Mercurial > repos > rnateam > structure_to_gspan

changeset 1:d62d7e98a68e draft

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planemo upload for repository https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN commit 6767a5ffb02052c844e9d862c79912f998f39d8e
author rnateam
date Mon, 20 Nov 2017 05:01:43 -0500
parents 4c7736b4d8ff
children 6648b5c2ce54
files structure_to_gspan.xml
diffstat 1 files changed, 45 insertions(+), 24 deletions(-) [+]
line wrap: on
line diff
--- a/structure_to_gspan.xml	Mon May 22 12:43:01 2017 -0400
+++ b/structure_to_gspan.xml	Mon Nov 20 05:01:43 2017 -0500
@@ -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="0.3" >
     <requirements>
-        <requirement type="package" version="0.2.0">graphclust-wrappers</requirement>
+        <requirement type="package" version="0.5.2">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"
@@ -49,33 +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: "rnafold"
-                        example of input-file for rnafold 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 
 
-   
-+ **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>