diff preprocessing.xml @ 6:e31c659be8bc draft

planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 6767a5ffb02052c844e9d862c79912f998f39d8e

--- a/preprocessing.xml	Wed May 24 09:56:11 2017 -0400
+++ b/preprocessing.xml	Mon Nov 20 05:01:21 2017 -0500
@@ -1,6 +1,9 @@
-<tool id="preproc" name="Preprocessing" version="0.2">
+<tool id="preproc" name="Preprocessing" version="0.4">
   <requirements>
-    <requirement type="package" version="0.1.12">graphclust-wrappers</requirement>
+    <requirement type="package" version="0.5.2">graphclust-wrappers</requirement>
+    <requirement type="package" version="3.0">zip</requirement>
+    <requirement type="package" version="1.70">biopython</requirement>
+
   </requirements>
     <stdio>
         <exit_code range="1:" />
@@ -17,13 +20,22 @@
             &&
             python '$__tool_directory__/splitSHAPE.py' 
                 '$SHAPEdata'
-                $max_length
+                
         #end if
+
+        #if $AlignmentData:
+            &&
+            python '$__tool_directory__/splitStockholm.py' 
+                '$AlignmentData'
+                
+        #end if
+             
 ]]>
 	</command>
     <inputs>
         <param type="data" name="fastaFile" format="fasta" />
         <param type="data" name="SHAPEdata" format="txt" optional="true" label="SHAPE data"/>
+        <param type="data" name="AlignmentData" format="stockholm" optional="true" label="Alignments file"/>
         <param name="max_length" type="integer" value="10000" size="5" label="window size"/>
         <param name="in_winShift" type="integer" value="100" size="5" label="window shift in percent"/>
         <param name="min_seq_length" type="integer" value="5" size="5" label="minimum sequence length"/>
@@ -34,7 +46,8 @@
         <data name="data.names" format="txt" from_work_dir="FASTA/data.names" label="data.names"/>
         <data name="data.fasta.scan" format="fasta" from_work_dir="FASTA/data.fasta.scan" label="data.fasta.scan"/>
         <data name="FASTA" format="zip" from_work_dir="FASTA.zip" label="FASTA.ZIP"/>
-        <data name="shape_data_split" format="txt" from_work_dir="shape_data_split.react" label="SHAPE data splited"/>
+        <data name="shape_data_split" format="txt" from_work_dir="shape_data_split.react" label="SHAPE.data.split"/>
+        <data name="alignment_data_split" format="stockholm" from_work_dir="alignment_data_split.stk" label="alignments.data.stk"/>
     </outputs>
     <tests>
         <test>
@@ -55,6 +68,14 @@
             <param name="in_winShift" value="50"/>
             <param name="min_seq_length" value="5"/>
             <output name="shape_data_split" file="sample_3_shape_data_split.react" />
+        </test> 
+        <test>
+            <param name="fastaFile" value="sample_4_representatives.fa"/>
+            <param name="AlignmentData" value="sample_4_all.stk"/>
+            <param name="max_length" value="50"/>
+            <param name="in_winShift" value="50"/>
+            <param name="min_seq_length" value="5"/>
+            <output name="alignment_data_split" file="sample_4_alignment_data_split.stk" />
         </test>        
     </tests>
     <help>