# HG changeset patch
# User greg
# Date 1496930501 14400
# Node ID 80996fca62c8f53d8276432a32cdb6c209786343
# Parent  1a54a0ba5a81237ed167c6cc32e306cc8b713f59
Uploaded

diff -r 1a54a0ba5a81 -r 80996fca62c8 gene_family_integrator.xml
--- a/gene_family_integrator.xml	Tue Jun 06 08:46:37 2017 -0400
+++ b/gene_family_integrator.xml	Thu Jun 08 10:01:41 2017 -0400
@@ -4,33 +4,31 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements_gene_family_integrator" />
-    <command detect_errors="exit_code">
-        <![CDATA[
-            #set input_format = $input_format_cond.input_format
-            #set scaffold = $input_format_cond.scaffold
-            #set method = $input_format_cond.method
+    <command detect_errors="exit_code"><![CDATA[
+#set input_format = $input_format_cond.input_format
+#set scaffold = $input_format_cond.scaffold
+#set method = $input_format_cond.method
 
-            python $__tool_directory__/gene_family_integrator.py
-            --scaffold '$scaffold.fields.path'
-            --method $method
-            #if str($input_format) == 'ptortho':
-                --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
-                --output '$output_ptortho'
-                --output_dir '$output_ptortho.files_path'
-            #else:
-                ## str($input_format) == 'ptorthocs'
-                --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
-                #if str($input_format_cond.orthogroup_fna) == 'yes':
-                    --orthogroup_fna 'true'
-                    --output '$output_ptorthocs'
-                    --output_dir '$output_ptorthocs.files_path'
-                #else:
-                    --output '$output_ptortho'
-                    --output_dir '$output_ptortho.files_path'
-                #end if
-            #end if
-        ]]>
-    </command>
+python $__tool_directory__/gene_family_integrator.py
+--scaffold '$scaffold.fields.path'
+--method $method
+#if str($input_format) == 'ptortho':
+    --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
+    --output '$output_ptortho'
+    --output_dir '$output_ptortho.files_path'
+#else:
+    ## str($input_format) == 'ptorthocs'
+    --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
+    #if str($input_format_cond.orthogroup_fna) == 'yes':
+        --orthogroup_fna 'true'
+        --output '$output_ptorthocs'
+        --output_dir '$output_ptorthocs.files_path'
+    #else:
+        --output '$output_ptortho'
+        --output_dir '$output_ptortho.files_path'
+    #end if
+#end if
+    ]]></command>
     <inputs>
         <conditional name="input_format_cond">
             <param name="input_format" type="select" label="Classified orthogroup fasta files">
@@ -63,15 +61,10 @@
         </data>
     </outputs>
     <tests>
+        <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.
         <test>
-            <param name="input_format" value="ptorthocs"/>
-            <param name="input_ptorthocs" value="input.ptorthocs" ftype="ptorthocs"/>
-            <param name="scaffold" value="22Gv1.1"/>
-            <param name="method" value="orthomcl"/>
-            <param name="classifier" value="both"/>
-            <param name="orthogroup_fna" value="yes"/>
-            <output name="output_ptorthocs" file="output.ptorthocs" ftype="ptorthocs"/>
         </test>
+        -->
     </tests>
     <help>
 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary
diff -r 1a54a0ba5a81 -r 80996fca62c8 macros.xml
--- a/macros.xml	Tue Jun 06 08:46:37 2017 -0400
+++ b/macros.xml	Thu Jun 08 10:01:41 2017 -0400
@@ -1,29 +1,29 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <macros>
-    <token name="@WRAPPER_VERSION@">0.8</token>
+    <token name="@WRAPPER_VERSION@">1.0</token>
     <xml name="requirements_assembly_post_processor">
         <requirements>
-            <requirement type="package" version="0.8">plant_tribes_assembly_post_processor</requirement>
+            <requirement type="package" version="1.0.0">plant_tribes_assembly_post_processor</requirement>
         </requirements>
     </xml>
     <xml name="requirements_gene_family_aligner">
         <requirements>
-            <requirement type="package" version="0.8">plant_tribes_gene_family_aligner</requirement>
+            <requirement type="package" version="1.0.0">plant_tribes_gene_family_aligner</requirement>
         </requirements>
     </xml>
     <xml name="requirements_gene_family_classifier">
         <requirements>
-            <requirement type="package" version="0.8">plant_tribes_gene_family_classifier</requirement>
+            <requirement type="package" version="1.0.0">plant_tribes_gene_family_classifier</requirement>
         </requirements>
     </xml>
     <xml name="requirements_gene_family_integrator">
         <requirements>
-            <requirement type="package" version="0.8">plant_tribes_gene_family_integrator</requirement>
+            <requirement type="package" version="1.0.0">plant_tribes_gene_family_integrator</requirement>
         </requirements>
     </xml>
     <xml name="requirements_kaks_analysis">
         <requirements>
-            <requirement type="package" version="0.8">plant_tribes_kaks_analysis</requirement>
+            <requirement type="package" version="1.0.0">plant_tribes_kaks_analysis</requirement>
         </requirements>
     </xml>
     <xml name="requirements_ks_distribution">
@@ -33,7 +33,7 @@
     </xml>
     <xml name="requirements_gene_family_phylogeny_builder">
         <requirements>
-            <requirement type="package" version="0.8">plant_tribes_gene_family_phylogeny_builder</requirement>
+            <requirement type="package" version="1.0.0">plant_tribes_gene_family_phylogeny_builder</requirement>
         </requirements>
     </xml>
     <xml name="param_codon_alignments">
diff -r 1a54a0ba5a81 -r 80996fca62c8 test-data/input.ptorthocs
--- a/test-data/input.ptorthocs	Tue Jun 06 08:46:37 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-<html><head><h3>Orthogroups and corresponding coding sequences files: 12 files</h3></head>
-<body><p/><table cellpadding="2">
-<tr><th>Size</th><th>Name</th></tr>
-<tr bgcolor="#D8D8D8"><td>145</td><td><a href="20.faa" type="text/plain">20.faa</a>
-</td></tr>
-<tr bgcolor="#FFFFFF"><td>145</td><td><a href="20.fna" type="text/plain">20.fna</a>
-</td></tr>
-<tr bgcolor="#D8D8D8"><td>99</td><td><a href="3494.faa" type="text/plain">3494.faa</a>
-</td></tr>
-<tr bgcolor="#FFFFFF"><td>12</td><td><a href="3494.fna" type="text/plain">3494.fna</a>
-</td></tr>
-<tr bgcolor="#D8D8D8"><td>111</td><td><a href="3722.faa" type="text/plain">3722.faa</a>
-</td></tr>
-<tr bgcolor="#FFFFFF"><td>111</td><td><a href="3722.fna" type="text/plain">3722.fna</a>
-</td></tr>
-<tr bgcolor="#D8D8D8"><td>183</td><td><a href="38889.faa" type="text/plain">38889.faa</a>
-</td></tr>
-<tr bgcolor="#FFFFFF"><td>183</td><td><a href="38889.fna" type="text/plain">38889.fna</a>
-</td></tr>
-<tr bgcolor="#D8D8D8"><td>138</td><td><a href="39614.faa" type="text/plain">39614.faa</a>
-</td></tr>
-<tr bgcolor="#FFFFFF"><td>11</td><td><a href="39614.fna" type="text/plain">39614.fna</a>
-</td></tr>
-<tr bgcolor="#D8D8D8"><td>128</td><td><a href="5235.faa" type="text/plain">5235.faa</a>
-</td></tr>
-<tr bgcolor="#FFFFFF"><td>11</td><td><a href="5235.fna" type="text/plain">5235.fna</a>
-</td></tr>
-</table></body></html>
diff -r 1a54a0ba5a81 -r 80996fca62c8 test-data/output.ptorthocs
--- a/test-data/output.ptorthocs	Tue Jun 06 08:46:37 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-<html><head><h3>Integrated gene family sequences: 12 files</h3></head>
-<body><p/><table cellpadding="2">
-<tr><th>Size</th><th>Name</th></tr>
-<tr bgcolor="#D8D8D8"><td>382392</td><td><a href="20.faa" type="text/plain">20.faa</a>
-</td></tr>
-<tr bgcolor="#FFFFFF"><td>1112659</td><td><a href="20.fna" type="text/plain">20.fna</a>
-</td></tr>
-<tr bgcolor="#D8D8D8"><td>21306</td><td><a href="3494.faa" type="text/plain">3494.faa</a>
-</td></tr>
-<tr bgcolor="#FFFFFF"><td>61243</td><td><a href="3494.fna" type="text/plain">3494.fna</a>
-</td></tr>
-<tr bgcolor="#D8D8D8"><td>9874</td><td><a href="3722.faa" type="text/plain">3722.faa</a>
-</td></tr>
-<tr bgcolor="#FFFFFF"><td>27053</td><td><a href="3722.fna" type="text/plain">3722.fna</a>
-</td></tr>
-<tr bgcolor="#D8D8D8"><td>765</td><td><a href="38889.faa" type="text/plain">38889.faa</a>
-</td></tr>
-<tr bgcolor="#FFFFFF"><td>1801</td><td><a href="38889.fna" type="text/plain">38889.fna</a>
-</td></tr>
-<tr bgcolor="#D8D8D8"><td>1222</td><td><a href="39614.faa" type="text/plain">39614.faa</a>
-</td></tr>
-<tr bgcolor="#FFFFFF"><td>3136</td><td><a href="39614.fna" type="text/plain">39614.fna</a>
-</td></tr>
-<tr bgcolor="#D8D8D8"><td>22617</td><td><a href="5235.faa" type="text/plain">5235.faa</a>
-</td></tr>
-<tr bgcolor="#FFFFFF"><td>65568</td><td><a href="5235.fna" type="text/plain">5235.fna</a>
-</td></tr>
-</table></body></html>