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changeset 9:93db2f9bca12

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upgrade to v0.1.7.2
author Wolfgang Maier wolfgang.maier@biologie.uni-freiburg.de
date Thu, 28 Jan 2016 17:26:58 +0100
parents d79fe626c6fd
children ac3eac581b83
files annotate_variants.xml bamsort.xml cloudmap.xml convert.xml covstats.xml deletion_predictor.xml fileinfo.xml reheader.xml sam_header.xml snap_caller.xml snp_caller_caller.xml snpeff_genomes.xml tool_dependencies.xml toolshed_macros.xml varextract.xml vcf_filter.xml
diffstat 16 files changed, 16 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/annotate_variants.xml	Thu Oct 22 15:34:23 2015 +0200
+++ b/annotate_variants.xml	Thu Jan 28 17:26:58 2016 +0100
@@ -1,4 +1,4 @@
-<tool id="annotate_variants" name="Variant Annotation" version="0.1.7.1">
+<tool id="annotate_variants" name="Variant Annotation" version="0.1.7.2">
   <description>Predict the effects of SNPs and indels on known genes in the reference genome using SnpEff</description>
   <macros>
     <import>toolshed_macros.xml</import>
--- a/bamsort.xml	Thu Oct 22 15:34:23 2015 +0200
+++ b/bamsort.xml	Thu Jan 28 17:26:58 2016 +0100
@@ -1,4 +1,4 @@
-<tool id="bamsort" name="Sort BAM file" version="0.1.7.1">
+<tool id="bamsort" name="Sort BAM file" version="0.1.7.2">
   <description>Sort a BAM file by coordinates (or names) of the mapped reads</description>
   <macros>
     <import>toolshed_macros.xml</import>
--- a/cloudmap.xml	Thu Oct 22 15:34:23 2015 +0200
+++ b/cloudmap.xml	Thu Jan 28 17:26:58 2016 +0100
@@ -1,4 +1,4 @@
-<tool id="nacreousmap" name="NacreousMap" version="0.1.7.1">
+<tool id="nacreousmap" name="NacreousMap" version="0.1.7.2">
   <description>Map causative mutations by multi-variant linkage analysis.</description>
   <expand macro="requirements"/>
   <version_command>mimodd version -q</version_command>
--- a/convert.xml	Thu Oct 22 15:34:23 2015 +0200
+++ b/convert.xml	Thu Jan 28 17:26:58 2016 +0100
@@ -1,4 +1,4 @@
-<tool id="convert" name="Convert" version="0.1.7.1">
+<tool id="convert" name="Convert" version="0.1.7.2">
   <description>between different sequence data formats</description>
   <macros>
     <import>toolshed_macros.xml</import>
--- a/covstats.xml	Thu Oct 22 15:34:23 2015 +0200
+++ b/covstats.xml	Thu Jan 28 17:26:58 2016 +0100
@@ -1,4 +1,4 @@
-<tool id="coverage_stats" name="Coverage Statistics" version="0.1.7.1">
+<tool id="coverage_stats" name="Coverage Statistics" version="0.1.7.2">
   <description>Calculate coverage statistics for a BCF file as generated by the Variant Calling tool</description>
   <macros>
     <import>toolshed_macros.xml</import>
--- a/deletion_predictor.xml	Thu Oct 22 15:34:23 2015 +0200
+++ b/deletion_predictor.xml	Thu Jan 28 17:26:58 2016 +0100
@@ -1,4 +1,4 @@
-<tool id="deletion_prediction" name="Deletion Prediction for paired-end data" version="0.1.7.1">
+<tool id="deletion_prediction" name="Deletion Prediction for paired-end data" version="0.1.7.2">
   <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>
--- a/fileinfo.xml	Thu Oct 22 15:34:23 2015 +0200
+++ b/fileinfo.xml	Thu Jan 28 17:26:58 2016 +0100
@@ -1,4 +1,4 @@
-<tool id="fileinfo" name="Retrieve File Information" version="0.1.7.1">
+<tool id="fileinfo" name="Retrieve File Information" version="0.1.7.2">
   <description>for supported data formats.</description>
   <macros>
     <import>toolshed_macros.xml</import>
--- a/reheader.xml	Thu Oct 22 15:34:23 2015 +0200
+++ b/reheader.xml	Thu Jan 28 17:26:58 2016 +0100
@@ -1,4 +1,4 @@
-<tool id="reheader" name="Reheader BAM file" version="0.1.7.1">
+<tool id="reheader" name="Reheader BAM file" version="0.1.7.2">
   <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>
--- a/sam_header.xml	Thu Oct 22 15:34:23 2015 +0200
+++ b/sam_header.xml	Thu Jan 28 17:26:58 2016 +0100
@@ -1,4 +1,4 @@
-<tool id="ngs_run_annotation" name="NGS Run Annotation" version="0.1.7.1">
+<tool id="ngs_run_annotation" name="NGS Run Annotation" version="0.1.7.2">
   <description>Create a SAM format header from run metadata for sample annotation.</description>
   <macros>
     <import>toolshed_macros.xml</import>
--- a/snap_caller.xml	Thu Oct 22 15:34:23 2015 +0200
+++ b/snap_caller.xml	Thu Jan 28 17:26:58 2016 +0100
@@ -1,4 +1,4 @@
-<tool id="read_alignment" name="SNAP Read Alignment" version="0.1.7.1">
+<tool id="read_alignment" name="SNAP Read Alignment" version="0.1.7.2">
   <description>Map sequence reads to a reference genome using SNAP</description>
   <macros>
     <import>toolshed_macros.xml</import>
--- a/snp_caller_caller.xml	Thu Oct 22 15:34:23 2015 +0200
+++ b/snp_caller_caller.xml	Thu Jan 28 17:26:58 2016 +0100
@@ -1,4 +1,4 @@
-<tool id="variant_calling" name="Variant Calling" version="0.1.7.1">
+<tool id="variant_calling" name="Variant Calling" version="0.1.7.2">
   <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>
--- a/snpeff_genomes.xml	Thu Oct 22 15:34:23 2015 +0200
+++ b/snpeff_genomes.xml	Thu Jan 28 17:26:58 2016 +0100
@@ -1,4 +1,4 @@
-<tool id="snpeff_genomes" name="List Installed SnpEff Genomes" version="0.1.7.1">
+<tool id="snpeff_genomes" name="List Installed SnpEff Genomes" version="0.1.7.2">
   <description>Checks the local SnpEff installation to compile a list of currently installed genomes</description>
   <macros>
     <import>toolshed_macros.xml</import>
--- a/tool_dependencies.xml	Thu Oct 22 15:34:23 2015 +0200
+++ b/tool_dependencies.xml	Thu Jan 28 17:26:58 2016 +0100
@@ -7,7 +7,7 @@
     <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="0.1.7.1">
+  <package name="mimodd" version="0.1.7.2">
     <install version="1.0">
       <actions>
         <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.1.tar.gz</action>
--- a/toolshed_macros.xml	Thu Oct 22 15:34:23 2015 +0200
+++ b/toolshed_macros.xml	Thu Jan 28 17:26:58 2016 +0100
@@ -1,7 +1,7 @@
 <macros>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="0.1.7.1">mimodd</requirement>
+      <requirement type="package" version="0.1.7.2">mimodd</requirement>
     </requirements>
   </xml>
 </macros>
--- a/varextract.xml	Thu Oct 22 15:34:23 2015 +0200
+++ b/varextract.xml	Thu Jan 28 17:26:58 2016 +0100
@@ -1,4 +1,4 @@
-<tool id="extract_variants" name="Extract Variant Sites" version="0.1.7.1">
+<tool id="extract_variants" name="Extract Variant Sites" version="0.1.7.2">
   <description>from a BCF file</description>
   <macros>
     <import>toolshed_macros.xml</import>
--- a/vcf_filter.xml	Thu Oct 22 15:34:23 2015 +0200
+++ b/vcf_filter.xml	Thu Jan 28 17:26:58 2016 +0100
@@ -1,4 +1,4 @@
-<tool id="vcf_filter" name="VCF Filter" version="0.1.7.1">
+<tool id="vcf_filter" name="VCF Filter" version="0.1.7.2">
   <description>Extracts lines from a vcf variant file based on field-specific filters</description>
   <macros>
     <import>toolshed_macros.xml</import>