# HG changeset patch
# User jaredgk
# Date 1562181124 14400
# Node ID 76d433f51d11fa42f88a2ccb6f1c954f7e76f421

Uploaded

diff -r 000000000000 -r 76d433f51d11 mega_galaxy_input.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mega_galaxy_input.py	Wed Jul 03 15:12:04 2019 -0400
@@ -0,0 +1,22 @@
+import sys
+import shutil
+import os
+
+def check_data_format(fn):
+    f = open(fn,'r')
+    l = f.readline()
+    if l[0:5] == '#mega':
+        return 'meg'
+        os.environ['MDTYPE'] = 1
+    return 'fasta'
+
+data_name = str(sys.argv[1])
+data_mod_name = 'mega_data.'+check_data_format(data_name)
+os.symlink(data_name,data_mod_name)
+if len(sys.argv) == 3:
+    tree_name = str(sys.argv[2])
+    tree_mod_name = 'mega_tree.nwk'
+    os.symlink(tree_name,tree_mod_name)
+lf = open('mega_data.txt','w')
+lf.write(data_mod_name+'\n')
+
diff -r 000000000000 -r 76d433f51d11 mega_galaxy_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mega_galaxy_wrapper.xml	Wed Jul 03 15:12:04 2019 -0400
@@ -0,0 +1,82 @@
+<tool id="megalaxy" name="MEGA for Galaxy" version="0.1">
+    <stdio>
+        <exit_code range="1:" level="fatal" />
+    </stdio>
+    <description>Galaxy interface for MEGA-CC</description>
+    <command>
+        <![CDATA[
+            python $__tool_directory__/mega_galaxy_input.py $data_input &&
+            $__tool_directory__/megacc -a $analysis_input -d mega_data.txt
+            #if $advf.calibration_input
+                -c $advf.calibration_input
+            #end if
+            #if $advf.groups_input
+                -g $advf.groups_input
+            #end if
+            #if $advf.tree_input
+                -t $advf.tree_input
+            #end if
+            #if $advo.format != "None"
+                -f $advo.format
+            #end if
+            #if $advo.gap_symbol
+                -gs $advo.gap_symbol
+            #end if
+            #if $advo.idbase_symbol
+                -is $advo.idbase_symbol
+            #end if
+            #if $advo.missing_symbol
+                -ms $advo.missing_symbol
+            #end if
+            -o MEGA/mega_galaxy_out 
+            
+        
+        ]]>
+    </command>
+
+    <inputs>
+        <param name="analysis_input" type="data" label="MEGA Analysis Options (.mao) File"/>
+        <param name="data_input" type="data" label="Data File"/>
+        <section name="advf" title="Optional Files" expanded="false">
+            <param name="calibration_input" type="data" label="Calibration file" help="Provides calibration
+            data for tree calling methods" optional="true"/>
+            <param name="groups_input" type="data" label="Groups file"
+            help="Organizes taxa into groups. Each line is a key-value pair of the form: taxonName=groupName" optional="true"/>
+            <param name="tree_input" type="data" label="Tree file" help="Required for some methods" optional="true"/>
+        </section>
+        <section name="advo" title="Optional Arguments" expanded="false">
+            <param name="concat" type="boolean" truevalue="-ca" falsevalue="" label="Concatenate Alignments"/>
+            <param name="format" type="select" label="Format (for sequence alignment only)">
+                <option value="None" selected="true">None</option>
+                <option value="MEGA">MEGA</option>
+                <option value="Fasta">Fasta</option>
+            </param>
+            <param name="gap_symbol" type="text" label="Gap Symbol in sequence data file" optional="true"/>
+            <param name="idbase_symbol" type="text" label="Character that represents identical bases in sequence data file" optional="true"/>
+            <param name="missing_symbol" type="text" label="Character that represents missing bases in sequence data file" optional="true"/>
+            <param name="pfc" type="float" min="0.0" max="1.0" label="Partition Frequency Cutoff: when boostrapping, will output partition frequencies that are over given frequency" optional="true"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="outputs" format="txt">
+            <discover_datasets pattern="__designation__" directory="MEGA" visible="true" format="txt"/>
+        </data>
+    </outputs>
+    <help>
+    <![CDATA[
+        Use of MEGA requires two files, a MEGA Analysis Options (.mao) file and a file with data for analysis,
+        which may be one of many, including FASTA files. The MAO file must be generated prior to use of 
+        MEGA. This file can be made with the MEGA prototyper, available from the `MEGA site`_. 
+    
+        .. _MEGA site: https://megasoftware.net
+    ]]>
+    </help>
+    <tests>
+        <test>
+            <param name="analysis_input" value="infer_NJ_nucleotine.mao"/>
+            <param name="data_input" value="Drosophilia_Adh.meg"/>
+            <assert_stdout has_text="Analysis Complete"/>
+            <assert_stdout has_text="MEGA-CC"/>
+        </test>
+    </tests>
+</tool>
diff -r 000000000000 -r 76d433f51d11 megacc
Binary file megacc has changed