Mercurial > repos > greg > phylogenomics_analysis

changeset 2:56ff8d706414 draft

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Uploaded
author greg
date Wed, 04 Jan 2017 09:31:35 -0500
parents b1e7de636060
children fd6773b7bb3f
files phylogenomics_analysis.xml
diffstat 1 files changed, 5 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- 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>