# HG changeset patch
# User iuc
# Date 1444771385 14400
# Node ID ce61d4876838fdcc5844540a1f15752a89745b2f
# Parent  65f742e605ecf4c8afe01a4908f6a1c26949ef20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e5a5ad091c621348dc6ce2df861475ebc54a380e

diff -r 65f742e605ec -r ce61d4876838 gemini_annotate.xml
--- 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">
diff -r 65f742e605ec -r ce61d4876838 gemini_autosomal_recessive.xml
--- 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>
diff -r 65f742e605ec -r ce61d4876838 gemini_burden.xml
--- 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>
diff -r 65f742e605ec -r ce61d4876838 gemini_macros.xml
--- 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>
diff -r 65f742e605ec -r ce61d4876838 gemini_pathways.xml
--- 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>
diff -r 65f742e605ec -r ce61d4876838 gemini_query.xml
--- 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>
diff -r 65f742e605ec -r ce61d4876838 gemini_roh.xml
--- 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>
 
diff -r 65f742e605ec -r ce61d4876838 gemini_windower.xml
--- 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>