# HG changeset patch
# User Wolfgang Maier
# Date 1438118471 -7200
# Node ID bdd1995c9e662127a1a42a803f8b18ff05bea304
# Parent  ffee8534a5c482ddfc9e42841c0cd9cab1b00cb4
upgrade to mimodd version 0.1.6.1

diff -r ffee8534a5c4 -r bdd1995c9e66 annotate_variants.xml
--- a/annotate_variants.xml	Thu Jun 04 17:52:04 2015 +0200
+++ b/annotate_variants.xml	Tue Jul 28 23:21:11 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="annotate_variants" name="Variant Annotation">
+<tool id="annotate_variants" name="Variant Annotation" version="0.1.6.1">
   <description>Predict the effects of SNPs and indels on known genes in the reference genome using SnpEff</description>
   <macros>
     <import>toolshed_macros.xml</import>
diff -r ffee8534a5c4 -r bdd1995c9e66 bamsort.xml
--- a/bamsort.xml	Thu Jun 04 17:52:04 2015 +0200
+++ b/bamsort.xml	Tue Jul 28 23:21:11 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="bamsort" name="Sort BAM file">
+<tool id="bamsort" name="Sort BAM file" version="0.1.6.1">
   <description>Sort a BAM file by coordinates (or names) of the mapped reads</description>
   <macros>
     <import>toolshed_macros.xml</import>
@@ -6,13 +6,27 @@
   <expand macro="requirements"/>
   <version_command>mimodd version -q</version_command>
   <command>
-	mimodd sort "$inputfile" -o "$output" --oformat $oformat $by_name
+	mimodd sort "$input.ifile" -o "$output" --iformat $input.iformat --oformat $oformat $by_name
   </command>
   
   <inputs>
-    <param name="inputfile" type="data" format="bam" label="Input file to sort" />
+    <conditional name="input">
+      <param name="iformat" type="select" label = "Input data format">
+        <option value="bam">bam</option>
+        <option value="sam">sam</option>
+      </param>
+      <when value="bam">
+        <param name="ifile" type="data" format="bam" label="BAM input file to sort" />
+      </when>
+      <when value="sam">
+        <param name="ifile" type="data" format="sam" label="SAM input file to sort" />
+      </when>
+    </conditional>
+    <param name="oformat" type="select" label = "Output format for the sorted data">
+      <option value="bam">bam</option>
+      <option value="sam">sam</option>
+    </param>
     <param name="by_name" type="boolean" truevalue = "-n" falsevalue ="" label="Sort by read names instead of coordinates" checked = "false" help="A less common option, but necessary, e.g., if you want to re-align sorted output from a previous run of the Snap Align Tool." />
-    <param name="oformat" type="boolean" truevalue = "sam" falsevalue = "bam" label = "Output in uncompressed SAM format" checked = "false" />
   </inputs>
   
   <outputs>
diff -r ffee8534a5c4 -r bdd1995c9e66 cloudmap.xml
--- a/cloudmap.xml	Thu Jun 04 17:52:04 2015 +0200
+++ b/cloudmap.xml	Tue Jul 28 23:21:11 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="cloudmap_prepare" name="Prepare variant data for mapping">
+<tool id="cloudmap_prepare" name="Prepare variant data for mapping" version="0.1.6.1">
   <description>with the CloudMap series of tools.</description>
   <macros>
     <import>toolshed_macros.xml</import>
diff -r ffee8534a5c4 -r bdd1995c9e66 convert.xml
--- a/convert.xml	Thu Jun 04 17:52:04 2015 +0200
+++ b/convert.xml	Tue Jul 28 23:21:11 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="convert" name="Convert">
+<tool id="convert" name="Convert" version="0.1.6.1">
   <description>between different sequence data formats</description>
   <macros>
     <import>toolshed_macros.xml</import>
diff -r ffee8534a5c4 -r bdd1995c9e66 covstats.xml
--- a/covstats.xml	Thu Jun 04 17:52:04 2015 +0200
+++ b/covstats.xml	Tue Jul 28 23:21:11 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="coverage_stats" name="Coverage Statistics">
+<tool id="coverage_stats" name="Coverage Statistics" version="0.1.6.1">
   <description>Calculate coverage statistics for a BCF file as generated by the Variant Calling tool</description>
   <macros>
     <import>toolshed_macros.xml</import>
diff -r ffee8534a5c4 -r bdd1995c9e66 deletion_predictor.xml
--- a/deletion_predictor.xml	Thu Jun 04 17:52:04 2015 +0200
+++ b/deletion_predictor.xml	Tue Jul 28 23:21:11 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="deletion_prediction" name="Deletion Prediction for paired-end data">
+<tool id="deletion_prediction" name="Deletion Prediction for paired-end data" version="0.1.6.1">
   <description>Predicts deletions in one or more aligned read samples based on coverage of the reference genome and on insert sizes</description>
   <macros>
     <import>toolshed_macros.xml</import>
diff -r ffee8534a5c4 -r bdd1995c9e66 fileinfo.xml
--- a/fileinfo.xml	Thu Jun 04 17:52:04 2015 +0200
+++ b/fileinfo.xml	Tue Jul 28 23:21:11 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="fileinfo" name="Retrieve File Information">
+<tool id="fileinfo" name="Retrieve File Information" version="0.1.6.1">
   <description>for supported data formats.</description>
   <macros>
     <import>toolshed_macros.xml</import>
diff -r ffee8534a5c4 -r bdd1995c9e66 reheader.xml
--- a/reheader.xml	Thu Jun 04 17:52:04 2015 +0200
+++ b/reheader.xml	Tue Jul 28 23:21:11 2015 +0200
@@ -1,5 +1,4 @@
-<tool id="reheader" name="Reheader BAM file">
-
+<tool id="reheader" name="Reheader BAM file" version="0.1.6.1">
   <description>From a BAM file generate a new file with the original header (if any) replaced or modified by that found in a second SAM file</description>
   <expand macro="requirements"/>
   <version_command>mimodd version -q</version_command>
@@ -83,7 +82,7 @@
 
     #set $restr = ""
     #for $rename in $rg_renaming
-      #set $restr = $restr + ($str($rename.from) and $str($rename.to) and '"' + $str($rename.from) + '" : "' + $str($rename.to) + '"')
+      #set $restr = $restr + ($str($rename.from) and $str($rename.to) and '"' + $str($rename.from) + '" : "' + $str($rename.to) + '" ')
     #end for
     #if $restr
       --rgm $restr
@@ -91,7 +90,7 @@
  
     #set $restr = ""
     #for $rename in $sq_renaming
-      #set $restr = $restr + ($str($rename.from) and $str($rename.to) and '"' + $str($rename.from) + '" : "' + $str($rename.to) + '"')
+      #set $restr = $restr + ($str($rename.from) and $str($rename.to) and '"' + $str($rename.from) + '" : "' + $str($rename.to) + '" ')
     #end for
     #if $restr
       --sqm $restr
diff -r ffee8534a5c4 -r bdd1995c9e66 sam_header.xml
--- a/sam_header.xml	Thu Jun 04 17:52:04 2015 +0200
+++ b/sam_header.xml	Tue Jul 28 23:21:11 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="ngs_run_annotation" name="NGS Run Annotation">
+<tool id="ngs_run_annotation" name="NGS Run Annotation" version="0.1.6.1">
   <description>Create a SAM format header from run metadata for sample annotation.</description>
   <macros>
     <import>toolshed_macros.xml</import>
diff -r ffee8534a5c4 -r bdd1995c9e66 snap_caller.xml
--- a/snap_caller.xml	Thu Jun 04 17:52:04 2015 +0200
+++ b/snap_caller.xml	Tue Jul 28 23:21:11 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="read_alignment" name="SNAP Read Alignment">
+<tool id="read_alignment" name="SNAP Read Alignment" version="0.1.6.1">
   <description>Map sequence reads to a reference genome using SNAP</description>
   <macros>
     <import>toolshed_macros.xml</import>
diff -r ffee8534a5c4 -r bdd1995c9e66 snp_caller_caller.xml
--- a/snp_caller_caller.xml	Thu Jun 04 17:52:04 2015 +0200
+++ b/snp_caller_caller.xml	Tue Jul 28 23:21:11 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="variant_calling" name="Variant Calling">
+<tool id="variant_calling" name="Variant Calling" version="0.1.6.1">
   <description>From a reference and aligned reads generate a BCF file with position-specific variant likelihoods and coverage information</description>
   <macros>
     <import>toolshed_macros.xml</import>
diff -r ffee8534a5c4 -r bdd1995c9e66 snpeff_genomes.xml
--- a/snpeff_genomes.xml	Thu Jun 04 17:52:04 2015 +0200
+++ b/snpeff_genomes.xml	Tue Jul 28 23:21:11 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="snpeff_genomes" name="List Installed SnpEff Genomes">
+<tool id="snpeff_genomes" name="List Installed SnpEff Genomes" version="0.1.6.1">
   <description>Checks the local SnpEff installation to compile a list of currently installed genomes</description>
   <macros>
     <import>toolshed_macros.xml</import>
diff -r ffee8534a5c4 -r bdd1995c9e66 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jun 04 17:52:04 2015 +0200
+++ b/tool_dependencies.xml	Tue Jul 28 23:21:11 2015 +0200
@@ -7,10 +7,10 @@
     <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
     
-  <package name="mimodd" version="0.1.6">
+  <package name="mimodd" version="0.1.6.1">
     <install version="1.0">
       <actions>
-        <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.6.tar.gz</action>
+        <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.6.1.tar.gz</action>
         <action type="set_environment_for_install">
           <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
             <package name="python3" version="3.4.1" />
diff -r ffee8534a5c4 -r bdd1995c9e66 toolshed_macros.xml
--- a/toolshed_macros.xml	Thu Jun 04 17:52:04 2015 +0200
+++ b/toolshed_macros.xml	Tue Jul 28 23:21:11 2015 +0200
@@ -1,7 +1,7 @@
 <macros>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="0.1.6">mimodd</requirement>
+      <requirement type="package" version="0.1.6.1">mimodd</requirement>
     </requirements>
   </xml>
 </macros>
diff -r ffee8534a5c4 -r bdd1995c9e66 varextract.xml
--- a/varextract.xml	Thu Jun 04 17:52:04 2015 +0200
+++ b/varextract.xml	Tue Jul 28 23:21:11 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="extract_variants" name="Extract Variant Sites">
+<tool id="extract_variants" name="Extract Variant Sites" version="0.1.6.1">
   <description>from a BCF file</description>
   <macros>
     <import>toolshed_macros.xml</import>
diff -r ffee8534a5c4 -r bdd1995c9e66 vcf_filter.xml
--- a/vcf_filter.xml	Thu Jun 04 17:52:04 2015 +0200
+++ b/vcf_filter.xml	Tue Jul 28 23:21:11 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="vcf_filter" name="VCF Filter">
+<tool id="vcf_filter" name="VCF Filter" version="0.1.6.1">
   <description>Extracts lines from a vcf variant file based on field-specific filters</description>
   <macros>
     <import>toolshed_macros.xml</import>
@@ -28,6 +28,10 @@
 	#for $i in $datasets
 	    "$i.GQ"
 	#end for
+	--af
+	#for $i in $datasets
+	    "#echo ($i.AF or "::")#"
+	#end for
 	#end if
 	#if len($regions):
 	-r
@@ -54,6 +58,7 @@
 	<param name="GT" type="text" label="genotype pattern(s) for the inclusion of variants" help="keep only variants for which the genotype of the sample matches the specified pattern; format: x/x where x = 0 is wildtype and x = 1 is mutant. Multiple genotypes can be specified as a comma-separated list." />
 	<param name="DP" type="integer" label="depth of coverage for the sample at the variant site" value = "0" help="keep only variants with at least this sample-specific coverage at the variant site" />
 	<param name="GQ" type="integer" label="genotype quality for the variant in the sample" value = "0" help="keep only variants for which the genotype prediction for the sample has at least this quality" />
+	<param name="AF" type="text" label="allelic fraction filter" help="expected format: [allele number]:[minimal fraction]:[maximal fraction]; keep only variants for which the fraction of sample-specific reads supporting a given allele number is between minimal and maximal fraction; if allele number is omitted, the filter operates on the most frequent non-reference allele instead" />
     </repeat>
     <repeat name="regions" title="Region Filter" default="0" min="0" help = "Filter variant sites by their position in the genome. If multiple Region Filters are specified, all variants that fall in ONE of the regions are reported.">
       <param name="chrom" type="text" label="Chromosome" />