# HG changeset patch
# User greg
# Date 1486389884 18000
# Node ID c4f809cd2f3893d23503de143e2f441366f412c8
# Parent  b63f96ff6708fcd7d0d9f3139d13a31e7472cf69
Uploaded

diff -r b63f96ff6708 -r c4f809cd2f38 gene_family_classifier.xml
--- a/gene_family_classifier.xml	Thu Feb 02 14:41:34 2017 -0500
+++ b/gene_family_classifier.xml	Mon Feb 06 09:04:44 2017 -0500
@@ -13,10 +13,10 @@
     </stdio>
     <command>
         <![CDATA[
-        	#import os
-        	#set scaffold_path = $scaffold.fields.path
-        	#set scaffold_dir = $os.path.split($scaffold_path)[0]
-        	#set scaffold_selection = $os.path.split($scaffold_path)[1]
+            #import os
+            #set scaffold_path = $scaffold.fields.path
+            #set scaffold_dir = $os.path.split($scaffold_path)[0]
+            #set scaffold_selection = $os.path.split($scaffold_path)[1]
 
             #if str($options_type.options_type_selector) == 'advanced':
                 #set create_orthogroup_cond = $options_type.create_orthogroup_cond
@@ -33,10 +33,10 @@
                     #set create_ortho_sequences = True
                     #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
                     #if $create_corresponding_coding_sequences:
-                    	#set dest_dir = $output_ptcgfcs.extra_files_path
+                        #set dest_dir = $output_ptcgfcs.extra_files_path
                     #else:
-                    	#set dest_dir = $output_ptcgf.extra_files_path
-                  	#end if
+                        #set dest_dir = $output_ptcgf.extra_files_path
+                      #end if
                     mkdir -p $dest_dir &&
                 #else:
                     #set create_ortho_sequences = False
@@ -79,11 +79,13 @@
 
             #if $create_ortho_sequences:
                 #if $create_corresponding_coding_sequences:
-                    && echo "# Precomputed orthologous gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_ptcgfcs
-                    && ls -al $orthogroups_fasta_src_dir | grep f >> $output_ptcgfcs
+                    && echo '#Precomputed orthologous gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files' > $output_ptcgfcs
+                    && echo '#Size    File' > $output_ptcgfcs
+                    && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptcgfcs
                 #else:
-                    && echo "# Precomputed orthologous gene family clusters: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_ptcgf
-                    && ls -al $orthogroups_fasta_src_dir | grep f >> $output_ptcgf
+                    && echo '#Precomputed orthologous gene family clusters: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files' > $output_ptcgf
+                    && echo '#Size    File' > $output_ptcgf
+                    && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptcgf
                 #end if
                 && mv $orthogroups_fasta_src_dir/* $dest_dir || true
             #end if
@@ -94,7 +96,7 @@
         <param name="input" format="fasta" type="data" label="Amino acids (proteins) sequences fasta file"/>
         <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."/>
+            <validator type="no_options" message="No PlantTribes scaffolds are available.  Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table."/>
         </param>
         <param name="method" type="select" label="Protein clustering method">
             <option value="gfam" selected="true">GFam</option>
@@ -180,8 +182,8 @@
         </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 -->
-    	<!--
+        <!-- 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"/>