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changeset 11:53a5647e5271 draft

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Uploaded
author iuc
date Wed, 18 Feb 2015 11:36:37 -0500
parents 0f1bcedd836f
children 59b31ca05a2b
files 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 tool-data/gemini_databases.loc.sample tool_dependencies.xml
diffstat 18 files changed, 69 insertions(+), 56 deletions(-) [+]
line wrap: on
line diff
--- a/gemini_annotate.xml	Mon Aug 25 16:37:46 2014 -0400
+++ b/gemini_annotate.xml	Wed Feb 18 11:36:37 2015 -0500
@@ -29,7 +29,7 @@
     </command>
     <expand macro="stdio" />
     <inputs>
-        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+        <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=""
@@ -79,7 +79,7 @@
 
     </inputs>
     <outputs>
-        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+        <data name="outfile" format="tabular" />
     </outputs>
     <tests>
         <test>
--- a/gemini_autosomal_recessive.xml	Mon Aug 25 16:37:46 2014 -0400
+++ b/gemini_autosomal_recessive.xml	Wed Feb 18 11:36:37 2015 -0500
@@ -9,7 +9,7 @@
 <![CDATA[
         gemini 
 
-            #if $rec_or_dom == 'recessive':
+            #if str($rec_or_dom) == 'recessive':
                 ## start autosomal_recessive
                 autosomal_recessive
             #else:
@@ -17,13 +17,11 @@
                 autosomal_dominant
             #end if
 
-            #if $report.report_selector != 'all':
+            #if str($report.report_selector) != 'all':
                 --columns "${report.columns}"
             #end if
 
-            #if $filter.filter_selector == 'yes':
-                --filter "${filter.filter}"
-            #end if
+            @CMDLN_SQL_FILTER_FILTER_OPTION@
 
             -d $d
             #if int($min_kindreds) > 0:
@@ -42,16 +40,16 @@
             <option value="dominant">dominant</option>
         </param>
 
-        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+        <expand macro="infile" />
         <expand macro="column_filter" />
         <expand macro="filter" />
         <expand macro="min_sequence_depth" />
-        <param name="min_kindreds" size="4" type="integer" value="-1" lebel="The min. number of kindreds that must have a candidate variant in a gene"
+        <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"
             help="-1 means default values (--min-kindreds)" />
 
     </inputs>
     <outputs>
-        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+        <data name="outfile" format="tabular" />
     </outputs>
     <tests>
         <test>
--- a/gemini_burden.xml	Mon Aug 25 16:37:46 2014 -0400
+++ b/gemini_burden.xml	Wed Feb 18 11:36:37 2015 -0500
@@ -28,7 +28,7 @@
     </command>
     <expand macro="stdio" />
     <inputs>
-        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+        <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)"/>
@@ -56,7 +56,7 @@
 
     </inputs>
     <outputs>
-        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+        <data name="outfile" format="tabular" />
     </outputs>
     <tests>
         <test>
--- a/gemini_comp_hets.xml	Mon Aug 25 16:37:46 2014 -0400
+++ b/gemini_comp_hets.xml	Wed Feb 18 11:36:37 2015 -0500
@@ -14,9 +14,8 @@
                 --columns "${report.columns}"
             #end if
 
-            #if $filter.filter_selector == 'yes':
-                --filter "${filter.filter}"
-            #end if
+            @CMDLN_SQL_FILTER_FILTER_OPTION@
+
             $only_affected
             $ignore_phasing
 
@@ -26,7 +25,7 @@
     </command>
     <expand macro="stdio" />
     <inputs>
-        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+        <expand macro="infile" />
         <expand macro="add_header_column" />
         <expand macro="column_filter" />
         <param name="only_affected" type="boolean" truevalue="--only-affected" falsevalue="" checked="False" 
@@ -36,7 +35,7 @@
         <expand macro="filter" />
     </inputs>
     <outputs>
-        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+        <data name="outfile" format="tabular" />
     </outputs>
     <tests>
         <test>
--- a/gemini_db_info.xml	Mon Aug 25 16:37:46 2014 -0400
+++ b/gemini_db_info.xml	Wed Feb 18 11:36:37 2015 -0500
@@ -15,10 +15,10 @@
     </command>
     <expand macro="stdio" />
     <inputs>
-        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+        <expand macro="infile" />
     </inputs>
     <outputs>
-        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+        <data name="outfile" format="tabular" />
     </outputs>
     <tests>
         <test>
--- a/gemini_de_novo.xml	Mon Aug 25 16:37:46 2014 -0400
+++ b/gemini_de_novo.xml	Wed Feb 18 11:36:37 2015 -0500
@@ -14,9 +14,8 @@
                 --columns "${report.columns}"
             #end if
 
-            #if $filter.filter_selector == 'yes':
-                --filter "${filter.filter}"
-            #end if
+            @CMDLN_SQL_FILTER_FILTER_OPTION@
+
             -d $d
             "${ infile }"
             > "${ outfile }"
@@ -24,14 +23,14 @@
     </command>
     <expand macro="stdio" />
     <inputs>
-        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+        <expand macro="infile" />
 
         <expand macro="column_filter" />
         <expand macro="filter" />
         <expand macro="min_sequence_depth" />
     </inputs>
     <outputs>
-        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+        <data name="outfile" format="tabular" />
     </outputs>
     <tests>
         <test>
--- a/gemini_interactions.xml	Mon Aug 25 16:37:46 2014 -0400
+++ b/gemini_interactions.xml	Wed Feb 18 11:36:37 2015 -0500
@@ -27,7 +27,7 @@
     </command>
     <expand macro="stdio" />
     <inputs>
-        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+        <expand macro="infile" />
 
         <conditional name="gene">
             <param name="gene_selector" type="select" label="Studying" help="">
@@ -44,7 +44,7 @@
         <expand macro="variant_mode" />
     </inputs>
     <outputs>
-        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+        <data name="outfile" format="tabular" />
     </outputs>
     <tests>
         <test>
--- a/gemini_load.xml	Mon Aug 25 16:37:46 2014 -0400
+++ b/gemini_load.xml	Wed Feb 18 11:36:37 2015 -0500
@@ -12,7 +12,9 @@
             --annotation-dir ${annotation_databases.fields.path}
             @BINARY@
             -v "${ infile }"
-            -t $annotation_type
+            #if str( $annotation_type ) != "None":
+                -t $annotation_type
+            #end if
 
             #if $ped:
                 -p $ped
@@ -34,7 +36,8 @@
         <param name="infile" type="data" format="vcf" label="VCF file to be loaded in the GEMINI database" />
 
         <param name="annotation_type" type="select" label="The annotations to be used with the input vcf" help="(-t)">
-            <option value="snpEff">snpEff annotated VCF file</option>
+            <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)" />
@@ -60,7 +63,7 @@
 
     </inputs>
     <outputs>
-        <data name="outfile" format="sqlite" label="${tool.name} on ${on_string}" />
+        <data name="outfile" format="gemini.sqlite" />
     </outputs>
     <tests>
         <test>
--- a/gemini_lof_sieve.xml	Mon Aug 25 16:37:46 2014 -0400
+++ b/gemini_lof_sieve.xml	Wed Feb 18 11:36:37 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@version@.0">
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
     <description>Filter LoF variants by transcript position and type</description>
     <expand macro="requirements" />
     <expand macro="version_command" />
@@ -15,10 +15,10 @@
     </command>
     <expand macro="stdio" />
     <inputs>
-        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+        <expand macro="infile" />
     </inputs>
     <outputs>
-        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+        <data name="outfile" format="tabular" />
     </outputs>
     <tests>
         <test>
--- a/gemini_macros.xml	Mon Aug 25 16:37:46 2014 -0400
+++ b/gemini_macros.xml	Wed Feb 18 11:36:37 2015 -0500
@@ -88,11 +88,17 @@
 
     <xml name="sanitize_query">
         <sanitizer invalid_char="">
-            <valid initial="string.printable">
-            </valid>
+            <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" size="5" label="The minimum aligned sequence depth (genotype DP) required for each sample"
                 help="default: 0 (-d)">
@@ -100,7 +106,7 @@
         </param>
     </xml>
 
-    <token name="@VERSION@">0.10.0</token>
+    <token name="@VERSION@">0.10.1</token>
 
     <token name="@CITATION@">------
 
@@ -115,4 +121,14 @@
         <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	Mon Aug 25 16:37:46 2014 -0400
+++ b/gemini_pathways.xml	Wed Feb 18 11:36:37 2015 -0500
@@ -19,7 +19,7 @@
     </command>
     <expand macro="stdio" />
     <inputs>
-        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+        <expand macro="infile" />
 
         <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)">
@@ -31,7 +31,7 @@
         <expand macro="annotation_dir" />
     </inputs>
     <outputs>
-        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+        <data name="outfile" format="tabular" />
     </outputs>
     <tests>
         <test>
--- a/gemini_query.xml	Mon Aug 25 16:37:46 2014 -0400
+++ b/gemini_query.xml	Wed Feb 18 11:36:37 2015 -0500
@@ -49,7 +49,7 @@
                         stratified by the given sample phenotype column-->
     <expand macro="stdio" />
     <inputs>
-        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+        <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" />
@@ -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" lebel="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" 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="dgidb" type="boolean" truevalue="--dgidb" falsevalue="" checked="False" 
             label="Request drug-gene interaction info from DGIdb" help="(--dgidb)"/>
@@ -90,7 +90,7 @@
 
     </inputs>
     <outputs>
-        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+        <data name="outfile" format="tabular" />
     </outputs>
     <tests>
         <test>
--- a/gemini_region.xml	Mon Aug 25 16:37:46 2014 -0400
+++ b/gemini_region.xml	Wed Feb 18 11:36:37 2015 -0500
@@ -24,9 +24,7 @@
                 --columns "${report.columns}"
             #end if
 
-            #if $filter.filter_selector == 'yes':
-                --filter "${filter.filter}"
-            #end if
+            @CMDLN_SQL_FILTER_FILTER_OPTION@
 
             $header
             "${ infile }"
@@ -35,7 +33,7 @@
     </command>
     <expand macro="stdio" />
     <inputs>
-        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+        <expand macro="infile" />
 
         <conditional name="region">
             <param name="region_selector" type="select" label="Select by ...?" help="">
@@ -58,7 +56,7 @@
 
     </inputs>
     <outputs>
-        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+        <data name="outfile" format="tabular" />
     </outputs>
     <tests>
         <test>
--- a/gemini_roh.xml	Mon Aug 25 16:37:46 2014 -0400
+++ b/gemini_roh.xml	Wed Feb 18 11:36:37 2015 -0500
@@ -24,7 +24,7 @@
     </command>
     <expand macro="stdio" />
     <inputs>
-        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+        <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)">
             <validator type="in_range" min="0"/>
@@ -51,7 +51,7 @@
     </inputs>
 
     <outputs>
-        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+        <data name="outfile" format="tabular" />
     </outputs>
     <tests>
         <test>
--- a/gemini_stats.xml	Mon Aug 25 16:37:46 2014 -0400
+++ b/gemini_stats.xml	Wed Feb 18 11:36:37 2015 -0500
@@ -16,7 +16,7 @@
     </command>
     <expand macro="stdio" />
     <inputs>
-        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+        <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>
@@ -30,7 +30,7 @@
 
     </inputs>
     <outputs>
-        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+        <data name="outfile" format="tabular" />
     </outputs>
     <tests>
         <test>
--- a/gemini_windower.xml	Mon Aug 25 16:37:46 2014 -0400
+++ b/gemini_windower.xml	Wed Feb 18 11:36:37 2015 -0500
@@ -19,7 +19,7 @@
     </command>
     <expand macro="stdio" />
     <inputs>
-        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+        <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>
@@ -47,7 +47,7 @@
     </inputs>
 
     <outputs>
-        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+        <data name="outfile" format="tabular" />
     </outputs>
     <tests>
         <test>
--- a/tool-data/gemini_databases.loc.sample	Mon Aug 25 16:37:46 2014 -0400
+++ b/tool-data/gemini_databases.loc.sample	Wed Feb 18 11:36:37 2015 -0500
@@ -1,3 +1,3 @@
 ## GEMINI databases
-#Version	dbkey	Description
-#08_08_2014	hg19	Database (08-08-2014)
+#Version	dbkey	Description	Path
+#08_08_2014	hg19	Database (08-08-2014)	/path/to/data
--- a/tool_dependencies.xml	Mon Aug 25 16:37:46 2014 -0400
+++ b/tool_dependencies.xml	Wed Feb 18 11:36:37 2015 -0500
@@ -4,15 +4,15 @@
         <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="c1743e071a28" name="package_tabix_0_2_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <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="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <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="75ffd114bf5f" name="package_gemini_0_10_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="a4eca4f434e6" name="package_gemini_0_10_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>