# HG changeset patch
# User iuc
# Date 1408916940 14400
# Node ID e6512af21622ce1cab89d96218f43e5670d7c19e
# Parent  5fec0c2b77c762c17e670921675900bd26801e4f
Uploaded

diff -r 5fec0c2b77c7 -r e6512af21622 gemini_burden.xml
--- 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" 
diff -r 5fec0c2b77c7 -r e6512af21622 gemini_comp_hets.xml
--- 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" 
diff -r 5fec0c2b77c7 -r e6512af21622 gemini_db_info.xml
--- 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>
diff -r 5fec0c2b77c7 -r e6512af21622 gemini_interactions.xml
--- 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)" />
diff -r 5fec0c2b77c7 -r e6512af21622 gemini_load.xml
--- 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>
diff -r 5fec0c2b77c7 -r e6512af21622 gemini_macros.xml
--- 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>
diff -r 5fec0c2b77c7 -r e6512af21622 gemini_pathways.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>
diff -r 5fec0c2b77c7 -r e6512af21622 gemini_query.xml
--- 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)"/>
diff -r 5fec0c2b77c7 -r e6512af21622 gemini_region.xml
--- 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':
diff -r 5fec0c2b77c7 -r e6512af21622 gemini_roh.xml
--- 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" />
diff -r 5fec0c2b77c7 -r e6512af21622 tool_dependencies.xml
--- 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>