# HG changeset patch
# User gandres
# Date 1455549978 18000
# Node ID ec22fcacb66cbb8bcc91137a6ae6028006354d84
# Parent  10627af23f10c5f54e3c2587854ea06400cec13d
planemo upload

diff -r 10627af23f10 -r ec22fcacb66c MDSplot/mdsplot.xml
--- a/MDSplot/mdsplot.xml	Tue Dec 15 05:18:02 2015 -0500
+++ b/MDSplot/mdsplot.xml	Mon Feb 15 10:26:18 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="sniplay_mdsplot" name="MDS plot" version="1.1.1">
+<tool id="sniplay_mdsplot" name="MDS plot" version="1.2.0">
     
     <!-- [REQUIRED] Tool description displayed after the tool name -->
     <description> IBS matrix / multi-dimensional scaling</description>
@@ -37,8 +37,8 @@
     
     <!-- [REQUIRED] Output files -->
     <outputs>
-	<data name="fileout_matrix" type="data" format="tabular" label="${fileout_label}.ibs_matrix.txt" />
-	<data name="fileout_plot" type="data" format="tabular" label="${fileout_label}.mds_plot.txt" />
+	<data name="fileout_matrix" type="data" format="txt" label="${fileout_label}.ibs_matrix.txt" />
+	<data name="fileout_plot" type="data" format="txt" label="${fileout_label}.mds_plot.txt" />
 	<data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
     </outputs>
     
diff -r 10627af23f10 -r ec22fcacb66c Rooting/rooting.xml
--- a/Rooting/rooting.xml	Tue Dec 15 05:18:02 2015 -0500
+++ b/Rooting/rooting.xml	Mon Feb 15 10:26:18 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="sniplay_rooting" name="Rooting" version="1.0.2">
+<tool id="sniplay_rooting" name="Rooting" version="1.0.3">
     
     <!-- [REQUIRED] Tool description displayed after the tool name -->
     <description> Midpoint rooting of newick tree </description>
@@ -30,14 +30,14 @@
    
     <!-- [REQUIRED] Input files and tool parameters -->
     <inputs>
-	<param name="filein" type="data" format="txt" optional="false" label="Fasta alignment input" />
+	<param name="filein" type="data" format="nwk" optional="false" label="Fasta alignment input" />
 	<param name="fileout_label" type="text" value="out tree" label="Output name" help="Output name for files" />
     </inputs> 
     
     <!-- [REQUIRED] Output files -->
     <outputs>
 	<data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
-	<data name="fileout" type="data" format="txt" label="${fileout_label}" />
+	<data name="fileout" type="data" format="nwk" label="${fileout_label}" />
     </outputs>
     
     <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
diff -r 10627af23f10 -r ec22fcacb66c SNP_density/calculateSlidingWindowsSNPdensitiesFromHapMap_wrapper.xml
--- a/SNP_density/calculateSlidingWindowsSNPdensitiesFromHapMap_wrapper.xml	Tue Dec 15 05:18:02 2015 -0500
+++ b/SNP_density/calculateSlidingWindowsSNPdensitiesFromHapMap_wrapper.xml	Mon Feb 15 10:26:18 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="sniplay_density" name="SNP density" version="1.3.0">
+<tool id="sniplay_density" name="SNP density" version="1.4.0">
     
     <!-- [REQUIRED] Tool description displayed after the tool name -->
     <description> Calculate SNP densities along chromosome from HapMap</description>
@@ -35,8 +35,8 @@
     
     <!-- [REQUIRED] Output files -->
     <outputs>
-	<data name="fileout" type="data" format="tabular" label="${fileout_label}" />
-	<data name="fileout_bysample" type="data" format="tabular" label="${fileout_label}.by_sample" />
+	<data name="fileout" type="data" format="txt" label="${fileout_label}" />
+	<data name="fileout_bysample" type="data" format="txt" label="${fileout_label}.by_sample" />
     </outputs>
 
     <tests>
diff -r 10627af23f10 -r ec22fcacb66c check_gwas_inputs/CheckGWASInputs.xml
--- a/check_gwas_inputs/CheckGWASInputs.xml	Tue Dec 15 05:18:02 2015 -0500
+++ b/check_gwas_inputs/CheckGWASInputs.xml	Mon Feb 15 10:26:18 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="check_GWAS_inputs" name="Check GWAS Inputs" version="1.0">
+<tool id="check_GWAS_inputs" name="Check GWAS Inputs" version="1.1">
 	<description>checks concordance between input files for GWAS analysis</description>
 
     <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
@@ -15,8 +15,8 @@
 	<command interpreter="bash">./CheckGWASInputs.sh $hapmap $trait $out_hapmap $out_trait $stats
     </command>
 	<inputs>
-		<param format="text" name="hapmap" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/>
-		<param format="text" name="trait" type="data" label="Trait file" help="Phenotypic file"/>
+		<param format="txt" name="hapmap" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/>
+		<param format="txt" name="trait" type="data" label="Trait file" help="Phenotypic file"/>
 	</inputs>
 	<outputs>
 		<data format="txt" name="out_hapmap" label="Hapmap output"/>