# HG changeset patch
# User greg
# Date 1487606161 18000
# Node ID 9969b17ae6567209d73442ddc5daa01ef669b048
# Parent  6e859426c8731bcc31f1b5a3c2389f58d8aa800e
Uploaded

diff -r 6e859426c873 -r 9969b17ae656 gene_family_classifier.xml
--- a/gene_family_classifier.xml	Fri Feb 17 14:00:43 2017 -0500
+++ b/gene_family_classifier.xml	Mon Feb 20 10:56:01 2017 -0500
@@ -118,14 +118,14 @@
                     && echo -e "#Size\tName" > $output_ptortho
                     && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptortho
                 #end if
-                && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir
+                && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir || true
             #end if
 
             #if $single_copy_orthogroup:
                 #if $create_ortho_sequences:
                     && echo -e "#Size\tName" > $output_ptsco
                     && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptsco
-                    && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir
+                    && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir || true
                 #end if
             #end if
         ]]>
@@ -256,8 +256,6 @@
         </collection>
     </outputs>
     <tests>
-        <!-- Not sure how to test this since the tool requires scaffolds data which is extremely large and installed using a Data Manager -->
-        <!--
         <test>
             <param name="input" value="transcripts.cleaned.nr.pep" ftype="fasta" />
             <param name="scaffold" value="22Gv1.1"/>
@@ -271,7 +269,6 @@
                 <element name="proteins.blastp.22Gv1.1.bestOrthos.summary" file="proteins.blastp.22Gv1.1.bestOrthos.summary" ftype="tabular"/>
             </output_collection>
         </test>
-        -->
     </tests>
     <help>
 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of