                        .({{...)}, [ -0.99]
+                        ..((...)). {  0.60 d=1.89}
+                        .(((...))) { -0.50 MEA=6.60}
+                         frequency of mfe structure in ensemble 0.452041; ensemble diversity 2.26 
+
    
 + **stack** : This adds an additional vertex (type P) for each pair of stacked base-pairs and four edges
   (type p) from each of the involved bases to the new vertex.