# HG changeset patch
# User greg
# Date 1483540295 18000
# Node ID 56ff8d7064144874a7f7f885191f21700b796ab9
# Parent  b1e7de636060c5a2b4520afee800ed3dc9be4bf1
Uploaded

diff -r b1e7de636060 -r 56ff8d706414 phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Wed Jan 04 08:24:13 2017 -0500
+++ b/phylogenomics_analysis.xml	Wed Jan 04 09:31:35 2017 -0500
@@ -60,7 +60,10 @@
                 #end if
             #end if
             --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
-            --num_threads \${GALAXY_SLOTS:-4}
+            --num_threads \${GALAXY_SLOTS:-4} &&
+            echo "Sequence alignments and corresponding phylogenies: `ls -l phylogenomicsAnalysis_dir/orthogroups_fasta | wc -l` files" > $output &&
+            ls phylogenomicsAnalysis_dir/orthogroups_fasta >> $output &&
+            mv phylogenomicsAnalysis_dir/orthogroups_fasta/* $output.extra_files_path
         ]]>
     </command>
     <inputs>
@@ -170,9 +173,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <collection name="transcripts" type="list">
-            <discover_datasets pattern="__name__" directory="phylogenomicsAnalysis_dir" visible="true" ext="fasta" />
-        </collection>
+        <data name="output" format="txt" label="Sequence alignments and corresponding phylogenies on ${on_string}"/>
     </outputs>
     <tests>
         <test>
@@ -183,7 +184,6 @@
             <param name="dereplicate" value="yes"/>
             <param name="min_length" value="200"/>
             <output_collection name="orthos" type="list">
-
             </output_collection>
         </test>
     </tests>