# HG changeset patch
# User cropgeeks
# Date 1488453286 18000
# Node ID 927533e85a6abf911a48941e1bafd2a5e59928ed
# Parent  414aa590a1de2951a5efc67d48aefea8d6f79f2b
Uploaded

diff -r 414aa590a1de -r 927533e85a6a flapjack.py
--- a/flapjack.py	Thu Mar 02 05:40:54 2017 -0500
+++ b/flapjack.py	Thu Mar 02 06:14:46 2017 -0500
@@ -9,7 +9,7 @@
         if super(FlapjackFormat, self).sniff(filename):
 			fj_table_names = ["objects", "project"]
             try:
-                conn = sqlite.connect( filename )
+                conn = sqlite.connect(filename)
                 c = conn.cursor()
                 tables_query = "SELECT name FROM sqlite_master WHERE type='table' ORDER BY name"
                 result = c.execute(tables_query).fetchall()
@@ -19,7 +19,7 @@
                         return False
                 return True
             except Exception as e:
-                log.warning( '%s, sniff Exception: %s', self, e )
+                log.warning('%s, sniff Exception: %s', self, e)
         return False
 
 class FlapjackMapFormat(Tabular):
diff -r 414aa590a1de -r 927533e85a6a hapmap2fj.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hapmap2fj.xml	Thu Mar 02 06:14:46 2017 -0500
@@ -0,0 +1,58 @@
+<tool id="flapjack_hapmap2fj" name="HapMap to Flapjack" version="0.0.1">
+
+<!--System.out.println("Usage: hapmap2flapjack <options>\n"
+			+ " where valid options are:\n"
+			+ "   -separator=<s or t>            (required separator used in input file)\n"
+			+ "   -hapmap=<hapmap_file>          (required input file)\n"
+			+ "   -map=<map_file>                (required output file)\n"
+			+ "   -genotypes=<genotype_file>     (required output file)\n");-->
+
+  <description>convert an HapMap formatted file into a Flapjack-formatted genotype file</description>
+  <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.HapMapToFJTabbedConverter 
+	  -hapmap=$hapmap
+	  -separator=$separator 
+	  -map=$map
+	  -genotypes=$genotypes
+  </command>
+  <inputs>
+    <param format="txt" name="hapmap" type="data" label="Source file"
+		help="HapMap Formatted File"/>
+	<param name="separator" type="boolean" label="File is tab-separated"
+		truevalue="t" falsevalue="s">
+	</param>
+	<param name="memory" type="select" label="Memory"
+		help="How much memory to use; larger files may require more memory">
+	  <option selected="true" value="64m">64MB</option>
+	  <option value="128m">128MB</option>
+	  <option value="256m">256MB</option>
+	</param>
+  </inputs>
+  <outputs>
+	<data format="fjmap" name="map" />
+    <data format="fjgenotype" name="genotypes" />
+  </outputs>
+  
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+
+  <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
+allowing for rapid navigation and comparisons between lines, markers and chromosomes.
+
+This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
+See Flapjack's documentation_ for more details on the various Flapjack data formats.
+
+.. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats 
+
+
+
+  ]]></help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btq580</citation>
+  </citations>
+</tool>
\ No newline at end of file
diff -r 414aa590a1de -r 927533e85a6a hdf52fj.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hdf52fj.xml	Thu Mar 02 06:14:46 2017 -0500
@@ -0,0 +1,55 @@
+<tool id="flapjack_hdf52fj" name="HDF5 to Flapjack" version="0.0.1">
+
+  <description>convert an HDF5 formatted genotype file into a Flapjack-formatted genotype file</description>
+  <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.Hdf5ToFJTabbedConverter 
+	  -hdf5=$hdf5 
+	  -lines=$lines
+	  -markers=$markers
+	  -missing_filter=$missing_filter
+	  -heterozygous_filter=$heterozygous_filter
+	  -genotypes=$genotypes
+  </command>
+  <inputs>
+    <param format="h5" name="hdf5" type="data" label="Source file"
+		help="Flapjack's flavour of HDF5 for storing genotype data."/>
+	<param format="txt" name="lines" type="data" label="Source file"
+		help="A list of lines desired in the output. One line name per line on each line of the file."/>
+	<param format="txt" name="markers" type="data" label="Source file"
+		help="A list of markers desired in the output. One line name per marker on each line of the file."/>
+	<param name="missing_filter" type="boolean" label="Filter out missing markers"
+		truevalue="true" falsevalue="false">
+	</param>
+	<param name="heterozygous_filter" type="boolean" label="Filter out heterozygous markers"
+		truevalue="true" falsevalue="false">
+	</param>
+	<param name="memory" type="select" label="Memory"
+		help="How much memory to use; larger files may require more memory">
+	  <option selected="true" value="64m">64MB</option>
+	  <option value="128m">128MB</option>
+	  <option value="256m">256MB</option>
+	</param>
+  </inputs>
+  <outputs>
+    <data format="fjgenotype" name="genotypes" />
+  </outputs>
+
+  <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
+allowing for rapid navigation and comparisons between lines, markers and chromosomes.
+
+This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
+See Flapjack's documentation_ for more details on the various Flapjack data formats.
+
+.. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats 
+
+
+
+  ]]></help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btq580</citation>
+  </citations>
+</tool>
\ No newline at end of file