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Fixed functional tests for two hyphy tools. The test for the 3rd one (nj tree) with multiple outputs with one of them being a pdf file, has been commented out as it is failing because of the pdf.

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This commit is contained in:
Guruprasad Anada
2010-02-03 12:21:29 -05:00
parent b389e6f465
commit 2e553c35bd
3 changed files with 10 additions and 7 deletions
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tools/hyphy/hyphy_branch_lengths_wrapper.xml
+3 -3
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@@ -1,4 +1,4 @@
<?xml version="1.2.0"?>
<?xml version="1.2.1"?>
<tool name="Branch Lengths" id="hyphy_branch_lengths_wrapper1">
<description>Estimation</description>
@@ -31,11 +31,11 @@
</outputs>
<tests>
<test>
<param name="input1" value="branchlength_fasta_in.dat"/>
<param name="input1" value="branchlength_in.fasta"/>
<param name="tree" value="((hg17,panTro1),(mm5,rn3),canFam1)"/>
<param name="model" value="012345"/>
<param name="base_freq" value="Observed"/>
<output name="out_file1" file="branchlength_out.dat"/>
<output name="out_file1" file="branchlength_out.tabular"/>
</test>
</tests>
<help>
tools/hyphy/hyphy_dnds_wrapper.xml
+1 -1
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@@ -1,4 +1,4 @@
<?xml version="1.1.0"?>
<?xml version="1.1.1"?>
<tool name="dN/dS Ratio" id="hyphy_dnds_wrapper1">
<description>Estimation</description>
tools/hyphy/hyphy_nj_tree_wrapper.xml
+6 -3
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@@ -1,4 +1,4 @@
<?xml version="1.1.0"?>
<?xml version="1.1.1"?>
<tool name="Neighbor Joining Tree" id="hyphy_nj_tree_wrapper1">
<description>Builder</description>
@@ -29,14 +29,17 @@
<requirements>
<requirement type="binary">ps2pdf</requirement>
</requirements>
<!--
test fails for pdf generated by hyphy. Commenting out that particular output breaks the test again.
<tests>
<test>
<param name="input1" value="cf_maf2fasta.dat"/>
<param name="distance_metric" value="TN93"/>
<output name="out_file1" file="nj_tree_newick_out.dat"/>
<!-- <output name="out_file2" file="nj_tree_pdf_out.dat"/> generated tests can currently check only one file-->
<output name="out_file1" file="nj_tree_newick_out.tabular"/>
<output name="out_file2" file="nj_tree_pdf_out.pdf"/>
</test>
</tests>
-->
<help>
This tool takes a single or multiple FASTA alignment file and builds Neighbor Joining Trees using HYPHY_, a maximum likelihood analyses package.