diff structure_to_gspan.xml @ 2:dcc336102d65 draft

planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e

--- a/structure_to_gspan.xml	Tue Jul 18 01:44:04 2017 -0400
+++ b/structure_to_gspan.xml	Mon Nov 20 04:55:20 2017 -0500
@@ -1,6 +1,6 @@
-<tool id="structure_to_gspan" name="Structure to GSPAN" version="0.2">
+<tool id="structure_to_gspan" name="Structure to GSPAN" version="0.3" >
     <requirements>
-        <requirement type="package" version="0.3.1">graphclust-wrappers</requirement>
+        <requirement type="package" version="0.5.2">graphclust-wrappers</requirement>
     </requirements>
     <command detect_errors="exit_code">
     <![CDATA[
@@ -53,49 +53,50 @@
     <help>
     <![CDATA[
 
-**What it does**
-For each pair of sequence and structure provided in the input file
-and convert them into GSPAN format graphs.
+        **What it does**
+        For each pair of sequence and structure provided in the input file
+        and convert them into GSPAN format graphs.
 
 
-**Parameters**
+        **Parameters**
 
-+ **input** : The sequence and structure data, the output of structure prediction tool.
+        + **input** : The sequence and structure data, the output of structure prediction tool.
 
-+ **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)
-                        >seq2
-                        GCGGUUGCCG
-                        .(((...))) ( -0.50)
+        + **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)
+            >seq2
+            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 
+            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.
+           
+        + **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.
 
-+ **abstr** : Add abstract structure graphs to the single shrep graph instances.
+        + **abstr** : Add abstract structure graphs to the single shrep graph instances.
 
-+ **seq-graph-t** : Add for each 't #' a graph which contains no structure
+        + **seq-graph-t** : Add for each 't #' a graph which contains no structure
 
-+ **group** : Combine/group that number of input seqs into 1 gspan file output name is then '<INT>.group.gspan.bz2'
+        + **group** : Combine/group that number of input seqs into 1 gspan file output name is then '<INT>.group.gspan.bz2'
 
     ]]>
     </help>