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changeset 15:6abd809cefdd draft

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Uploaded v0.2.4, added unit tests for Promoter 2
author peterjc
date Thu, 25 Apr 2013 12:25:52 -0400
parents 6365217cd3de
children 7de64c8b258d
files test-data/Adenovirus.fasta test-data/Adenovirus.promoter2.tabular test-data/empty_promoter2.tabular tools/protein_analysis/README tools/protein_analysis/promoter2.xml
diffstat 5 files changed, 36 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Adenovirus.fasta	Thu Apr 25 12:25:52 2013 -0400
@@ -0,0 +1,21 @@
+>gi_209811_gb_J01917_ADRCG Adenovirus type 2, complete genome.
+CATCATCATAATATACCTTATTTTGGATTGAAGCCAATATGATAATGAGGGGGTGGAGTT
+TGTGACGTGGCGCGGGGCGTGGGAACGGGGCGGGTGACGTAGTAGTGTGGCGGAAGTGTG
+ATGTTGCAAGTGTGGCGGAACACATGTAAGCGCCGGATGTGGTAAAAGTGACGTTTTTGG
+TGTGCGCCGGTGTATACGGGAAGTGACAATTTTCGCGCGGTTTTAGGCGGATGTTGTAGT
+AAATTTGGGCGTAACCAAGTAATGTTTGGCCATTTTCGCGGGAAAACTGAATAAGAGGAA
+GTGAAATCTGAATAATTCTGTGTTACTCATAGCGCGTAATATTTGTCTAGGGCCGCGGGG
+ACTTTGACCGTTTACGTGGAGACTCGCCCAGGTGTTTTTCTCAGGTGTTTTCCGCGTTCC
+GGGTCAAAGTTGGCGTTTTATTATTATAGTCAGCTGACGCGCAGTGTATTTATACCCGGT
+GAGTTCCTCAAGAGGCCACTCTTGAGTGCCAGCGAGTAGAGTTTTCTCCTCCGAGCCGCT
+CCGACACCGGGACTGAAAATGAGACATATTATCTGCCACGGAGGTGTTATTACCGAAGAA
+ATGGCCGCCAGTCTTTTGGACCAGCTGATCGAAGAGGTACTGGCTGATAATCTTCCACCT
+CCTAGCCATTTTGAACCACCTACCCTTCACGAACTGTATGATTTAGACGTGACGGCCCCC
+GAAGATCCCAACGAGGAGGCGGTTTCGCAGATTTTTCCCGAGTCTGTAATGTTGGCGGTG
+CAGGAAGGGATTGACTTATTCACTTTTCCGCCGGCGCCCGGTTCTCCGGAGCCGCCTCAC
+CTTTCCCGGCAGCCCGAGCAGCCGGAGCAGAGAGCCTTGGGTCCGGTTTCTATGCCAAAC
+CTTGTGCCGGAGGTGATCGATCTTACCTGCCACGAGGCTGGCTTTCCACCCAGTGACGAC
+GAGGATGAAGAGGGTGAGGAGTTTGTGTTAGATTATGTGGAGCACCCCGGGCACGGTTGC
+AGGTCTTGTCATTATCACCGGAGGAATACGGGGGACCCAGATATTATGTGTTCGCTTTGC
+TATATGAGGACCTGTGGCATGTTTGTCTACAGTAAGTGAAAATTATGGGCAGTCGGTGAT
+AGAGTGGTGGGTTTGGTGTGGTAATTTTTTTTTAATTTTTACAGTTTTGTGGTTTAAAGA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Adenovirus.promoter2.tabular	Thu Apr 25 12:25:52 2013 -0400
@@ -0,0 +1,2 @@
+#Identifier	Position	Score	Likelihood
+gi_209811_gb_J01917_ADRCG	600	1.063	Highly likely prediction
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/empty_promoter2.tabular	Thu Apr 25 12:25:52 2013 -0400
@@ -0,0 +1,1 @@
+#Identifier	Position	Score	Likelihood
--- a/tools/protein_analysis/README	Thu Apr 25 11:54:47 2013 -0400
+++ b/tools/protein_analysis/README	Thu Apr 25 12:25:52 2013 -0400
@@ -142,6 +142,7 @@
          files accidentally included previously via a wildcard).
 v0.2.2 - Include missing test files.
 v0.2.3 - Added unit tests for WoLF PSORT.
+v0.2.4 - Added unit tests for Promoter 2
 
 
 Developers
--- a/tools/protein_analysis/promoter2.xml	Thu Apr 25 11:54:47 2013 -0400
+++ b/tools/protein_analysis/promoter2.xml	Thu Apr 25 12:25:52 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="promoter2" name="Promoter 2.0" version="0.0.3">
+<tool id="promoter2" name="Promoter 2.0" version="0.0.4">
     <description>Find eukaryotic PolII promoters in DNA sequences</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <!-- Using 2000 per chunk so 4 threads each doing 500 is ideal -->
@@ -23,6 +23,16 @@
     <requirements>
         <requirement type="binary">promoter</requirement>
     </requirements>
+    <tests>
+        <test>
+            <param name="fasta_file" value="Adenovirus.fasta" ftype="fasta"/>
+            <output name="tabular_file" file="Adenovirus.promoter2.tabular" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="fasta_file" value="empty.fasta" ftype="fasta"/>
+            <output name="tabular_file" file="empty_promoter2.tabular" ftype="tabular"/>
+        </test>
+    </tests>
     <help>
     
 **What it does**