Mercurial > repos > peterjc > mira4_assembler

diff tools/mira4/mira4_de_novo.xml @ 21:4abe8d59a438 draft

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Uploaded v0.0.4 preview 1; fix getting BAM without MAF
author peterjc
date Tue, 28 Oct 2014 08:29:59 -0400
parents aeb3e35f8236
children
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--- a/tools/mira4/mira4_de_novo.xml	Tue Jun 10 10:11:58 2014 -0400
+++ b/tools/mira4/mira4_de_novo.xml	Tue Oct 28 08:29:59 2014 -0400
@@ -180,7 +180,8 @@
             <param name="bam_wanted" value="true"/>
             <output name="out_fasta" file="U13small_m.mira4_de_novo.fasta" ftype="fasta" />
             <output name="out_bam" file="empty_file.dat" compare="contains" />
-            <output name="out_maf" file="empty_file.dat" compare="contains" />
+            <!-- TODO: Suggest startswith as a compare method? -->
+            <output name="out_maf" file="header.mira" compare="contains" />
             <output name="out_log" file="empty_file.dat" compare="contains" />
         </test>
         <!-- Simple assembly based on MIRA's minidemo/solexa1 example
@@ -192,11 +193,9 @@
             <param name="job_quality" value="accurate" />
             <param name="type" value="none" />
             <param name="filenames" value="ecoli.fastq" ftype="fastqsanger" />
-            <param name="maf_wanted" value="true"/>
-            <param name="bam_wanted" value="true"/>
+            <param name="maf_wanted" value="false"/>
+            <param name="bam_wanted" value="false"/>
             <output name="out_fasta" file="ecoli.mira4_de_novo.fasta" ftype="fasta" />
-            <output name="out_bam" file="empty_file.dat" compare="contains" />
-            <output name="out_maf" file="empty_file.dat" compare="contains" />
             <output name="out_log" file="empty_file.dat" compare="contains" />
         </test>
     </tests>