# HG changeset patch
# User greg
# Date 1483625517 18000
# Node ID 37b56c1befaa40afecde63336e7ac7bef36e58cb
# Parent  fd6773b7bb3fff1181c246b99294813282b0fce0
Uploaded

diff -r fd6773b7bb3f -r 37b56c1befaa phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Wed Jan 04 09:40:42 2017 -0500
+++ b/phylogenomics_analysis.xml	Thu Jan 05 09:11:57 2017 -0500
@@ -64,14 +64,14 @@
                 #end if
             #end if
             --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
-            --num_threads \${GALAXY_SLOTS:-4} &&
-            echo "Sequence alignments and corresponding phylogenies: `ls $src_dir | wc -l` files" > $output &&
-            ls $src_dir >> $output &&
-            mv $src_dir/* $dest_dir
+            --num_threads \${GALAXY_SLOTS:-4}
+            && echo "Sequence alignments and corresponding phylogenies: `ls $src_dir | wc -l` files" > $output
+            && ls $src_dir >> $output
+            && mv $src_dir/* $dest_dir
         ]]>
     </command>
     <inputs>
-        <param name="orthogroup_fna" format="fasta" type="data" label="Gene family classification coding sequences (CDS) fasta file for which orthogroup fasta files were created"/>
+        <param name="orthogroup_fna" format="txt" type="data" label="Select sequences classified into gene family clusters"/>
         <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
             <options from_data_table="plant_tribes_scaffolds" />
             <validator type="no_options" message="No PlantTribes scaffolds are available.  Use the PlantTribes Scaffolds Download Data Manager tool to install and populate the PlantTribes scaffolds data table."/>