| Previous changeset 5:bdd1995c9e66 (2015-07-28) Next changeset 7:3619e85a5477 (2015-09-22) |
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Commit message:
upgrade to mimodd version 0.1.7.0 |
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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 bdd1995c9e66 -r 85214e4428fd annotate_variants.xml --- a/annotate_variants.xml Tue Jul 28 23:21:11 2015 +0200 +++ b/annotate_variants.xml Fri Sep 11 16:25:49 2015 +0200 |
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| @@ -1,4 +1,4 @@ -<tool id="annotate_variants" name="Variant Annotation" version="0.1.6.1"> +<tool id="annotate_variants" name="Variant Annotation" version="0.1.7.0"> <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 bdd1995c9e66 -r 85214e4428fd bamsort.xml --- a/bamsort.xml Tue Jul 28 23:21:11 2015 +0200 +++ b/bamsort.xml Fri Sep 11 16:25:49 2015 +0200 |
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| @@ -1,4 +1,4 @@ -<tool id="bamsort" name="Sort BAM file" version="0.1.6.1"> +<tool id="bamsort" name="Sort BAM file" version="0.1.7.0"> <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 bdd1995c9e66 -r 85214e4428fd cloudmap.xml --- a/cloudmap.xml Tue Jul 28 23:21:11 2015 +0200 +++ b/cloudmap.xml Fri Sep 11 16:25:49 2015 +0200 |
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| b'@@ -1,54 +1,247 @@\n-<tool id="cloudmap_prepare" name="Prepare variant data for mapping" version="0.1.6.1">\n- <description>with the CloudMap series of tools.</description>\n+<tool id="nacreousmap" name="NacreousMap" version="0.1.7.0">\n+ <description>Map causative mutations by multi-variant linkage analysis.</description>\n <macros>\n <import>toolshed_macros.xml</import>\n </macros>\n <expand macro="requirements"/>\n <version_command>mimodd version -q</version_command>\n <command>\n- mimodd cloudmap "$ifile" ${run.mode} "$sample"\n- \n- #if $str($run.related_parent_sample):\n- -r "${run.related_parent_sample}"\n+ mimodd map "${opt.source.ifile}" ${opt.mode}\n+ #if $str($opt.source.sample):\n+ -m "${opt.source.sample}"\n+ #end if\n+ #if $str($opt.source.related_parent_sample):\n+ -r "${opt.source.related_parent_sample}"\n+ #end if\n+ #if $str($opt.source.unrelated_parent_sample):\n+ -u "${opt.source.unrelated_parent_sample}"\n+ #end if\n+ $opt.source.infer_missing\n+ -o "$ofile"\n+ #if $str($opt.source.seqdict_required.required) == "yes":\n+ -s "${opt.source.seqdict_required.seqdict}"\n+ #end if\n+ $opt.source.norm\n+ #if $len($opt.source.bin_sizes):\n+ --bin-sizes\n+ #for $size in $opt.source.bin_sizes:\n+ "${size.bin_size}"\n+ #end for\n+ #end if\n+ #if $str($opt.source.tabfile):\n+ $str($opt.source.tabfile) $tfile\n #end if\n- #if $str($run.unrelated_parent_sample):\n- -u "${run.unrelated_parent_sample}"\n+ #if $str($opt.source.plotopts.plots):\n+ $str($opt.source.plotopts.plots) "$pfile"\n+ $str($opt.source.plotopts.xlim)\n+ #if $str($opt.source.plotopts.hylim):\n+ --ylim-hist $str($opt.source.plotopts.hylim)\n+ #end if\n+ #if $str($opt.source.plotopts.hcols) and $len($opt.source.plotopts.hcols):\n+ --hist-colors\n+ #for $color in $opt.source.plotopts.hcols:\n+ "${color.hcolor}"\n+ #end for\n+ #end if\n+ #if $str($opt.source.plotopts.sylim):\n+ --ylim-scatter $str($opt.source.plotopts.sylim)\n+ #end if\n+ #if $str($opt.source.plotopts.pcol):\n+ --points-color "$str($opt.source.plotopts.pcol)"\n+ #end if\n+ #if $str($opt.source.plotopts.lcol):\n+ --loess-color "$str($opt.source.plotopts.lcol)"\n+ #end if\n+ #if $str($opt.source.plotopts.span):\n+ --loess-span "$str($opt.source.plotopts.span)"\n+ #end if \n #end if\n \n- $run.infer_missing\n- -o "$ofile"\n- \n- #if $seqdict:\n- -s "$dictfile"\n- #end if\n </command>\n \n+ <macros>\n+ <macro name="svd_unconditional">\n+ <expand macro="hidden_vaf_algo_params" />\n+ <expand macro="seqdict_param" />\n+ <expand macro="bins" />\n+ <param name="norm" type="boolean" label="normalize variant counts to bin-width" truevalue="" falsevalue="--no-normalize" checked="true" help="without normalization the tool will just report the number of nucleotides per bin; with normalization the results for different bin-widths will be comparable." />\n+ <conditional name="plotopts">\n+ <param name="plots" type="select" label="graphical output settings">\n+ <option value="">Do not generate graphs.</option>\n+ <option value="-p">Give me graphics.</option>\n+ </param>\n+ <when value="-p">\n+ <expand macro="scatter_default" />\n+ <param name="hylim" type="text" label="upper limit for the histogram y-axis (leave blank for automatic scaling)" />\n+ <param name="xlim" type="select" label="x-axis scaling">\n+ <option value="">preserve relative contig sizes</option>\n+ <option value="--fit-width">scale each contig to fit the plot width</option>\n+ </param>\n+ <expand macro="hist_colors" />\n+ </when>\n+ </conditional>\n+ </macro>\n+ <macro name="vaf_unconditional">\n+ <expand macro="bins" />\n+ <param name="norm" type="boolean" label='..b's the width of the regions along each chromosome, in which variants are counted and analyzed together. \n+ \n+ Several bin sizes can be specified and for each size you will get a corresponding report section in the binned variant counts file and a histogram plot in the linkage plots file.\n+ \n+ *normalize variant counts to bin-width* - if selected (as per default) the variant counts for different bin sizes are not absolute, but normalized to the bin width\n+ \n+ *sample names (in VAF mode only)* - to analyze inheritance patterns, VAF mode needs information about the relationship between the samples defined in the input VCF file:\n+ \n+ The *mapping sample name* should be set to the name of the sample for which the inheritance pattern is to be analyzed (the pooled progeny population). \n+ \n+ The *name of the related sample* should be that of the parent sample that carried and brought in the unknown mutation to be mapped (or, alternatively, that of a closely related ancestor). \n+ \n+ Finally, the *name of the unrelated sample* should be that of the other parent strain used in the cross. \n+ \n+ At least one of the parent samples MUST be specified, but if the input file contains variant information for both parents, they can be analyzed together for higher mapping accuracy. If you are reanalyzing a tabular report file from a previous tool run or from CloudMap, the association between variants and samples is already incorporated into the input file and cannot be specified again.\n \n-2) Variant Allele Frequency (VAF) Mapping mode generates output for use with the CloudMap Variant Discovery or Hawaiian Variant Mapping tools. The aim of VAF analysis is to identify clusters of variants with (near) homozygous inheritance in a F2 population obtained from a cross between a mutant strain of interest and an unrelated mapping strain. Here, the "mapping sample" is the pooled F2 population. To analyze inheritance patterns this mode **requires either** a list of variants that could have been inherited through the mapping strain, i.e. the "unrelated parent strain", or through the mutant parent, i.e. through the "related parent strain". If variants are available for both parents, they can be analyzed together for higher mapping accuracy.\n+2) Graphical output settings\n+\n+ .. class:: warningmark\n+ \n+ To be able to generate plots the system running MiModD needs to have the statistical programming environment R and its Python interface rpy2 installed.\n+\n \n-3) More information on combining MiModD and CloudMap in mapping-by-sequencing analyses can be found in the `corresponding section of the MiModD User Guide`_.\n+ *y-axes scaling* - if you want to override the defaults\n+\n+ *x-axis scaling* - choose *preserve relative contig sizes* if you want the largest chromosome to fit the page width and smaller chromosomes to appear according to their relative size or choose *scale each contig to fit the plot width* if all chromosomes should exploit the available space\n+\n+ *span value to be used in calculating the Loess regression line* - this value determines the degree of smoothing of the regression line through the scatterplot data. Information on loess regression and the loess span parameter can be found at http://en.wikipedia.org/wiki/Local_regression. The default is 0.1 as in CloudMap.\n+\n+ *colors used for plotting* - can be selected freely from the offered palette. For histogram colors, the list of selected colors will be used to provide the colors for the different histograms plotted. If less colors than histograms (determined by the number of bin sizes selected) are specified, colors from the list will be recycled.\n+\n \n .. _CloudMap: https://usegalaxy.org/u/gm2123/p/cloudmap\n-.. _corresponding section of the MiModD User Guide: http://mimodd.readthedocs.org/en/latest/cloudmap.html\n-\n+.. _mapping-by-sequencing analysis workflows in MiModD: http://mimodd.readthedocs.org/en/latest/cloudmap.html\n </help>\n </tool>\n' |
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| diff -r bdd1995c9e66 -r 85214e4428fd convert.xml --- a/convert.xml Tue Jul 28 23:21:11 2015 +0200 +++ b/convert.xml Fri Sep 11 16:25:49 2015 +0200 |
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| @@ -1,4 +1,4 @@ -<tool id="convert" name="Convert" version="0.1.6.1"> +<tool id="convert" name="Convert" version="0.1.7.0"> <description>between different sequence data formats</description> <macros> <import>toolshed_macros.xml</import> |
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| diff -r bdd1995c9e66 -r 85214e4428fd covstats.xml --- a/covstats.xml Tue Jul 28 23:21:11 2015 +0200 +++ b/covstats.xml Fri Sep 11 16:25:49 2015 +0200 |
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| @@ -1,4 +1,4 @@ -<tool id="coverage_stats" name="Coverage Statistics" version="0.1.6.1"> +<tool id="coverage_stats" name="Coverage Statistics" version="0.1.7.0"> <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 bdd1995c9e66 -r 85214e4428fd deletion_predictor.xml --- a/deletion_predictor.xml Tue Jul 28 23:21:11 2015 +0200 +++ b/deletion_predictor.xml Fri Sep 11 16:25:49 2015 +0200 |
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| @@ -1,4 +1,4 @@ -<tool id="deletion_prediction" name="Deletion Prediction for paired-end data" version="0.1.6.1"> +<tool id="deletion_prediction" name="Deletion Prediction for paired-end data" version="0.1.7.0"> <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 bdd1995c9e66 -r 85214e4428fd fileinfo.xml --- a/fileinfo.xml Tue Jul 28 23:21:11 2015 +0200 +++ b/fileinfo.xml Fri Sep 11 16:25:49 2015 +0200 |
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| @@ -1,4 +1,4 @@ -<tool id="fileinfo" name="Retrieve File Information" version="0.1.6.1"> +<tool id="fileinfo" name="Retrieve File Information" version="0.1.7.0"> <description>for supported data formats.</description> <macros> <import>toolshed_macros.xml</import> |
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| diff -r bdd1995c9e66 -r 85214e4428fd reheader.xml --- a/reheader.xml Tue Jul 28 23:21:11 2015 +0200 +++ b/reheader.xml Fri Sep 11 16:25:49 2015 +0200 |
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| @@ -1,4 +1,4 @@ -<tool id="reheader" name="Reheader BAM file" version="0.1.6.1"> +<tool id="reheader" name="Reheader BAM file" version="0.1.7.0"> <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 bdd1995c9e66 -r 85214e4428fd sam_header.xml --- a/sam_header.xml Tue Jul 28 23:21:11 2015 +0200 +++ b/sam_header.xml Fri Sep 11 16:25:49 2015 +0200 |
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| @@ -1,4 +1,4 @@ -<tool id="ngs_run_annotation" name="NGS Run Annotation" version="0.1.6.1"> +<tool id="ngs_run_annotation" name="NGS Run Annotation" version="0.1.7.0"> <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 bdd1995c9e66 -r 85214e4428fd snap_caller.xml --- a/snap_caller.xml Tue Jul 28 23:21:11 2015 +0200 +++ b/snap_caller.xml Fri Sep 11 16:25:49 2015 +0200 |
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| @@ -1,4 +1,4 @@ -<tool id="read_alignment" name="SNAP Read Alignment" version="0.1.6.1"> +<tool id="read_alignment" name="SNAP Read Alignment" version="0.1.7.0"> <description>Map sequence reads to a reference genome using SNAP</description> <macros> <import>toolshed_macros.xml</import> @@ -18,7 +18,7 @@ #end if --ofile '$outputfile' --iformat ${i.mode_choose.input.iformat} --oformat $oformat --idx-seedsize '$set.seedsize' ---idx-slack '$set.slack' --maxseeds '$set.maxseeds' --maxhits '$set.maxhits' --clipping=$set.clipping --maxdist '$set.maxdist' --confdiff '$set.confdiff' --confadapt '$set.confadpt' +--idx-slack '$set.slack' --maxseeds '$set.maxseeds' --maxhits '$set.maxhits' --clipping $set.clipping --maxdist '$set.maxdist' --confdiff '$set.confdiff' --confadapt '$set.confadpt' #if $i.mode_choose.input.header: --header '${i.mode_choose.input.header}' #end if @@ -168,9 +168,9 @@ <param name="maxseeds" type="integer" value="25" label="maximum seeds per read (default: 25)" help="Number of seeds to use per read (SNAP option -n) when trying to match it to the reference genome; higher numbers will increase the rate of aligned reads and reduce the rate of misalignments, but will reduce performance."/> <param name="clipping" type="select" label="read clipping (default: from back and front)" help="Specifies from which end of a read low-quality bases should be clipped (SNAP option -Cxx)"> <option value="++">from back and front</option> - <option value="-+">from back only</option> - <option value="+-">from front only</option> - <option value="--">no clipping</option> + <option value="x+">from back only</option> + <option value="+x">from front only</option> + <option value="xx">no clipping</option> </param> <param name="selectivity" type="integer" value="1" label="selectivity (default: 1)" help="randomly choose 1/selectivity of the reads to score (SNAP option -S). The tool uses the default of 1 (or a 0 setting) to indicate that all reads should be worked with." /> <param name="filter_output" type="select" label="filter output (default: no filtering)" help="filter output (SNAP option -F for certain classes of reads."> |
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| diff -r bdd1995c9e66 -r 85214e4428fd snp_caller_caller.xml --- a/snp_caller_caller.xml Tue Jul 28 23:21:11 2015 +0200 +++ b/snp_caller_caller.xml Fri Sep 11 16:25:49 2015 +0200 |
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| @@ -1,4 +1,4 @@ -<tool id="variant_calling" name="Variant Calling" version="0.1.6.1"> +<tool id="variant_calling" name="Variant Calling" version="0.1.7.0"> <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 bdd1995c9e66 -r 85214e4428fd snpeff_genomes.xml --- a/snpeff_genomes.xml Tue Jul 28 23:21:11 2015 +0200 +++ b/snpeff_genomes.xml Fri Sep 11 16:25:49 2015 +0200 |
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| @@ -1,4 +1,4 @@ -<tool id="snpeff_genomes" name="List Installed SnpEff Genomes" version="0.1.6.1"> +<tool id="snpeff_genomes" name="List Installed SnpEff Genomes" version="0.1.7.0"> <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 bdd1995c9e66 -r 85214e4428fd tool_dependencies.xml --- a/tool_dependencies.xml Tue Jul 28 23:21:11 2015 +0200 +++ b/tool_dependencies.xml Fri Sep 11 16:25:49 2015 +0200 |
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| @@ -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="0.1.6.1"> + <package name="mimodd" version="0.1.7.0"> <install version="1.0"> <actions> - <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.6.1.tar.gz</action> + <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.0.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" /> |
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| diff -r bdd1995c9e66 -r 85214e4428fd toolshed_macros.xml --- a/toolshed_macros.xml Tue Jul 28 23:21:11 2015 +0200 +++ b/toolshed_macros.xml Fri Sep 11 16:25:49 2015 +0200 |
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| @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="0.1.6.1">mimodd</requirement> + <requirement type="package" version="0.1.7.0">mimodd</requirement> </requirements> </xml> </macros> |
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| diff -r bdd1995c9e66 -r 85214e4428fd varextract.xml --- a/varextract.xml Tue Jul 28 23:21:11 2015 +0200 +++ b/varextract.xml Fri Sep 11 16:25:49 2015 +0200 |
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| @@ -1,4 +1,4 @@ -<tool id="extract_variants" name="Extract Variant Sites" version="0.1.6.1"> +<tool id="extract_variants" name="Extract Variant Sites" version="0.1.7.0"> <description>from a BCF file</description> <macros> <import>toolshed_macros.xml</import> |
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| diff -r bdd1995c9e66 -r 85214e4428fd vcf_filter.xml --- a/vcf_filter.xml Tue Jul 28 23:21:11 2015 +0200 +++ b/vcf_filter.xml Fri Sep 11 16:25:49 2015 +0200 |
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| @@ -1,4 +1,4 @@ -<tool id="vcf_filter" name="VCF Filter" version="0.1.6.1"> +<tool id="vcf_filter" name="VCF Filter" version="0.1.7.0"> <description>Extracts lines from a vcf variant file based on field-specific filters</description> <macros> <import>toolshed_macros.xml</import> |