| Previous changeset 8:d79fe626c6fd (2015-10-22) Next changeset 10:ac3eac581b83 (2016-01-28) |
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Commit message:
upgrade to v0.1.7.2 |
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modified:
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 |
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| diff -r d79fe626c6fd -r 93db2f9bca12 annotate_variants.xml --- a/annotate_variants.xml Thu Oct 22 15:34:23 2015 +0200 +++ b/annotate_variants.xml Thu Jan 28 17:26:58 2016 +0100 |
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| @@ -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> |
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| diff -r d79fe626c6fd -r 93db2f9bca12 bamsort.xml --- a/bamsort.xml Thu Oct 22 15:34:23 2015 +0200 +++ b/bamsort.xml Thu Jan 28 17:26:58 2016 +0100 |
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| @@ -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> |
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| diff -r d79fe626c6fd -r 93db2f9bca12 cloudmap.xml --- a/cloudmap.xml Thu Oct 22 15:34:23 2015 +0200 +++ b/cloudmap.xml Thu Jan 28 17:26:58 2016 +0100 |
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| @@ -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> |
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| diff -r d79fe626c6fd -r 93db2f9bca12 convert.xml --- a/convert.xml Thu Oct 22 15:34:23 2015 +0200 +++ b/convert.xml Thu Jan 28 17:26:58 2016 +0100 |
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| @@ -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> |
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| diff -r d79fe626c6fd -r 93db2f9bca12 covstats.xml --- a/covstats.xml Thu Oct 22 15:34:23 2015 +0200 +++ b/covstats.xml Thu Jan 28 17:26:58 2016 +0100 |
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| @@ -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> |
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| diff -r d79fe626c6fd -r 93db2f9bca12 deletion_predictor.xml --- a/deletion_predictor.xml Thu Oct 22 15:34:23 2015 +0200 +++ b/deletion_predictor.xml Thu Jan 28 17:26:58 2016 +0100 |
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| @@ -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> |
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| diff -r d79fe626c6fd -r 93db2f9bca12 fileinfo.xml --- a/fileinfo.xml Thu Oct 22 15:34:23 2015 +0200 +++ b/fileinfo.xml Thu Jan 28 17:26:58 2016 +0100 |
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| @@ -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> |
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| diff -r d79fe626c6fd -r 93db2f9bca12 reheader.xml --- a/reheader.xml Thu Oct 22 15:34:23 2015 +0200 +++ b/reheader.xml Thu Jan 28 17:26:58 2016 +0100 |
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| @@ -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> |
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| diff -r d79fe626c6fd -r 93db2f9bca12 sam_header.xml --- a/sam_header.xml Thu Oct 22 15:34:23 2015 +0200 +++ b/sam_header.xml Thu Jan 28 17:26:58 2016 +0100 |
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| @@ -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> |
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| diff -r d79fe626c6fd -r 93db2f9bca12 snap_caller.xml --- a/snap_caller.xml Thu Oct 22 15:34:23 2015 +0200 +++ b/snap_caller.xml Thu Jan 28 17:26:58 2016 +0100 |
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| @@ -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> |
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| diff -r d79fe626c6fd -r 93db2f9bca12 snp_caller_caller.xml --- 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 |
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| @@ -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> |
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| diff -r d79fe626c6fd -r 93db2f9bca12 snpeff_genomes.xml --- a/snpeff_genomes.xml Thu Oct 22 15:34:23 2015 +0200 +++ b/snpeff_genomes.xml Thu Jan 28 17:26:58 2016 +0100 |
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| @@ -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> |
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| diff -r d79fe626c6fd -r 93db2f9bca12 tool_dependencies.xml --- a/tool_dependencies.xml Thu Oct 22 15:34:23 2015 +0200 +++ b/tool_dependencies.xml Thu Jan 28 17:26:58 2016 +0100 |
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| @@ -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> |
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| diff -r d79fe626c6fd -r 93db2f9bca12 toolshed_macros.xml --- a/toolshed_macros.xml Thu Oct 22 15:34:23 2015 +0200 +++ b/toolshed_macros.xml Thu Jan 28 17:26:58 2016 +0100 |
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| @@ -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> |
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| diff -r d79fe626c6fd -r 93db2f9bca12 varextract.xml --- a/varextract.xml Thu Oct 22 15:34:23 2015 +0200 +++ b/varextract.xml Thu Jan 28 17:26:58 2016 +0100 |
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| @@ -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> |
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| diff -r d79fe626c6fd -r 93db2f9bca12 vcf_filter.xml --- a/vcf_filter.xml Thu Oct 22 15:34:23 2015 +0200 +++ b/vcf_filter.xml Thu Jan 28 17:26:58 2016 +0100 |
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| @@ -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> |