# HG changeset patch
# User greg
# Date 1495480858 14400
# Node ID 048fcfb76dfabe929d7e83e4e7f591b62034f0f8
# Parent  93a69f4573a600dfe386caa052036b714135a791
Uploaded

diff -r 93a69f4573a6 -r 048fcfb76dfa gene_family_classifier.xml
--- a/gene_family_classifier.xml	Mon May 22 15:20:39 2017 -0400
+++ b/gene_family_classifier.xml	Mon May 22 15:20:58 2017 -0400
@@ -208,16 +208,16 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="hmmscan_log" format="txt" label="Protein classification hmmscan.log on ${on_string}">
+        <data name="hmmscan_log" format="txt" label="${tool.name} (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_ptortho" format="ptortho" label="Gene family clusters on ${on_string}">
+        <data name="output_ptortho" format="ptortho" label="${tool.name} (gene family clusters) on ${on_string}">
             <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['create_orthogroup_cond']['create_corresponding_coding_sequences_cond']['create_corresponding_coding_sequences'] == 'no'</filter>
         </data>
-        <data name="output_ptorthocs" format="ptorthocs" label="Gene family clusters and corresponding coding sequences on ${on_string}">
+        <data name="output_ptorthocs" format="ptorthocs" label="${tool.name} (gene family clusters and corresponding coding sequences) on ${on_string}">
             <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['create_orthogroup_cond']['create_corresponding_coding_sequences_cond']['create_corresponding_coding_sequences'] == 'yes'</filter>
         </data>
-        <data name="output_ptsco" format="tabular" label="Single copy orthogroups on ${on_string}">
+        <data name="output_ptsco" format="tabular" label="${tool.name} (single copy orthogroups) on ${on_string}">
             <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'</filter>
             <change_format>
                 <when input="options_type.create_orthogroup_cond.create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences" value="no" format="ptortho" />
@@ -229,19 +229,24 @@
         </collection>
     </outputs>
     <tests>
-        <!-- Need to figure out how to test using scaffolds data.
         <test>
-            <param name="input" value="transcripts.cleaned.nr.pep" ftype="fasta" />
-            <param name="scaffold" value="plant_tribes/scaffolds/22Gv1.1"/>
+            <param name="input" value="transcripts.cleaned.nr.pep" ftype="fasta"/>
+            <param name="scaffold" value="22Gv1.1"/>
             <param name="method" value="orthomcl"/>
-            <param name="classifier" value="blastp"/>
+            <param name="classifier" value="both"/>
+            <param name="options_type_selector" value="advanced"/>
+            <param name="create_orthogroup" value="yes"/>
+            <param name="create_corresponding_coding_sequences" value="yes"/>
+            <output name="output_ptorthocs" file="output.ptorthocs" ftype="ptorthocs"/>
             <output_collection name="orthos" type="list">
                 <element name="proteins.blastp.22Gv1.1" file="proteins.blastp.22Gv1.1" ftype="tabular" compare="contains"/>
-                <element name="proteins.blastp.22Gv1.1.bestOrthos" file="proteins.blastp.22Gv1.1.bestOrthos" ftype="tabular"/>
-                <element name="proteins.blastp.22Gv1.1.bestOrthos.summary" file="proteins.blastp.22Gv1.1.bestOrthos.summary" ftype="tabular"/>
+                <element name="proteins.blastp.22Gv1.1.bestOrthos" file="proteins.blastp.22Gv1.1.bestOrthos" ftype="tabular" compare="contains"/>
+                <element name="proteins.both.22Gv1.1.bestOrthos" file="proteins.both.22Gv1.1.bestOrthos" ftype="tabular" compare="contains"/>
+                <element name="proteins.both.22Gv1.1.bestOrthos.summary" file="proteins.both.22Gv1.1.bestOrthos.summary" ftype="tabular" compare="contains"/>
+                <element name="proteins.hmmscan.22Gv1.1" file="proteins.hmmscan.22Gv1.1" ftype="tabular" compare="contains"/>
+                <element name="proteins.hmmscan.22Gv1.1.bestOrthos" file="proteins.hmmscan.22Gv1.1.bestOrthos" ftype="tabular" compare="contains"/>
             </output_collection>
         </test>
-        -->
     </tests>
     <help>
 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary