Mercurial > repos > iuc > gemini
changeset 20:b5207530f991 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
| author | iuc |
|---|---|
| date | Tue, 29 Dec 2015 10:19:47 -0500 |
| parents | 27ce3de83007 |
| children | |
| files | data_manager/data_manager_gemini_download.py data_manager/data_manager_gemini_download.xml data_manager_conf.xml gemini_annotate.xml gemini_autosomal_recessive.xml gemini_burden.xml gemini_comp_hets.xml gemini_db_info.xml gemini_de_novo.xml gemini_interactions.xml gemini_load.xml gemini_lof_sieve.xml gemini_macros.xml gemini_pathways.xml gemini_query.xml gemini_region.xml gemini_roh.xml gemini_stats.xml gemini_windower.xml readme.rst repository_dependencies.xml tool-data/gemini_databases.loc.sample tool_dependencies.xml |
| diffstat | 23 files changed, 93 insertions(+), 1269 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_gemini_download.py Tue Dec 29 10:19:47 2015 -0500 @@ -0,0 +1,32 @@ +#!/usr/bin/env python + +import sys +import os +import json +import shlex +import datetime +import subprocess + +def main(): + + today = datetime.date.today() + params = json.loads( open( sys.argv[1] ).read() ) + target_directory = params[ 'output_data' ][0]['extra_files_path'] + os.mkdir( target_directory ) + cmd = "gemini --annotation-dir %s update --dataonly %s %s" % (target_directory, params['param_dict']['gerp_bp'], params['param_dict']['cadd'] ) + ret = subprocess.check_call( cmd, shell=True ) + data_manager_dict = { + 'data_tables': + {'gemini_databases': [ + {'value': today.isoformat(), 'dbkey': 'hg19', 'name': 'GEMINI annotations (%s)' % today.isoformat(), 'path': './%s' % today.isoformat() } + ] + } + } + + #save info to json file + with open( sys.argv[1], 'wb' ) as out: + out.write( json.dumps( data_manager_dict ) ) + +if __name__ == "__main__": + main() +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_gemini_download.xml Tue Dec 29 10:19:47 2015 -0500 @@ -0,0 +1,36 @@ +<tool id="data_manager_gemini_download" name="GEMINI Download" version="0.18.1" tool_type="manage_data"> + <description>Download a new database</description> + <requirements> + <requirement type="package" version="0.18.1">gemini</requirement> + </requirements> + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + <command interpreter="python"> + data_manager_gemini_download.py "$out_file" + </command> + <inputs> + <param name="cadd" type="boolean" truevalue="--extra cadd_score" falsevalue="" checked="True" + label="Download CADD scores for GEMINI database annotation" help="(--extra cadd_score)"/> + <param name="gerp_bp" type="boolean" truevalue="--extra gerp_bp" falsevalue="" checked="True" + label="Download GERP for GEMINI database annotation" help="(--extra gerp_bp)"/> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" label="${tool.name}"/> + </outputs> + <tests> + </tests> + <help> + +This tool downloads the GEMINI databases. + +For details about this tool, please go to http://gemini.readthedocs.org + + </help> + <citations> + <citation type="doi">10.1371/journal.pcbi.1003153</citation> + <yield /> + </citations> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Tue Dec 29 10:19:47 2015 -0500 @@ -0,0 +1,21 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/data_manager_gemini_download.xml" id="data_manager_gemini_download" > + <data_table name="gemini_databases"> <!-- Defines a Data Table to be modified. --> + <output> <!-- Handle the output of the Data Manager Tool --> + <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="dbkey" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="path" output_ref="out_file" > + <move type="directory" relativize_symlinks="True"> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">gemini/data/${dbkey}/${value}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/gemini/data/${dbkey}/${value}/gemini/data/</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> +</data_managers> + +
--- a/gemini_annotate.xml Fri Oct 16 13:55:09 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,96 +0,0 @@ -<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> - <description>adding your own custom annotations</description> - <macros> - <import>gemini_macros.xml</import> - <token name="@BINARY@">annotate</token> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <expand macro="version_command" /> - <command> -<![CDATA[ - -bgzip -c $annotate_source > tabixed.gz; -tabix -p bed tabixed.gz; - - gemini @BINARY@ - -f tabixed.gz - -c $column_name - -a $a.a_selector - #if $a.a_selector == 'extract': - -t $a.column_type - -e $a.column_extracts - -o $a.operation - #end if - - "${ infile }" - > "${ outfile }" -]]> - - </command> - <inputs> - <expand macro="infile" /> - <param name="annotate_source" type="data" format="bed" label="File containing the annotations in BED format" help="(-f)"/> - - <param name="column_name" type="text" value="" - label="The name of the column to be added to the variant table" help="(-c)"> - <sanitizer invalid_char=" "> - <valid initial="string.letters,string.digits"> - <add value="_" /> - </valid> - </sanitizer> - </param> - <conditional name="a"> - <param name="a_selector" type="select" label="How should the annotation file be used?" help="(-a)"> - <option value="boolean">Did a variant overlap a region or not? (boolean)</option> - <option value="count">How many regions did a variant overlap? (count)</option> - <option value="extract" selected="True">Extract specific values from a BED file. (extract)</option> - </param> - <when value="extract"> - - <param name="column_extracts" label="Column to extract information from for list annotations" - type="data_column" data_ref="annotate_source" force_select="true" help="(-e)"/> - - - <param name="column_type" type="select" label="What data type(s) should be used to represent the new values in the database?" - help="(-t)"> - <option value="float">Decimal precision number (float)</option> - <option value="integer">Integer number (integer)</option> - <option value="text">Text columns such as “valid”, “yes” (text)</option> - </param> - - <param name="operation" type="select" label="Operation to apply to the extract column values ..." - help="in the event that a variant overlaps multiple annotations in your annotation file. (-o)"> - <option value="mean">Compute the average of the (numeric) values</option> - <option value="median">Compute the median of the (numeric) values</option> - <option value="mix">Compute the minimum of the (numeric) values</option> - <option value="max">Compute the maximum of the (numeric) values</option> - <option value="mode">Compute the maximum of the (numeric) values</option> - <option value="first">Use the value from the first record in the annotation file</option> - <option value="last">Use the value from the last record in the annotation file</option> - <option value="list">Create a comma-separated list of the observed (text) values</option> - <option value="uniq_list">Create a comma-separated list of non-redundant observed (text) values</option> - </param> - - </when> - <when value="boolean"/> - <when value="count"/> - </conditional> - - </inputs> - <outputs> - <data name="outfile" format="tabular" /> - </outputs> - <tests> - <test> - </test> - </tests> - <help> -**What it does** - -It is inevitable that researchers will want to enhance the gemini framework with their own, custom annotations. gemini provides a sub-command called annotate for exactly this purpose. - -@CITATION@ - </help> - <expand macro="citations"/> -</tool>
--- a/gemini_autosomal_recessive.xml Fri Oct 16 13:55:09 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,68 +0,0 @@ -<tool id="gemini_recessive_and_dominant" name="GEMINI autosomal recessive/dominant" version="@VERSION@.0"> - <description>Find variants meeting an autosomal recessive/dominant model</description> - <macros> - <import>gemini_macros.xml</import> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <expand macro="version_command" /> - <command> -<![CDATA[ - gemini - - #if str($rec_or_dom) == 'recessive': - ## start autosomal_recessive - autosomal_recessive - #else: - ## start autosomal_dominant - autosomal_dominant - #end if - - #if str($report.report_selector) != 'all': - --columns "${report.columns}" - #end if - - @CMDLN_SQL_FILTER_FILTER_OPTION@ - - -d $d - #if int($min_kindreds) > 0: - --min-kindreds $min_kindreds - #end if - - "${ infile }" - > "${ outfile }" -]]> - </command> - <inputs> - - <param name="rec_or_dom" type="select" label="Autosomal ..." help=""> - <option value="recessive">recessive</option> - <option value="dominant">dominant</option> - </param> - - <expand macro="infile" /> - <expand macro="column_filter" /> - <expand macro="filter" /> - <expand macro="min_sequence_depth" /> - <param name="min_kindreds" type="integer" value="-1" label="The min. number of kindreds that must have a candidate variant in a gene" - help="-1 means default values (--min-kindreds)" /> - - </inputs> - <outputs> - <data name="outfile" format="tabular" /> - </outputs> - <tests> - <test> - </test> - </tests> - <help> -**What it does** - -Assuming you have defined the familial relationships between samples when loading your VCF into GEMINI, one can leverage a -built-in tool for identifying variants that meet an autosomal recessive or dominant inheritance pattern. -The reported variants will be restricted to those variants having the potential to impact the function of affecting protein coding transcripts. - -@CITATION@ - </help> - <expand macro="citations"/> -</tool>
--- a/gemini_burden.xml Fri Oct 16 13:55:09 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ -<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> - <description>perform sample-wise gene-level burden calculations</description> - <macros> - <import>gemini_macros.xml</import> - <token name="@BINARY@">burden</token> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <expand macro="version_command" /> - <command> -<![CDATA[ - gemini @BINARY@ - --cases $cases - --controls $controls - $save_tscores - $nonsynonymous - $calpha - --permutations $permutations - #if float( str($min_aaf) ) >= 0.0: - --min-aaf $min_aaf - #end if - #if float( str($max_aaf) ) >= 0.0: - --max-aaf $max_aaf - #end if - "${ infile }" - > "${ outfile }" -]]> - - </command> - <inputs> - <expand macro="infile" /> - - <param name="cases" type="text" value="" label="Space separated list of cases for association testing" help="(--cases)"/> - <param name="controls" type="text" value="" label="Space separated list of controls for association testing" help="(--controls)"/> - - <param name="save_tscores" type="boolean" truevalue="--save_tscores" falsevalue="" checked="False" - label="Save the permuted T-scores in the output file" help="(--save_tscores)"/> - - <param name="nonsynonymous" type="boolean" truevalue="--nonsynonymous" falsevalue="" checked="False" - label="Count all nonsynonymous variants as contributing burden" help="(--nonsynonymous)"/> - <param name="calpha" type="boolean" truevalue="--calpha" falsevalue="" checked="False" - label="Run the C-alpha association test" help="(--calpha)"/> - <param name="min_aaf" type="float" value="-1" label="The min. alt. allele frequency for a variant to be included" - help="(--min-aaf)"> - <!--validator type="in_range" min="0.0"/--> - </param> - <param name="max_aaf" type="float" value="-1" label="The max. alt. allele frequency for a variant to be included" - help="(--max-aaf)"> - <!--validator type="in_range" min="0.0"/--> - </param> - - <param name="permutations" type="integer" value="1000" label="Number of permutations to run for the C-alpha test" - help="(--permutations)"> - <validator type="in_range" min="0"/> - </param> - - </inputs> - <outputs> - <data name="outfile" format="tabular" /> - </outputs> - <tests> - <test> - </test> - </tests> - <help> -**What it does** - -The burden tool provides a set of utilities to perform burden summaries on a per-gene, per sample basis. -By default, it outputs a table of gene-wise counts of all high impact variants in coding regions for each sample. - -$ gemini burden test.burden.db -gene M10475 M10478 M10500 M128215 -WDR37 2 2 2 2 -CTBP2 0 0 0 1 -DHODH 1 0 0 0 - -@CITATION@ - </help> - <expand macro="citations"> - <citation type="doi">10.1371/journal.pgen.1001322</citation><!-- c-alpha citation --> - </expand> -</tool>
--- a/gemini_comp_hets.xml Fri Oct 16 13:55:09 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,60 +0,0 @@ -<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> - <description>Identifying potential compound heterozygotes</description> - <macros> - <import>gemini_macros.xml</import> - <token name="@BINARY@">comp_hets</token> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <expand macro="version_command" /> - <command> -<![CDATA[ - gemini @BINARY@ - - #if $report.report_selector != 'all': - --columns "${report.columns}" - #end if - - @CMDLN_SQL_FILTER_FILTER_OPTION@ - - $only_affected - $ignore_phasing - - "${ infile }" - > "${ outfile }" -]]> - </command> - <inputs> - <expand macro="infile" /> - <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" - label="Ignore phasing when screening for compound hets" help="Candidates are inherently putative. (--ignore-phasing)"/> - <expand macro="filter" /> - </inputs> - <outputs> - <data name="outfile" format="tabular" /> - </outputs> - <tests> - <test> - </test> - </tests> - <help> -**What it does** - -Many recessive disorders are caused by compound heterozygotes. Unlike canonical recessive sites where the same recessive allele is -inherited from both parents at the _same_ site in the gene, compound heterozygotes occur when the individual’s phenotype is caused -by two heterozygous recessive alleles at _different_ sites in a particular gene. - -So basically, we are looking for two (typically loss-of-function (LoF)) heterozygous variants impacting the same gene at different loci. -The complicating factor is that this is _recessive_ and as such, we must also require that the consequential alleles at each heterozygous -site were inherited on different chromosomes (one from each parent). As such, in order to use this tool, we require that all variants are phased. -Once this has been done, the comp_hets tool will provide a report of candidate compound heterozygotes for each sample/gene. - - -@CITATION@ - </help> - <expand macro="citations"/> -</tool>
--- a/gemini_db_info.xml Fri Oct 16 13:55:09 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ -<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> - <description>List the gemini database tables and columns</description> - <macros> - <import>gemini_macros.xml</import> - <token name="@BINARY@">db_info</token> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <expand macro="version_command" /> - <command> -<![CDATA[ - gemini @BINARY@ - "${ infile }" | tr -s ' ' '\t' - > "${ outfile }" -]]> - </command> - <inputs> - <expand macro="infile" /> - </inputs> - <outputs> - <data name="outfile" format="tabular" /> - </outputs> - <tests> - <test> - </test> - </tests> - <help> -**What it does** - -Because of the sheer number of annotations that are stored in gemini, there are admittedly too many columns to remember by rote. -If you can’t recall the name of particular column, just use the db_info tool. It will report all of the tables and all of the columns / types in each table. - -@CITATION@ - </help> - <expand macro="citations"/> -</tool>
--- a/gemini_de_novo.xml Fri Oct 16 13:55:09 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,48 +0,0 @@ -<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> - <description>Identifying potential de novo mutations</description> - <macros> - <import>gemini_macros.xml</import> - <token name="@BINARY@">de_novo</token> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <expand macro="version_command" /> - <command> -<![CDATA[ - gemini @BINARY@ - - #if $report.report_selector != 'all': - --columns "${report.columns}" - #end if - - @CMDLN_SQL_FILTER_FILTER_OPTION@ - - -d $d - "${ infile }" - > "${ outfile }" -]]> - </command> - <inputs> - <expand macro="infile" /> - - <expand macro="column_filter" /> - <expand macro="filter" /> - <expand macro="min_sequence_depth" /> - </inputs> - <outputs> - <data name="outfile" format="tabular" /> - </outputs> - <tests> - <test> - </test> - </tests> - <help> -**What it does** - -Assuming you have defined the familial relationships between samples when loading your VCF into GEMINI, -you can use this tool for identifying de novo (a.k.a spontaneous) mutations that arise in offspring. - -@CITATION@ - </help> - <expand macro="citations"/> -</tool>
--- a/gemini_interactions.xml Fri Oct 16 13:55:09 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,68 +0,0 @@ -<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> - <description>Find genes among variants that are interacting partners</description> - <macros> - <import>gemini_macros.xml</import> - <token name="@BINARY@">interactions</token> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <expand macro="version_command" /> - <command> -<![CDATA[ - gemini - --annotation-dir ${annotation_databases.fields.path} - #if $gene.gene_selector == 'lof': - ## lof interactions is a separate program - lof_interactions - #else: - ## use normal gemini interactions program - @BINARY@ - -g "${gene.gene}" - #end if - - -r "${radius}" - $variant_mode - "${ infile }" - > "${ outfile }" -]]> - </command> - <inputs> - <expand macro="infile" /> - - <conditional name="gene"> - <param name="gene_selector" type="select" label="Studying" help=""> - <option value="gene">Interesting gene</option> - <option value="lof">All loss-of-function variants</option> - </param> - <when value="gene"> - <param name="gene" type="text" label="Specify gene name" help="e.g. PTPN22 (-g)" /> - </when> - <when value="lof"/> - </conditional> - <expand macro="annotation_dir" /> - <expand macro="radius" /> - <expand macro="variant_mode" /> - </inputs> - <outputs> - <data name="outfile" format="tabular" /> - </outputs> - <tests> - <test> - </test> - </tests> - <help> -**What it does** - -Integrating the knowledge of the known protein-protein interactions would be useful in explaining variation data. -Meaning to say that a damaging variant in an interacting partner of a potential protein may be equally interesting as the -protein itself. We have used the HPRD_ binary interaction data to build a p-p network graph which can be explored by GEMINI. - -.. _HPRD: http://www.ncbi.nlm.nih.gov/pubmed/18988627 - - -@CITATION@ - </help> - <expand macro="citations"> - <citation type="doi">10.1093/nar/gkn892</citation><!-- HPRD citation --> - </expand> -</tool>
--- a/gemini_load.xml Fri Oct 16 13:55:09 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,91 +0,0 @@ -<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> - <description>Loading a VCF file into GEMINI</description> - <macros> - <import>gemini_macros.xml</import> - <token name="@BINARY@">load</token> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <expand macro="version_command" /> - <command> -<![CDATA[ - ln -s "${ infile }" input.vcf && - - gemini - --annotation-dir ${annotation_databases.fields.path} - @BINARY@ - -v input.vcf - #if str( $annotation_type ) != "None": - -t $annotation_type - #end if - - #if $ped: - -p $ped - #end if - - $skip_gerp_bp - $skip_cadd - $skip_gene_tables - $no_load_genotypes - $no_genotypes - $passonly - --cores \${GALAXY_SLOTS:-4} - - "${ outfile }" -]]> - </command> - <inputs> - <param name="infile" type="data" format="vcf" label="VCF file to be loaded in the GEMINI database" help="Only build 37 (aka hg19) of the human genome is supported."> - <options> - <filter type="add_value" value="hg19" /> - <filter type="add_value" value="Homo_sapiens_nuHg19_mtrCRS" /> - <filter type="add_value" value="hg_g1k_v37" /> - </options> - </param> - - <param name="annotation_type" type="select" label="The annotations to be used with the input vcf" help="(-t)"> - <option value="None">None (not recommended)</option> - <option value="snpEff" selected="True">snpEff annotated VCF file</option> - <option value="VEP">VEP annotated VCF file</option> - </param> - <param name="ped" type="data" format="tablar" optional="True" label="Sample information file in PED+ format" help="(-p)" /> - <expand macro="annotation_dir" /> - - <param name="skip_gerp_bp" type="boolean" truevalue="--skip-gerp-bp" falsevalue="" checked="False" - label="Do not load GERP scores at base pair resolution" help="(--skip-gerp-bp)"/> - - <param name="skip_cadd" type="boolean" truevalue="--skip-cadd" falsevalue="" checked="False" - label="Do not load CADD scores" help="(--skip-cadd)"/> - - <param name="skip_gene_tables" type="boolean" truevalue="--skip-gene-tables" falsevalue="" checked="False" - label="Do not load gene tables" help="(--skip-gene-tables)"/> - - <param name="no_load_genotypes" type="boolean" truevalue="--no-load-genotypes" falsevalue="" checked="False" - label="Genotypes exist in the file, but should not be stored" help="(--no-load-genotypes)"/> - - <param name="no_genotypes" type="boolean" truevalue="--no-load-genotypes" falsevalue="" checked="False" - label="There are no genotypes in the file" help="e.g. some 1000G VCFs (--no-genotypes)"/> - - <param name="passonly" type="boolean" truevalue="--passonly" falsevalue="" checked="False" - label="Keep only variants that pass all filters" help="e.g. some 1000G VCFs (--passonly)"/> - - </inputs> - <outputs> - <data name="outfile" format="gemini.sqlite" /> - </outputs> - <tests> - <test> - </test> - </tests> - <help> -**What it does** - -Before we can use GEMINI to explore genetic variation, we must first load our VCF file into the GEMINI database framework. -We expect you to have first annotated the functional consequence of each variant in your VCF using either VEP or snpEff. - -http://gemini.readthedocs.org/en/latest/content/loading.html - -@CITATION@ - </help> - <expand macro="citations"/> -</tool>
--- a/gemini_lof_sieve.xml Fri Oct 16 13:55:09 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,39 +0,0 @@ -<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> - <description>Filter LoF variants by transcript position and type</description> - <macros> - <import>gemini_macros.xml</import> - <token name="@BINARY@">lof_sieve</token> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <expand macro="version_command" /> - <command> -<![CDATA[ - gemini @BINARY@ - "${ infile }" - > "${ outfile }" -]]> - </command> - <inputs> - <expand macro="infile" /> - </inputs> - <outputs> - <data name="outfile" format="tabular" /> - </outputs> - <tests> - <test> - </test> - </tests> - <help> -**What it does** - -Not all candidate LoF variants are created equal. For e.g, a nonsense (stop gain) variant impacting the first 5% of a polypeptide is far -more likely to be deleterious than one affecting the last 5%. Assuming you’ve annotated your VCF with snpEff v3.0+, the lof_sieve tool -reports the fractional position (e.g. 0.05 for the first 5%) of the mutation in the amino acid sequence. -In addition, it also reports the predicted function of the transcript so that one can segregate candidate -LoF variants that affect protein_coding transcripts from processed RNA, etc. - -@CITATION@ - </help> - <expand macro="citations"/> -</tool>
--- a/gemini_macros.xml Fri Oct 16 13:55:09 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,134 +0,0 @@ -<macros> - <xml name="requirements"> - <requirements> - <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> - <yield /> - </requirements> - </xml> - - <xml name="version_command"> - <version_command>gemini --version</version_command> - </xml> - - <xml name="stdio"> - <stdio> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> - </xml> - - <xml name="annotation_dir"> - <param name="annotation_databases" type="select" label="Choose a gemini annotation database"> - <options from_data_table="gemini_databases"> - <filter type="sort_by" column="0" /> - <validator type="no_options" message="No annotation database is available" /> - </options> - </param> - </xml> - - <xml name="add_header_column"> - <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" - label="Add a header of column names to the output" help="(--header)"/> - </xml> - - <xml name="radius"> - <param name="radius" type="integer" value="3" label="Set filter for Breadth-first search (BFS) in the Protein-Protein Interaction network" help="(-r)" > - <validator type="in_range" min="0"/> - </param> - </xml> - <xml name="variant_mode"> - <param name="variant_mode" type="boolean" truevalue="--var" falsevalue="" checked="False" - label="Returns variant info (e.g. impact, biotype) for interacting genes" help="(--var)"/> - </xml> - - <xml name="column_filter"> - <conditional name="report"> - <param name="report_selector" type="select" label="Columns to include in the report" - help="By default, this tool reports all columns in the variants table. One may choose to report only a subset of the columns."> - <option value="all" selected="True">all</option> - <option value="column_filter">User given columns</option> - </param> - <when value="all"/> - <when value="column_filter"> - <param name="columns" type="select" display="checkboxes" multiple="True" label="Choose columns to include in the report" help="(--columns)"> - <option value="gene">gene</option> - <option value="chrom">chrom</option> - <option value="start">start</option> - <option value="end">end</option> - <option value="ref">ref</option> - <option value="alt">alt</option> - <option value="impact">impact</option> - <option value="impact_severity">impact_severity</option> - </param> - </when> - </conditional> - </xml> - - <xml name="filter"> - <conditional name="filter"> - <param name="filter_selector" type="select" label="Apply additional constraints" - help="By default, this tool will report all variants regardless of their putative functional impact. In order to apply additional constraints on the variants returned, you can this optional filter."> - <option value="no">No additional constraints</option> - <option value="yes">Apply additional constraints</option> - </param> - <when value="no"/> - <when value="yes"> - <param name="filter" type="text" label="Contraints in SQL syntax" help="Conditions applied here will become WHERE clauses in the query issued to the GEMINI database. E.g. alt='G' or impact_severity = 'HIGH'. (--filter)"> - <expand macro="sanitize_query" /> - </param> - </when> - </conditional> - </xml> - - <xml name="sanitize_query"> - <sanitizer invalid_char=""> - <valid initial="string.printable"/> - </sanitizer> - </xml> - - <token name="@CMDLN_SQL_FILTER_FILTER_OPTION@"> - #if str($filter.filter_selector) == 'yes' and $filter.filter: - #import pipes - --filter ${ pipes.quote( str( $filter.filter ) ) or "''" } - #end if - </token> - - <xml name="min_sequence_depth"> - <param name="d" type="integer" value="0" label="The minimum aligned sequence depth (genotype DP) required for each sample" - help="default: 0 (-d)"> - <validator type="in_range" min="0"/> - </param> - </xml> - - <token name="@VERSION@">0.10.1</token> - - <token name="@CITATION@">------ - -**Citation** - -If you use GEMINI in your research, please cite the following manuscript: - - </token> - <xml name="citations"> - <citations> - <citation type="doi">10.1371/journal.pcbi.1003153</citation> - <yield /> - </citations> - </xml> - - <xml name="infile"> - <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." > - <options options_filter_attribute="metadata.gemini_version" > - <filter type="add_value" value="@VERSION@" /> - </options> - <validator type="expression" message="This version of Gemini will only work with Gemini files that are for version @VERSION@.">value is not None and value.metadata.gemini_version == "@VERSION@"</validator> - </param> - </xml> - -</macros>
--- a/gemini_pathways.xml Fri Oct 16 13:55:09 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,52 +0,0 @@ -<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> - <description>Map genes and variants to KEGG pathways</description> - <macros> - <import>gemini_macros.xml</import> - <token name="@BINARY@">pathways</token> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <expand macro="version_command" /> - <command> -<![CDATA[ - gemini - --annotation-dir ${annotation_databases.fields.path} - @BINARY@ - -v $ensembl - $lof - "${ infile }" - > "${ outfile }" -]]> - </command> - <inputs> - <expand macro="infile" /> - - <param name="ensembl" type="integer" value="68" label="Version of ensembl genes to use" - help="Supported versions: 66 to 71. use versions that match the VEP/snpEff versions of the annotated vcf for correctness. For e.g VEP v2.6 and snpEff v3.1 use Ensembl 68 version of the genomes. (-v)"> - <validator type="in_range" min="66" max="71"/> - </param> - - <param name="lof" type="boolean" truevalue="--lof" falsevalue="" checked="False" - label="Report only pathways with loss-of-function variants" help="(--lof)"/> - <expand macro="annotation_dir" /> - </inputs> - <outputs> - <data name="outfile" format="tabular" /> - </outputs> - <tests> - <test> - </test> - </tests> - <help> -**What it does** - -Mapping genes to biological pathways is useful in understanding the function/role played by a gene. -Likewise, genes involved in common pathways is helpful in understanding heterogeneous diseases. -We have integrated the KEGG pathway mapping for gene variants, to explain/annotate variation. - -This requires your VCF be annotated with either snpEff/VEP. - -@CITATION@ - </help> - <expand macro="citations"/> -</tool>
--- a/gemini_query.xml Fri Oct 16 13:55:09 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,110 +0,0 @@ -<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> - <description>Querying the GEMINI database</description> - <macros> - <import>gemini_macros.xml</import> - <token name="@BINARY@">query</token> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <expand macro="version_command" /> - <command> -<![CDATA[ - gemini @BINARY@ - - --in "${in}" - - #if $gt_filter.strip(): - --gt-filter "${gt_filter}" - #end if - - #if $sample_filter.strip(): - --sample-filter "${sample_filter}" - #end if - - $show_samples - $show_families - $family_wise - $header - $dgidb - #if $region.strip(): - --region "${region}" - #end if - #if int($min_kindreds) > 0: - --min-kindreds $min_kindreds - #end if - ##--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 }" -]]> - </command> - <!-- - ##TODO: - - -carrier-summary-by-phenotype CARRIER_SUMMARY - Output columns of counts of carriers and non-carriers - stratified by the given sample phenotype column--> - <inputs> - <expand macro="infile" /> - - <param name="q" type="text" area="True" size="5x50" label="The query to be issued to the database" help="(-q)"> - <expand macro="sanitize_query" /> - </param> - <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filer)"> - <expand macro="sanitize_query" /> - </param> - <param name="sample_filter" type="text" area="True" size="5x50" label="SQL filter to use to filter the sample table" help="(--sample-filter)"> - <expand macro="sanitize_query" /> - </param> - - <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)"/> - - <param name="show_families" type="boolean" truevalue="--show-families" falsevalue="" checked="False" - label="Add a column listing all of the families with a variant to each variant" help="(--show-families)"/> - - <param name="family_wise" type="boolean" truevalue="--family-wise" falsevalue="" checked="False" - label="Perform the sample-filter on a family-wise basis" help="(--family-wise)"/> - - <expand macro="add_header_column" /> - - <!-- TODO: is there any default values set? --> - <param name="min_kindreds" type="integer" value="-1" label="Minimum number of families for a variant passing a family-wise filter to be in" help="-1 means default values (--min-kindreds)" /> - - <param name="dgidb" type="boolean" truevalue="--dgidb" falsevalue="" checked="False" - 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">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" type="text" value="" label="Restrict query to this region" help="e.g. chr1:10-20 (--region)"/> - - - </inputs> - <outputs> - <data name="outfile" format="tabular" /> - </outputs> - <tests> - <test> - </test> - </tests> - <help> -**What it does** - -The real power in the GEMINI framework lies in the fact that all of your genetic variants have been stored in a convenient database in the context of a wealth of genome annotations that facilitate variant interpretation. -The expressive power of SQL allows one to pose intricate questions of one’s variation data. This tool offers you an easy way to query your variants! - -http://gemini.readthedocs.org/en/latest/content/querying.html - -@CITATION@ - </help> - <expand macro="citations"/> -</tool>
--- a/gemini_region.xml Fri Oct 16 13:55:09 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,73 +0,0 @@ -<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> - <description>Extracting variants from specific regions or genes</description> - <macros> - <import>gemini_macros.xml</import> - <token name="@BINARY@">region</token> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <expand macro="version_command" /> - <command> -<![CDATA[ - gemini @BINARY@ - - #if $region.region_selector == '--reg': - #if str(${region.region}) != '': - --reg "${region.region}" - #end if - #else: - #if str(${region.gene}) != '': - --gene "${region.gene}" - #end if - #end if - - #if $report.report_selector != 'all': - --columns "${report.columns}" - #end if - - @CMDLN_SQL_FILTER_FILTER_OPTION@ - - $header - "${ infile }" - > "${ outfile }" -]]> - </command> - <inputs> - <expand macro="infile" /> - - <conditional name="region"> - <param name="region_selector" type="select" label="Select by ...?" help=""> - <option value="--reg">genomic coordinates</option> - <option value="--gene">gene name</option> - </param> - <when value="--reg"> - <param name="region" type="text" label="Specify genomic region" help="e.g. chr1:100-200 (--reg)"/> - </when> - <when value="--gene"> - <param name="gene" type="text" label="Specify gene name" help="e.g. PTPN22 (--gene)" /> - </when> - </conditional> - - <expand macro="column_filter" /> - <expand macro="filter" /> - - - <expand macro="add_header_column" /> - - </inputs> - <outputs> - <data name="outfile" format="tabular" /> - </outputs> - <tests> - <test> - </test> - </tests> - <help> -**What it does** - -One often is concerned with variants found solely in a particular gene or genomic region. - -@CITATION@ - </help> - <expand macro="citations"/> -</tool>
--- a/gemini_roh.xml Fri Oct 16 13:55:09 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,106 +0,0 @@ -<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> - <description>Identifying runs of homozygosity</description> - <macros> - <import>gemini_macros.xml</import> - <token name="@BINARY@">roh</token> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <expand macro="version_command" /> - <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 - #if $samples.strip() != '': - -s "${samples}" - #end if - "${ infile }" - > "${ outfile }" -]]> - </command> - <inputs> - <expand macro="infile" /> - - <param name="min_snps" type="integer" value="25" label="Minimum number of expected homozygous SNPs" help="default: 25 (--min-snps)"> - <validator type="in_range" min="0"/> - </param> - <param name="min_total_depth" type="integer" value="20" label="The minimum overall sequencing depth requiredfor a SNP to be considered" help="default: 20 (--min-total-depth)"> - <validator type="in_range" min="0"/> - </param> - <param name="min_gt_depth" type="integer" value="0" label="The minimum required sequencing depth underlying a given sample's genotype for a SNP to be considered" - help="default: 0 (--min-gt-depth)"> - <validator type="in_range" min="0"/> - </param> - <param name="min_size" type="integer" value="100000" label="Minimum run size in base pairs" help="default: 100000 (--min-size)"> - <validator type="in_range" min="1"/> - </param> - <param name="max_hets" type="integer" value="1" label="Maximum number of allowed hets in the run" help="default: 1 (--max-hets)"> - <validator type="in_range" min="1"/> - </param> - <param name="max_unknowns" type="integer" value="3" label="Maximum number of allowed unknowns in the run" help="default: 3 (-max-unknowns)"> - <validator type="in_range" min="0"/> - </param> - - <param name="samples" type="text" value="" label="Comma separated list of samples to screen for ROHs" help="e.g S120,S450 (-s)"/> - - </inputs> - - <outputs> - <data name="outfile" format="tabular" /> - </outputs> - <tests> - <test> - </test> - </tests> - <help> - -**What it does** - -=========================================================================== -``ROH``: Identifying runs of homozygosity -=========================================================================== -Runs of homozygosity are long stretches of homozygous genotypes that reflect -segments shared identically by descent and are a result of consanguinity or -natural selection. Consanguinity elevates the occurrence of rare recessive -diseases (e.g. cystic fibrosis) that represent homozygotes for strongly deleterious -mutations. Hence, the identification of these runs holds medical value. - -The 'roh' tool in GEMINI returns runs of homozygosity identified in whole genome data. -The tool basically looks at every homozygous position on the chromosome as a possible -start site for the run and looks for those that could give rise to a potentially long -stretch of homozygous genotypes. - -For e.g. for the given example allowing ``1 HET`` genotype (h) and ``2 UKW`` genotypes (u) -the possible roh runs (H) would be: - - -:: - - genotype_run = H H H H h H H H H u H H H H H u H H H H H H H h H H H H H h H H H H H - roh_run1 = H H H H h H H H H u H H H H H u H H H H H H H - roh_run2 = H H H H u H H H H H u H H H H H H H h H H H H H - roh_run3 = H H H H H u H H H H H H H h H H H H H - roh_run4 = H H H H H H H h H H H H H - -roh returned for --min-snps = 20 would be: - -:: - - roh_run1 = H H H H h H H H H u H H H H H u H H H H H H H - roh_run2 = H H H H u H H H H H u H H H H H H H h H H H H H - - -As you can see, the immediate homozygous position right of a break (h or u) would be the possible -start of a new roh run and genotypes to the left of a break are pruned since they cannot -be part of a longer run than we have seen before. - - -@CITATION@ - </help> - <expand macro="citations"/> -</tool>
--- a/gemini_stats.xml Fri Oct 16 13:55:09 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,57 +0,0 @@ -<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> - <description>Compute useful variant statistics</description> - <macros> - <import>gemini_macros.xml</import> - <token name="@BINARY@">stats</token> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <expand macro="version_command" /> - <command> -<![CDATA[ - gemini @BINARY@ - $stats_type - "${ infile }" - > "${ outfile }" -]]> - </command> - <inputs> - <expand macro="infile" /> - - <param name="stats_type" type="select" label="Studying ..." help=""> - <option value="--tstv">Compute the transition and transversion ratios for the snps (--tstv)</option> - <option value="--tstv-coding">Compute the transition/transversion ratios for the snps in the coding regions (--tstv-coding)</option> - <option value="--tstv-noncoding">Compute the transition/transversion ratios for the snps in the non-coding regions (--tstv-noncoding)</option> - <option value="--snp-counts">Compute the type and count of the snps (--snp-counts)</option> - <option value="--sfs">Calculate the site frequency spectrum of the variants (--sfs)</option> - <option value="--mds">Compute the pair-wise genetic distance between each sample (--mds)</option> - <option value="--vars_by_sample">Return the total variants per sample, sum of homozygous and heterozygous variants (--vars-by-sample)</option> - </param> - - </inputs> - <outputs> - <data name="outfile" format="tabular" /> - </outputs> - <tests> - <test> - </test> - </tests> - <help> -**What it does** - -The stats tool computes some useful variant statistics for a GEMINI database. - - -$ gemini stats --summarize "select * from variants where in_dbsnp=1 and chrom='chr1'" my.db -sample total num_het num_hom_alt -M10475 1 1 0 -M128215 1 1 0 -M10478 2 2 0 -M10500 2 1 1 - - - -@CITATION@ - </help> - <expand macro="citations"/> -</tool>
--- a/gemini_windower.xml Fri Oct 16 13:55:09 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,64 +0,0 @@ -<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> - <description>Conducting analyses on genome "windows"</description> - <macros> - <import>gemini_macros.xml</import> - <token name="@BINARY@">windower</token> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <expand macro="version_command" /> - <command> -<![CDATA[ - gemini @BINARY@ - -w $w - -s $s - -t $window_analysis - -o $operation - "${ infile }" - > "${ outfile }" -]]> - </command> - <inputs> - <expand macro="infile" /> - - <param name="window_analysis" type="select" label="The type of window analysis requested?" help="(-t)"> - <option value="nucl_div">(nucl_div)</option> - <option value="hwe">(hwe)</option> - </param> - - <param name="operation" type="select" label="The operation that should be applied to the -t values" help="(-o)"> - <option value="mean">mean</option> - <option value="median">median</option> - <option value="min">min</option> - <option value="max">max</option> - <option value="collapse">collapse</option> - </param> - - <param name="w" type="integer" value="10000" label="The window size in bp" - help="(-w)"> - <validator type="in_range" min="0"/> - </param> - - <param name="s" type="integer" value="1000" label="The step size for the windows in bp" - help="(-s)"> - <validator type="in_range" min="0"/> - </param> - - </inputs> - - <outputs> - <data name="outfile" format="tabular" /> - </outputs> - <tests> - <test> - </test> - </tests> - <help> -**What it does** - -It computs variation metrics across genomic windows (both fixed and sliding). - -@CITATION@ - </help> - <expand macro="citations"/> -</tool>
--- a/readme.rst Fri Oct 16 13:55:09 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ -========================= -Galaxy wrapper for GEMINI -========================= - - -GEMINI: a flexible framework for exploring genome variation - -GEMINI (GEnome MINIng) is designed to be a flexible framework for exploring genetic variation in the context of -the wealth of genome annotations available for the human genome. By placing genetic variants, sample genotypes, -and useful genome annotations into an integrated database framework, GEMINI provides a simple, flexible, yet very -powerful system for exploring genetic variation for for disease and population genetics. - -Using the GEMINI framework begins by loading a VCF file into a database. Each variant is automatically -annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, -OMIM, dbSNP, KEGG, and HPRD. All of this information is stored in portable SQLite database that allows -one to explore and interpret both coding and non-coding variation using “off-the-shelf” tools or an -enhanced SQL engine. - -Please also see the original [manuscript](http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003153). - - -============ -Installation -============ - -It is recommended to install this wrapper via the `Galaxy Tool Shed`. - -.. _`Galaxy Tool Shed`: https://testtoolshed.g2.bx.psu.edu/view/iuc/gemini - - -======= -History -======= -- 0.9.1: Initial public release - - -==================== -Detailed description -==================== - -View the original GEMINI documentation: http://gemini.readthedocs.org/en/latest/index.html - - -=============================== -Wrapper Licence (MIT/BSD style) -=============================== - -Permission to use, copy, modify, and distribute this software and its -documentation with or without modifications and for any purpose and -without fee is hereby granted, provided that any copyright notices -appear in all copies and that both those copyright notices and this -permission notice appear in supporting documentation, and that the -names of the contributors or copyright holders not be used in -advertising or publicity pertaining to distribution of the software -without specific prior permission. - -THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL -WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED -WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE -CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT -OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS -OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE -OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE -OR PERFORMANCE OF THIS SOFTWARE. -
--- a/repository_dependencies.xml Fri Oct 16 13:55:09 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories description="This requires the GEMINI data manager definition to install all required annotation databases."> - <repository changeset_revision="da5f9fc20153" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> -</repositories>
--- a/tool-data/gemini_databases.loc.sample Fri Oct 16 13:55:09 2015 -0400 +++ b/tool-data/gemini_databases.loc.sample Tue Dec 29 10:19:47 2015 -0500 @@ -1,3 +1,3 @@ ## GEMINI databases -#Version dbkey Description Path -#08_08_2014 hg19 Database (08-08-2014) /path/to/data +#Version dbkey Description +#08_08_2014 hg19 Database (08-08-2014)
--- a/tool_dependencies.xml Fri Oct 16 13:55:09 2015 -0400 +++ b/tool_dependencies.xml Tue Dec 29 10:19:47 2015 -0500 @@ -1,18 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="grabix" version="0.1.3"> - <repository changeset_revision="8a1184d30e64" name="package_grabix_0_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="tabix" version="0.2.6"> - <repository changeset_revision="54f8b9bf9b6c" name="package_tabix_0_2_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="samtools" version="0.1.19"> - <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="bedtools" version="2.19.1"> - <repository changeset_revision="3ad963111153" name="package_bedtools_2_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="gemini" version="0.10.0"> - <repository changeset_revision="701523a25faa" name="package_gemini_0_10_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="gemini" version="0.18.1"> + <repository changeset_revision="4afa532941cb" name="package_gemini_0_18_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>