Mercurial > repos > iuc > gemini
changeset 18:ce61d4876838 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e5a5ad091c621348dc6ce2df861475ebc54a380e
| author | iuc |
|---|---|
| date | Tue, 13 Oct 2015 17:23:05 -0400 |
| parents | 65f742e605ec |
| children | 27ce3de83007 |
| files | gemini_annotate.xml gemini_autosomal_recessive.xml gemini_burden.xml gemini_macros.xml gemini_pathways.xml gemini_query.xml gemini_roh.xml gemini_windower.xml |
| diffstat | 8 files changed, 22 insertions(+), 22 deletions(-) [+] |
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--- a/gemini_annotate.xml Mon May 04 22:46:38 2015 -0400 +++ b/gemini_annotate.xml Tue Oct 13 17:23:05 2015 -0400 @@ -32,7 +32,7 @@ <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" size="20" type="text" value="" + <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">
--- a/gemini_autosomal_recessive.xml Mon May 04 22:46:38 2015 -0400 +++ b/gemini_autosomal_recessive.xml Tue Oct 13 17:23:05 2015 -0400 @@ -44,7 +44,7 @@ <expand macro="column_filter" /> <expand macro="filter" /> <expand macro="min_sequence_depth" /> - <param name="min_kindreds" size="4" type="integer" value="-1" label="The min. number of kindreds that must have a candidate variant in a gene" + <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>
--- a/gemini_burden.xml Mon May 04 22:46:38 2015 -0400 +++ b/gemini_burden.xml Tue Oct 13 17:23:05 2015 -0400 @@ -30,8 +30,8 @@ <inputs> <expand macro="infile" /> - <param name="cases" size="30" type="text" value="" label="Space separated list of cases for association testing" help="(--cases)"/> - <param name="controls" size="30" type="text" value="" label="Space separated list of controls for association testing" help="(--controls)"/> + <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)"/> @@ -40,16 +40,16 @@ 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" size="5" label="The min. alt. allele frequency for a variant to be included" + <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" size="5" label="The max. alt. allele frequency for a variant to be included" + <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" size="10" label="Number of permutations to run for the C-alpha test" + <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>
--- a/gemini_macros.xml Mon May 04 22:46:38 2015 -0400 +++ b/gemini_macros.xml Tue Oct 13 17:23:05 2015 -0400 @@ -38,7 +38,7 @@ </xml> <xml name="radius"> - <param name="radius" type="integer" value="3" size="5" label="Set filter for Breadth-first search (BFS) in the Protein-Protein Interaction network" help="(-r)" > + <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> @@ -79,7 +79,7 @@ </param> <when value="no"/> <when value="yes"> - <param name="filter" type="text" size="20" 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)"> + <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> @@ -100,7 +100,7 @@ </token> <xml name="min_sequence_depth"> - <param name="d" type="integer" value="0" size="5" label="The minimum aligned sequence depth (genotype DP) required for each sample" + <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>
--- a/gemini_pathways.xml Mon May 04 22:46:38 2015 -0400 +++ b/gemini_pathways.xml Tue Oct 13 17:23:05 2015 -0400 @@ -21,7 +21,7 @@ <inputs> <expand macro="infile" /> - <param name="ensembl" type="integer" value="68" size="5" label="Version of ensembl genes to use" + <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>
--- a/gemini_query.xml Mon May 04 22:46:38 2015 -0400 +++ b/gemini_query.xml Tue Oct 13 17:23:05 2015 -0400 @@ -73,7 +73,7 @@ <expand macro="add_header_column" /> <!-- TODO: is there any default values set? --> - <param name="min_kindreds" size="4" 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="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)"/> @@ -85,7 +85,7 @@ <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)"/> + <param name="region" type="text" value="" label="Restrict query to this region" help="e.g. chr1:10-20 (--region)"/> </inputs>
--- a/gemini_roh.xml Mon May 04 22:46:38 2015 -0400 +++ b/gemini_roh.xml Tue Oct 13 17:23:05 2015 -0400 @@ -26,27 +26,27 @@ <inputs> <expand macro="infile" /> - <param name="min_snps" type="integer" value="25" size="5" label="Minimum number of expected homozygous SNPs" help="default: 25 (--min-snps)"> + <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" size="10" label="The minimum overall sequencing depth requiredfor a SNP to be considered" help="default: 20 (--min-total-depth)"> + <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" size="10" label="The minimum required sequencing depth underlying a given sample's genotype for a SNP to be considered" + <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" size="10" label="Minimum run size in base pairs" help="default: 100000 (--min-size)"> + <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" size="5" label="Maximum number of allowed hets in the run" help="default: 1 (--max-hets)"> + <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" size="5" label="Maximum number of allowed unknowns in the run" help="default: 3 (-max-unknowns)"> + <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" size="30" type="text" value="" label="Comma separated list of samples to screen for ROHs" help="e.g S120,S450 (-s)"/> + <param name="samples" type="text" value="" label="Comma separated list of samples to screen for ROHs" help="e.g S120,S450 (-s)"/> </inputs>
--- a/gemini_windower.xml Mon May 04 22:46:38 2015 -0400 +++ b/gemini_windower.xml Tue Oct 13 17:23:05 2015 -0400 @@ -34,12 +34,12 @@ <option value="collapse">collapse</option> </param> - <param name="w" type="integer" value="10000" size="10" label="The window size in bp" + <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" size="10" label="The step size for the windows in bp" + <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>