Mercurial > repos > rnateam > graphclust_preprocessing

changeset 8:a04e93fdb40a draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 9a3dc91fa984be18fabc0d968360634d787c9589
author rnateam
date Wed, 24 May 2017 09:57:18 -0400
parents 07ad2d77f28a
children 0690d59881b9
files preprocessing.xml splitSHAPE.py test-data/sample_3.fa test-data/sample_3.react test-data/sample_3_shape_data_split.react
diffstat 5 files changed, 1134 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/preprocessing.xml	Mon May 22 12:45:22 2017 -0400
+++ b/preprocessing.xml	Wed May 24 09:57:18 2017 -0400
@@ -47,6 +47,15 @@
             <output name="data.names" file="FASTA/data.names"/>
             <output name="data.fasta.scan" file="FASTA/data.fasta.scan" />
         </test>
+
+        <test>
+            <param name="fastaFile" value="sample_3.fa"/>
+            <param name="SHAPEdata" value="sample_3.react"/>
+            <param name="max_length" value="100"/>
+            <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>        
     </tests>
     <help>
 <![CDATA[
--- a/splitSHAPE.py	Mon May 22 12:45:22 2017 -0400
+++ b/splitSHAPE.py	Wed May 24 09:57:18 2017 -0400
@@ -56,8 +56,8 @@
     for j in react_val[int(chunks[1])-1:int(chunks[2])]:
         id_s = int(j.split()[0])
 
-        if id_s > win_size:
-            id_s = id_s - int(chunks[1])
+
+        id_s = id_s - int(chunks[1]) + 1
         toWrite += str(id_s) + '\t' + j.split()[1] + "\n"
 
 with open("shape_data_split.react", 'w') as out:
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_3.fa	Wed May 24 09:57:18 2017 -0400
@@ -0,0 +1,6 @@
+>SECIS_1 test
+AUUUUAUCCAUGAAAGUGUUUCCUCUAAACCUAUGUGGAGGAACACCUGAUGUCCAGGAAAAU
+>6S_1 test1
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+>6S_2
+UUGUCCCUGCCGUGCUCGUGACUUGGCCAUACAUUCUCUGAACCUAUGUCUUACGGCAUAUGGGUUGCGGGAGUGUAGAGCUGGAGUGAUCGUCUACUCGUAGACGAACCCGAUGCUCUUCGGAUCGCGACCACCUUGAACCUCAGGGUUCGAGAUGCCGGCCUUGACGGCACAGGCGGGGCAUC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_3.react	Wed May 24 09:57:18 2017 -0400
@@ -0,0 +1,447 @@
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\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_3_shape_data_split.react	Wed May 24 09:57:18 2017 -0400
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