# HG changeset patch
# User greg
# Date 1483559490 18000
# Node ID 9d4ec11028031d8011df33479c022ee526115959
# Parent  595088cc480ae216c2f2d3fa35b966c09d120023
Uploaded

diff -r 595088cc480a -r 9d4ec1102803 gene_family_classifier.xml
--- a/gene_family_classifier.xml	Wed Jan 04 14:30:12 2017 -0500
+++ b/gene_family_classifier.xml	Wed Jan 04 14:51:30 2017 -0500
@@ -15,7 +15,7 @@
             #if str($options_type.options_type_selector) == 'advanced' and str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes':
                 #import os
                 #set create_ortho_sequences = True
-                #set src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
+                #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
                 #set dest_dir = $output.extra_files_path
                 mkdir -p $dest_dir &&
             #else:
@@ -41,14 +41,14 @@
             --num_threads \${GALAXY_SLOTS:-4}
             #if str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both':
                 #if str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes':
-                    && mv $src_dir/hmmscan.log $hmmscan_log
+                    && mv geneFamilyClassification_dir/hmmscan.log $hmmscan_log
                 #else:
-                    && rm $src_dir/hmmscan.log
+                    && rm geneFamilyClassification_dir/hmmscan.log
                 #end if
             #end if
             #if $create_ortho_sequences:
-                && echo "Sequences classified into pre-computed orthologous plant gene family clusters: `ls $src_dir | wc -l` files" > $output
-                && mv $src_dir/* $dest_dir
+                && echo "Sequences classified into pre-computed orthologous plant gene family clusters: `ls $orthogroups_fasta_src_dir | wc -l` files" > $output
+                && mv $orthogroups_fasta_src_dir/* $dest_dir
             #end if
         ]]>
     </command>
@@ -119,12 +119,12 @@
         </conditional>
     </inputs>
     <outputs>
+        <data name="hmmscan_log" format="txt" label="Protein classification hmmscan.log on ${on_string}">
+            <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter>
+        </data>
         <data name="output" format="txt" label="Sequences classified into gene family clusters on ${on_string}">
             <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes'</filter>
         </data>
-        <data name="hmmscan_log" format="txt" label="Protein classification hmmscan.log on ${on_string}">
-            <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter>
-        </data>
         <collection name="transcripts" type="list">
             <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
         </collection>