Mercurial > repos > greg > gene_family_aligner

changeset 65:71619c9e01d3 draft

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Uploaded
author greg
date Wed, 13 Dec 2017 14:09:03 -0500
parents 8d71c1dff476
children bb3a5d50da92
files gene_family_aligner.xml
diffstat 1 files changed, 5 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/gene_family_aligner.xml	Mon Oct 30 08:56:01 2017 -0400
+++ b/gene_family_aligner.xml	Wed Dec 13 14:09:03 2017 -0500
@@ -47,7 +47,11 @@
         #end if
     #end if
 #end if
-&>proc.log
+&>gene_family_aligner_log.txt;
+if [[ $? -ne 0 ]]; then
+    find geneFamilyAlignments_dir -type d -maxdepth 1 -exec cp gene_family_aligner_log.txt {} \;
+    exit 1;
+fi
     ]]></command>
     <inputs>
         <param name="input" format="fasta" type="data_collection" collection_type="list" label="Integrated orthogroup fasta files" />
@@ -129,7 +133,6 @@
             <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_fna" format="fasta" />
             <filter>codon_alignments == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
         </collection>
-
     </outputs>
     <tests>
         <test>