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changeset 8:d79fe626c6fd

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upgrade to v0.1.7.1
author Wolfgang Maier
date Thu, 22 Oct 2015 15:34:23 +0200
parents 3619e85a5477
children 93db2f9bca12
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, 20 insertions(+), 20 deletions(-) [+]
line wrap: on
line diff
--- a/annotate_variants.xml	Tue Sep 22 22:36:41 2015 +0200
+++ b/annotate_variants.xml	Thu Oct 22 15:34:23 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="annotate_variants" name="Variant Annotation" version="0.1.7.0">
+<tool id="annotate_variants" name="Variant Annotation" version="0.1.7.1">
   <description>Predict the effects of SNPs and indels on known genes in the reference genome using SnpEff</description>
   <macros>
     <import>toolshed_macros.xml</import>
--- a/bamsort.xml	Tue Sep 22 22:36:41 2015 +0200
+++ b/bamsort.xml	Thu Oct 22 15:34:23 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="bamsort" name="Sort BAM file" version="0.1.7.0">
+<tool id="bamsort" name="Sort BAM file" version="0.1.7.1">
   <description>Sort a BAM file by coordinates (or names) of the mapped reads</description>
   <macros>
     <import>toolshed_macros.xml</import>
--- a/cloudmap.xml	Tue Sep 22 22:36:41 2015 +0200
+++ b/cloudmap.xml	Thu Oct 22 15:34:23 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="nacreousmap" name="NacreousMap" version="0.1.7.0">
+<tool id="nacreousmap" name="NacreousMap" version="0.1.7.1">
   <description>Map causative mutations by multi-variant linkage analysis.</description>
   <expand macro="requirements"/>
   <version_command>mimodd version -q</version_command>
@@ -105,7 +105,7 @@
             <option value="">preserve relative contig sizes</option>
             <option value="--fit-width">scale each contig to fit the plot width</option>
           </param>
-          <param name="span" type="text" label="span value to be used in calculating the Loess regression line through the scatter data (default=0.1)" help="smaller values give a more responsive curve that often picks up local evidence for tight linkage better, but too small values lead to plotting failures (in that case just rerun the tool with a larger value)." />
+          <param name="span" type="text" label="span value to be used in calculating the Loess regression line through the scatter data (default=0.1, specify 0 to prevent calculation)" help="smaller values give a more responsive curve that often picks up local evidence for tight linkage better, but too small values lead to plotting failures (in that case just rerun the tool with a larger value)." />
           <expand macro="scatter_colors" />
         </when>
         <when value="-p">
@@ -156,7 +156,7 @@
         <option value="">preserve relative contig sizes</option>
         <option value="--fit-width">scale each contig to fit the plot width</option>
       </param>
-      <param name="span" type="text" label="span value to be used in calculating the Loess regression line through the scatter data (default=0.1)" help="smaller values give a more responsive curve that often picks up local evidence for tight linkage better, but too small values lead to plotting failures (in that case just rerun the tool with a larger value)." />
+      <param name="span" type="text" label="span value to be used in calculating the Loess regression line through the scatter data (default=0.1, specify 0 to prevent calculation)" help="smaller values give a more responsive curve that often picks up local evidence for tight linkage better, but too small values lead to plotting failures (in that case just rerun the tool with a larger value)." />
       <expand macro="hist_colors" />
       <expand macro="scatter_colors" />
     </macro>
@@ -213,7 +213,7 @@
             <param name="sample" type="text" label="mapping sample name" help="the sample to perform mutation mapping for" />
             <param name="related_parent_sample" type="text" label="name of the related parent sample" help="the sample that provides variants present in your original mutant strain or in an ancestor (like the pre-mutagenesis strain); leave blank if not available" />
             <param name="unrelated_parent_sample" type="text" label="name of the unrelated parent sample" help="the sample that provides variants present in the unrelated mapping strain (or in an ancestor of it) used in the mapping cross; leave blank if not available" />
-            <param name="infer_missing" type="boolean" checked="false" truevalue="--infer-missing" falsevalue="" label="Infer alleles for missing parent" help="if variant data for either the related or the unrelated parent strain is not available, the tool can try to infer the alleles present in that parent from the allele spectrum found in the mapping sample. This is an EXPERIMENTAL option that will give a benefit only in certain situations. Enable at your own risk." />
+            <param name="infer_missing" type="boolean" checked="false" truevalue="--infer-missing" falsevalue="" label="Infer alleles for missing parent" help="if variant data for either the related or the unrelated parent strain is not available, the tool can try to infer the alleles present in that parent from the allele spectrum found in the mapping sample. Use with caution on carefully filtered variant lists only!" />
             <expand macro="vaf_unconditional" />
             <param name="tabfile" type="select" label="additional per-variant output file" help="You can either choose to produce a tabular per-variant report, which is useful for fast replotting with different plot settings or a vcf-like CloudMap-compatibility file that can be used as input for the CloudMap Hawaiian Variant Mapping tool as an alternative plotting tool.">
               <option value="">Do not generate per-variant output</option>
--- a/convert.xml	Tue Sep 22 22:36:41 2015 +0200
+++ b/convert.xml	Thu Oct 22 15:34:23 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="convert" name="Convert" version="0.1.7.0">
+<tool id="convert" name="Convert" version="0.1.7.1">
   <description>between different sequence data formats</description>
   <macros>
     <import>toolshed_macros.xml</import>
--- a/covstats.xml	Tue Sep 22 22:36:41 2015 +0200
+++ b/covstats.xml	Thu Oct 22 15:34:23 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="coverage_stats" name="Coverage Statistics" version="0.1.7.0">
+<tool id="coverage_stats" name="Coverage Statistics" version="0.1.7.1">
   <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	Tue Sep 22 22:36:41 2015 +0200
+++ b/deletion_predictor.xml	Thu Oct 22 15:34:23 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="deletion_prediction" name="Deletion Prediction for paired-end data" version="0.1.7.0">
+<tool id="deletion_prediction" name="Deletion Prediction for paired-end data" version="0.1.7.1">
   <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>
--- a/fileinfo.xml	Tue Sep 22 22:36:41 2015 +0200
+++ b/fileinfo.xml	Thu Oct 22 15:34:23 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="fileinfo" name="Retrieve File Information" version="0.1.7.0">
+<tool id="fileinfo" name="Retrieve File Information" version="0.1.7.1">
   <description>for supported data formats.</description>
   <macros>
     <import>toolshed_macros.xml</import>
--- a/reheader.xml	Tue Sep 22 22:36:41 2015 +0200
+++ b/reheader.xml	Thu Oct 22 15:34:23 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="reheader" name="Reheader BAM file" version="0.1.7.0">
+<tool id="reheader" name="Reheader BAM file" version="0.1.7.1">
   <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>
--- a/sam_header.xml	Tue Sep 22 22:36:41 2015 +0200
+++ b/sam_header.xml	Thu Oct 22 15:34:23 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="ngs_run_annotation" name="NGS Run Annotation" version="0.1.7.0">
+<tool id="ngs_run_annotation" name="NGS Run Annotation" version="0.1.7.1">
   <description>Create a SAM format header from run metadata for sample annotation.</description>
   <macros>
     <import>toolshed_macros.xml</import>
--- a/snap_caller.xml	Tue Sep 22 22:36:41 2015 +0200
+++ b/snap_caller.xml	Thu Oct 22 15:34:23 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="read_alignment" name="SNAP Read Alignment" version="0.1.7.0">
+<tool id="read_alignment" name="SNAP Read Alignment" version="0.1.7.1">
   <description>Map sequence reads to a reference genome using SNAP</description>
   <macros>
     <import>toolshed_macros.xml</import>
--- a/snp_caller_caller.xml	Tue Sep 22 22:36:41 2015 +0200
+++ b/snp_caller_caller.xml	Thu Oct 22 15:34:23 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="variant_calling" name="Variant Calling" version="0.1.7.0">
+<tool id="variant_calling" name="Variant Calling" version="0.1.7.1">
   <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>
--- a/snpeff_genomes.xml	Tue Sep 22 22:36:41 2015 +0200
+++ b/snpeff_genomes.xml	Thu Oct 22 15:34:23 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="snpeff_genomes" name="List Installed SnpEff Genomes" version="0.1.7.0">
+<tool id="snpeff_genomes" name="List Installed SnpEff Genomes" version="0.1.7.1">
   <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	Tue Sep 22 22:36:41 2015 +0200
+++ b/tool_dependencies.xml	Thu Oct 22 15:34:23 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="0.1.7.0">
+  <package name="mimodd" version="0.1.7.1">
     <install version="1.0">
       <actions>
-        <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.0.tar.gz</action>
+        <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.1.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" />
--- a/toolshed_macros.xml	Tue Sep 22 22:36:41 2015 +0200
+++ b/toolshed_macros.xml	Thu Oct 22 15:34:23 2015 +0200
@@ -1,7 +1,7 @@
 <macros>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="0.1.7.0">mimodd</requirement>
+      <requirement type="package" version="0.1.7.1">mimodd</requirement>
     </requirements>
   </xml>
 </macros>
--- a/varextract.xml	Tue Sep 22 22:36:41 2015 +0200
+++ b/varextract.xml	Thu Oct 22 15:34:23 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="extract_variants" name="Extract Variant Sites" version="0.1.7.0">
+<tool id="extract_variants" name="Extract Variant Sites" version="0.1.7.1">
   <description>from a BCF file</description>
   <macros>
     <import>toolshed_macros.xml</import>
--- a/vcf_filter.xml	Tue Sep 22 22:36:41 2015 +0200
+++ b/vcf_filter.xml	Thu Oct 22 15:34:23 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="vcf_filter" name="VCF Filter" version="0.1.7.0">
+<tool id="vcf_filter" name="VCF Filter" version="0.1.7.1">
   <description>Extracts lines from a vcf variant file based on field-specific filters</description>
   <macros>
     <import>toolshed_macros.xml</import>