Mercurial > repos > rnateam > graphclust_preprocessing

diff preprocessing.xml @ 11:c0c9d19bc7b2 draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
author rnateam
date Tue, 18 Jul 2017 01:43:49 -0400
parents 16bcaef3dc1e
children 8a1786cdcf95
line wrap: on
line diff
--- a/preprocessing.xml	Thu Jun 01 12:11:37 2017 -0400
+++ b/preprocessing.xml	Tue Jul 18 01:43:49 2017 -0400
@@ -1,7 +1,8 @@
-<tool id="preproc" name="Preprocessing" version="0.2">
+<tool id="preproc" name="Preprocessing" version="0.3">
   <requirements>
-    <requirement type="package" version="0.1.12">graphclust-wrappers</requirement>
+    <requirement type="package" version="0.3.1">graphclust-wrappers</requirement>
     <requirement type="package" version="3.0">zip</requirement>
+    <requirement type="package" version="1.70">biopython</requirement>
 
   </requirements>
     <stdio>
@@ -19,13 +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"/>
@@ -36,7 +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>
@@ -57,6 +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>