# HG changeset patch
# User trinity_ctat
# Date 1523645871 14400
# Node ID e5182440ba1763924e26318f311d035e42a5c515
# Parent  1c8d5eb15ed12065b582851d751827afa79af6f5
Trying to fix problems with ctat_star_fusion and ctat_metagenomics.

diff -r 1c8d5eb15ed1 -r e5182440ba17 ctat_metagenomics.xml
--- a/ctat_metagenomics.xml	Thu Apr 12 10:46:59 2018 -0400
+++ b/ctat_metagenomics.xml	Fri Apr 13 14:57:51 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="ctat_metagenomics" name="ctat_metagenomics" version=1.0.0 profile="17.05">
+<tool id="ctat_metagenomics" name="ctat_metagenomics" version="1.0.0" profile="17.05">
 
     <description>Centrifuge - Classifier for metagenomic sequences (RNA-Seq)</description>
     <requirements>
@@ -61,7 +61,7 @@
         </conditional>
 
         <param name="index" type="select" label="Choose reference genome index :" help="Select genome index">
-            <options from_data_table="ctat_centrifuge_indexes">
+            <options from_data_table="ctat_centrifuge_indexes" />
         </param>
       
     </inputs>
@@ -89,42 +89,6 @@
             <output name="classification_report" file="centrifuge/SRR2219890_1.classification.report.txt" />
             <output name="kraken_style_report" file="centrifuge/SRR2219890_1.kraken_style_report.txt" />
         </test>
-        <test>
-            <!-- The following test uses two files that are left/right paired reads.
-            -->
-            <param name="format" value="fastq" />
-            <param name="type" value="paired" />
-            <param name="left_fq" value="centrifuge/SRR073747_1.fastq" />
-            <param name="right_fq" value="centrifuge/SRR073747_2.fastq" />
-            <!-- FIX - How are we going to set the index value when we don't know what is in the table? How do we find it for testing?
-            <param name="index.fields.path" value="/N/dc2/projects/galaxyshared/trinity/dev/Trinity_CTAT/metagenomics/phv" />
-            -->
-            <output name="classification_results" >
-                <assert_contents>
-                    <has_line_matching expression=".+" />
-                    <has_line line="readID&#009;seqID&#009;taxID&#009;score&#009;2ndBestScore&#009;hitLength&#009;queryLength&#009;numMatches" />
-                </assert_contents>
-            </output>
-            <output name="classification_report" file="centrifuge/SRR073747_1_2.classification.report.txt" />
-            <output name="kraken_style_report" file="centrifuge/SRR073747_1_2.kraken_style_report.txt" />
-        </test>
-        <test>
-            <!-- The following test uses an unpaired Trinity fasta file.
-            -->
-            <param name="format_type.format" value="fasta" />
-            <param name="fasta_file" value="centrifuge/TrinitySRR2219890.fasta" />
-            <!-- FIX - How are we going to set the index value when we don't know what is in the table? How do we find it for testing?
-            <param name="index" value="/N/dc2/projects/galaxyshared/trinity/dev/Trinity_CTAT/metagenomics/phv" />
-            -->
-            <output name="classification_results" >
-                <assert_contents>
-                    <has_line_matching expression=".+" />
-                    <has_line line="readID&#009;seqID&#009;taxID&#009;score&#009;2ndBestScore&#009;hitLength&#009;queryLength&#009;numMatches" />
-                </assert_contents>
-            </output>
-            <output name="classification_report" file="centrifuge/TrinitySRR2219890.classification.report.txt" />>
-            <output name="kraken_style_report" file="centrifuge/TrinitySRR2219890.kraken_style_report.txt" />
-        </test>
     </tests>
 
     <help>