Mercurial > repos > iuc > gemini
changeset 2:e6512af21622 draft
Uploaded
| author | iuc |
|---|---|
| date | Sun, 24 Aug 2014 17:49:00 -0400 |
| parents | 5fec0c2b77c7 |
| children | 2ebcf5c69c5e |
| files | gemini_burden.xml gemini_comp_hets.xml gemini_db_info.xml gemini_interactions.xml gemini_load.xml gemini_macros.xml gemini_pathways.xml gemini_query.xml gemini_region.xml gemini_roh.xml tool_dependencies.xml |
| diffstat | 11 files changed, 43 insertions(+), 40 deletions(-) [+] |
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--- a/gemini_burden.xml Mon Aug 11 07:45:22 2014 -0400 +++ b/gemini_burden.xml Sun Aug 24 17:49:00 2014 -0400 @@ -42,11 +42,11 @@ label="Run the C-alpha association test" help="(--calpha)"/> <param name="min_aaf" type="float" value="-1" size="5" label="The min. alt. allele frequency for a variant to be included" help="(--min-aaf)"> - <validator type="in_range" min="0.0"/> + <!--validator type="in_range" min="0.0"/--> </param> <param name="max_aaf" type="float" value="-1" size="5" label="The max. alt. allele frequency for a variant to be included" help="(--max-aaf)"> - <validator type="in_range" min="0.0"/> + <!--validator type="in_range" min="0.0"/--> </param> <param name="permutations" type="integer" value="1000" size="10" label="Number of permutations to run for the C-alpha test"
--- a/gemini_comp_hets.xml Mon Aug 11 07:45:22 2014 -0400 +++ b/gemini_comp_hets.xml Sun Aug 24 17:49:00 2014 -0400 @@ -28,6 +28,7 @@ <inputs> <param name="infile" type="data" format="sqlite" label="GEMINI database" /> <expand macro="add_header_column" /> + <expand macro="column_filter" /> <param name="only_affected" type="boolean" truevalue="--only-affected" falsevalue="" checked="False" label="Report solely those compund heterozygotes impacted a sample labeled as affected" help="(--only-affected)"/> <param name="ignore_phasing" type="boolean" truevalue="--ignore-phasing" falsevalue="" checked="False"
--- a/gemini_db_info.xml Mon Aug 11 07:45:22 2014 -0400 +++ b/gemini_db_info.xml Sun Aug 24 17:49:00 2014 -0400 @@ -9,7 +9,7 @@ <command> <![CDATA[ gemini @BINARY@ - "${ infile }" + "${ infile }" | tr -s ' ' '\t' > "${ outfile }" ]]> </command>
--- a/gemini_interactions.xml Mon Aug 11 07:45:22 2014 -0400 +++ b/gemini_interactions.xml Sun Aug 24 17:49:00 2014 -0400 @@ -19,22 +19,19 @@ #end if -r "${radius}" - $var + $variant_mode "${ infile }" > "${ outfile }" ]]> - - loss-of-function - </command> <expand macro="stdio" /> <inputs> <param name="infile" type="data" format="sqlite" label="GEMINI database" /> <conditional name="gene"> - <param name="gene_selector" type="select" label="Studying ..." help=""> + <param name="gene_selector" type="select" label="Studying" help=""> <option value="gene">Interesting gene</option> - <option value="lof">All loss-of-function variants</option> + <option value="lof">All loss-of-function variants</option> </param> <when value="gene"> <param name="gene" type="text" label="Specify gene name" help="e.g. PTPN22 (-g)" />
--- a/gemini_load.xml Mon Aug 11 07:45:22 2014 -0400 +++ b/gemini_load.xml Sun Aug 24 17:49:00 2014 -0400 @@ -1,5 +1,5 @@ <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> - <description></description> + <description>Loading a VCF file into GEMINI</description> <expand macro="requirements" /> <expand macro="version_command" /> <macros>
--- a/gemini_macros.xml Mon Aug 11 07:45:22 2014 -0400 +++ b/gemini_macros.xml Sun Aug 24 17:49:00 2014 -0400 @@ -1,12 +1,11 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="0.9.1">gemini</requirement> + <requirement type="package" version="0.10.0">gemini</requirement> <requirement type="package" version="0.1.3">grabix</requirement> <requirement type="package" version="0.2.6">tabix</requirement> <requirement type="package" version="0.1.19">samtools</requirement> <requirement type="package" version="2.19.1">bedtools</requirement> - <requirement type="package" version="0.6.6">pybedtools</requirement> <yield /> </requirements> </xml>
--- a/gemini_pathways.xml Mon Aug 11 07:45:22 2014 -0400 +++ b/gemini_pathways.xml Sun Aug 24 17:49:00 2014 -0400 @@ -19,7 +19,7 @@ <inputs> <param name="infile" type="data" format="sqlite" label="GEMINI database" /> - <param name="ensemble" type="integer" value="68" size="5" label="Version of ensembl genes to use" + <param name="ensembl" type="integer" value="68" size="5" label="Version of ensembl genes to use" help="Supported versions: 66 to 71. use versions that match the VEP/snpEff versions of the annotated vcf for correctness. For e.g VEP v2.6 and snpEff v3.1 use Ensembl 68 version of the genomes. (-v)"> <validator type="in_range" min="66" max="71"/> </param>
--- a/gemini_query.xml Mon Aug 11 07:45:22 2014 -0400 +++ b/gemini_query.xml Sun Aug 24 17:49:00 2014 -0400 @@ -1,5 +1,5 @@ <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> - <description></description> + <description>Querying the GEMINI database</description> <expand macro="requirements" /> <expand macro="version_command" /> <macros> @@ -10,9 +10,7 @@ <![CDATA[ gemini @BINARY@ - #if $q.strip(): - -q "${q}" - #end if + --in "${in}" #if $gt_filter.strip(): --gt-filter "${gt_filter}" @@ -27,7 +25,6 @@ $family_wise $header $dgidb - --in $in #if $region.strip(): --region "${region}" #end if @@ -37,8 +34,9 @@ ##--format FORMAT Format of output (JSON, TPED or default) # we will take default for the time being ## --sample-delim STRING The delimiter to be used with the --show-samples option. - - + #if $q.strip(): + -q "${q}" + #end if "${ infile }" > "${ outfile }" @@ -53,10 +51,9 @@ <inputs> <param name="infile" type="data" format="sqlite" label="GEMINI database" /> - <param name="q" type="text" area="True" size="5x50" label="The query to be issued to the database"/> - <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values"/> - <param name="sample_filter" type="text" area="True" size="5x50" label="SQL filter to use to filter the sample table"/> - <param name="sample_filter" type="text" area="True" size="5x50" label="SQL filter to use to filter the sample table"/> + <param name="q" type="text" area="True" size="5x50" label="The query to be issued to the database" help="(-q)"/> + <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filer)"/> + <param name="sample_filter" type="text" area="True" size="5x50" label="SQL filter to use to filter the sample table" help="(--sample-filter)"/> <param name="show_samples" type="boolean" truevalue="--show-samples" falsevalue="" checked="False" label="Add a column of all sample names with a variant to each variant" help="(--show-samples)"/> @@ -76,10 +73,10 @@ label="Request drug-gene interaction info from DGIdb" help="(--dgidb)"/> <param name="in" type="select" label="A variant must be in either all, none or any samples passing the sample-query filter" help="(--in)"> - <option value="all">all</option> - <option value="none">none</option> - <option value="any">any</option> - <option value="only">only</option> + <option value="all">Return a variant if all samples matching the query have the variant. (all)</option> + <option value="none">Return a variant if the variant does not appear in any of the matching samples. (none)</option> + <option value="any">Return all of the variant which are in all of the matching samples and not in any of the non-matching samples. (any)</option> + <option value="only">Return a variant if the variant is only in the matching samples and not in any of the non-matching samples. (only)</option> </param> <param name="region" size="30" type="text" value="" label="Restrict query to this region" help="e.g. chr1:10-20 (--region)"/>
--- a/gemini_region.xml Mon Aug 11 07:45:22 2014 -0400 +++ b/gemini_region.xml Sun Aug 24 17:49:00 2014 -0400 @@ -11,9 +11,13 @@ gemini @BINARY@ #if $region.region_selector == '--reg': - --reg "${region.region}" + #if "${region.region}" == '' + --reg "${region.region}" + #end if #else: - --gene "${region.gene} + #if "${region.gene}" != '': + --gene "${region.gene}" + #end if #end if #if $report.report_selector != 'all':
--- a/gemini_roh.xml Mon Aug 11 07:45:22 2014 -0400 +++ b/gemini_roh.xml Sun Aug 24 17:49:00 2014 -0400 @@ -9,15 +9,17 @@ <command> <![CDATA[ gemini @BINARY@ - --min-snps $min_snps - --min-total-depth $min_total_depth - --min-gt-depth $min_gt_depth - --min-size $min_size - --max-hets §max_hets - --max-unknowns $max_unknowns - -s $samples + --min-snps $min_snps + --min-total-depth $min_total_depth + --min-gt-depth $min_gt_depth + --min-size $min_size + --max-hets $max_hets + --max-unknowns $max_unknowns + #if $samples.strip() != '': + -s "${samples}" + #end if "${ infile }" - -> "${ outfile }" + > "${ outfile }" ]]> </command> <expand macro="stdio" />
--- a/tool_dependencies.xml Mon Aug 11 07:45:22 2014 -0400 +++ b/tool_dependencies.xml Sun Aug 24 17:49:00 2014 -0400 @@ -15,7 +15,10 @@ <package name="pybedtools" version="0.6.6"> <repository changeset_revision="cc2ed79fc537" name="package_pybedtools_0_6_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="gemini" version="0.9.1"> - <repository changeset_revision="8000d616c600" name="package_gemini_0_9_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="gemini" version="0.10.0"> + <repository changeset_revision="75ffd114bf5f" name="package_gemini_0_10_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="sqlite" version="3.8.3"> + <repository changeset_revision="e3729818491f" name="package_sqlite_3_8_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>