Repository 'gemini_windower'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/gemini_windower

Changeset 5:3b5b1ebc8423 (2019-01-11)
Previous changeset 4:9aad9ef0502c (2018-12-14) Next changeset 6:c15b615cdc3b (2020-01-24)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
modified:
gemini_macros.xml
gemini_windower.xml
repository_dependencies.xml
test-data/gemini_amend_input.db
test-data/gemini_annotate_result.db
test-data/gemini_auto_dom_input.db
test-data/gemini_auto_rec_input.db
test-data/gemini_comphets_input.db
test-data/gemini_de_novo_input.db
test-data/gemini_is_somatic_result.db
test-data/gemini_load_result1.db
test-data/gemini_load_result2.db
test-data/gemini_versioned_databases.loc
test-data/test-cache/gemini-config.yaml
added:
test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz
test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz.tbi
test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz
test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz.tbi
test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz
test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz.tbi
removed:
test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz
test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz.tbi
test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz
test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz.tbi
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 gemini_macros.xml
--- a/gemini_macros.xml Fri Dec 14 12:41:48 2018 -0500
+++ b/gemini_macros.xml Fri Jan 11 17:38:04 2019 -0500
[
b'@@ -1,15 +1,12 @@\n <macros>\n     <!-- gemini version to be used -->\n-    <token name="@VERSION@">0.18.1</token>\n+    <token name="@VERSION@">0.20.1</token>\n     <!-- minimal annotation files version required by this version of gemini -->\n-    <token name="@DB_VERSION@">181</token>\n+    <token name="@DB_VERSION@">200</token>\n \n     <xml name="requirements">\n         <requirements>\n             <requirement type="package" version="@VERSION@">gemini</requirement>\n-            <requirement type="package" version="0.2.6">tabix</requirement>\n-            <!-- for conda useage -->\n-            <!--requirement type="package" version="1.3.1">htslib</requirement-->\n             <yield />\n         </requirements>\n     </xml>\n@@ -24,9 +21,17 @@\n             <exit_code range=":-1" />\n             <regex match="Error:" />\n             <regex match="Exception:" />\n+            <yield />\n         </stdio>\n     </xml>\n \n+    <xml name="citations">\n+        <citations>\n+            <citation type="doi">10.1371/journal.pcbi.1003153</citation>\n+            <yield />\n+        </citations>\n+    </xml>\n+\n     <xml name="annotation_dir">\n         <param name="annotation_databases" type="select" label="Choose a gemini annotation source">\n             <options from_data_table="gemini_versioned_databases">\n@@ -36,31 +41,36 @@\n         </param>\n     </xml>\n \n-    <xml name="add_header_column">\n-        <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" \n-            label="Add a header of column names to the output" help="(--header)"/>\n-    </xml>\n-\n-    <xml name="radius">\n-        <param name="radius" type="integer" value="3" label="Set filter for Breadth-first search (BFS) in the Protein-Protein Interaction network" help="(-r)" >\n-            <validator type="in_range" min="0"/>\n+    <xml name="infile">\n+        <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." >\n+            <options options_filter_attribute="metadata.gemini_version" >\n+                <filter type="add_value" value="@VERSION@" />\n+            </options>\n         </param>\n     </xml>\n-    <xml name="variant_mode">\n-        <param name="variant_mode" type="boolean" truevalue="--var" falsevalue="" checked="False" \n-            label="Returns variant info (e.g. impact, biotype) for interacting genes" help="(--var)"/>\n+\n+    <xml name="add_header_column">\n+        <param argument="--header" name="header" type="boolean" truevalue="--header" falsevalue="" checked="True" \n+        label="Add a header of column names to the output" />\n     </xml>\n \n-    <xml name="column_filter">\n+    <xml name="column_filter" token_help="" token_minimalset="variant_id, gene">\n         <conditional name="report">\n-            <param name="report_selector" type="select" label="Columns to include in the report"\n-                help="By default, this tool reports all columns in the variants table. One may choose to report only a subset of the columns.">\n-                <option value="all" selected="True">all</option>\n-                <option value="column_filter">User given columns</option>\n+            <param name="report_selector" type="select"\n+            label="Set of columns to include in the variant report table"\n+            help="@HELP@">\n+                <option value="minimal">Minimal (report only a preconfigured minimal set of columns)</option>\n+                <option value="full">Full (report all columns defined in the GEMINI database variants table)</option>\n+                <option value="custom">Custom (report user-specified columns)</option>\n             </param>\n-            <when value="all"/>\n-            <when value="column_filter">\n-                <param name="columns" type="select" display="checkboxes" multiple="True" label="Choose columns to include in the report" help="(--columns)">\n+            <when value="full" />\n+            <when value="minimal">\n+         '..b'r($report.extra_cols).strip():\n+                #if $cols:\n+                    #set $cols = $cols + \', \' + str($report.extra_cols)\n+                #else:\n+                    #set $cols = str($report.extra_cols)\n+                #end if\n+            #end if\n+            #if not $cols:\n+                #set $cols = "variant_id, gene"\n+            #end if\n         #end if\n     </token>\n \n     <token name="@COLUMN_SELECT@">\n-        #if $report.report_selector != \'all\':\n-            --columns "${report.columns}\n-            #if str($report.extra_cols).strip()\n-                #echo \',\'+\',\'.join(str($report.extra_cols).split()) \n-            #end if\n-            "\n+        @SET_COLS@\n+        #if $cols != "*"\n+            --columns \'$cols\'\n         #end if\n     </token>\n \n-    <xml name="family">\n-        <param name="families" type="text" value="" label="Comma seperated list of families to restrict the analysis to." help="e.g. Family1,Family3 (--families)"/>\n-    </xml>\n-\n-    <xml name="lenient">\n-        <param name="lenient" type="boolean" truevalue="--lenient" falsevalue="" checked="False" label="Loosen the restrictions on family structure"/>\n-    </xml>\n-\n-    <xml name="unaffected">\n-        <param name="allow_unaffected" type="boolean" truevalue="--allow-unaffected" falsevalue="" checked="False" label="Report candidates that also impact samples labeled as unaffected." help="(--allow-unaffected)"/>\n-    </xml>\n-\n-    <xml name="min_kindreds">\n-        <param name="min_kindreds" type="integer" value="1" label="The min. number of kindreds that must have a candidate variant in a gene" help="default: 1 (--min-kindreds)" />\n-    </xml>\n-\n-    <xml name="min_sequence_depth">\n-        <param name="d" type="integer" value="0" min="0" label="The minimum aligned sequence depth (genotype DP) required for each sample"\n-                help="default: 0 (-d)" />\n-    </xml>\n-\n-    <xml name="min_gq">\n-        <param name="min_gq" type="integer" value="0" label="the minimum genotype quality required for each sample in a family" help="default: 0 (--min-gq)">\n-            <validator type="in_range" min="0"/>\n-        </param>\n-    </xml>\n-\n-    <xml name="gt_pl_max">\n-        <param name="gt_pl_max" type="integer" value="-1" min="-1" label="The maximum phred-scaled genotype likelihod (PL) allowed for each sample in a family" help="default: -1 (not set) (--gt-pl-max)" />\n-    </xml>\n-\n-    <xml name="citations">\n-        <citations>\n-            <citation type="doi">10.1371/journal.pcbi.1003153</citation>\n-            <yield />\n-        </citations>\n-    </xml>\n-\n-    <xml name="infile">\n-        <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." >\n-            <options options_filter_attribute="metadata.gemini_version" >\n-                <filter type="add_value" value="@VERSION@" />\n-            </options>\n-            <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>\n-        </param>\n-    </xml>\n-\n+    <token name="@PARSE_REGION_ELEMENTS@"><![CDATA[\n+        #set $region_elements = []\n+        #for $r in $regions:\n+            ## The actual chromosome name needs to be single-quoted\n+            ## in SQL, so we need to quote the single quotes like the\n+            ## sanitize_query macro would if the whole was a parameter.\n+            #set $r_elements = ["chrom = \'\\"\'\\"\'%s\'\\"\'\\"\'" % str($r.chrom).strip()]\n+            #if str($r.start).strip():\n+                #silent $r_elements.append("start >= %d" % int($r.start))\n+            #end if\n+            #if str($r.stop).strip():\n+                #silent $r_elements.append("end <= %d" % int($r.stop))\n+            #end if\n+            #silent $region_elements.append("(%s)" % " AND ".join($r_elements))\n+        #end for\n+    ]]>\n+    </token>\n </macros>\n'
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 gemini_windower.xml
--- a/gemini_windower.xml Fri Dec 14 12:41:48 2018 -0500
+++ b/gemini_windower.xml Fri Jan 11 17:38:04 2019 -0500
[
@@ -1,5 +1,5 @@
-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
-    <description>Conducting analyses on genome "windows"</description>
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
+    <description>Compute sliding window statistics from variants</description>
     <macros>
         <import>gemini_macros.xml</import>
         <token name="@BINARY@">windower</token>
@@ -14,19 +14,21 @@
             -s $s
             -t $window_analysis
             -o $operation
-            "${ infile }"
-            > "${ outfile }"
+            '$infile'
+            > '$outfile'
 ]]>
     </command>
     <inputs>
         <expand macro="infile" />
 
-        <param name="window_analysis" type="select" label="The type of window analysis requested?" help="(-t)">
+        <param argument="-t" name="window_analysis" type="select"
+        label="The type of window analysis requested?" help="">
             <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)">
+        <param argument="-o" name="operation" type="select"
+        label="The operation that should be applied to the -t values" help="">
             <option value="mean">mean</option>
             <option value="median">median</option>
             <option value="min">min</option>
@@ -34,18 +36,11 @@
             <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>
-
+        <param argument="-w" name="w" type="integer" value="10000" min="2"
+        label="Window size in bp" help="" />
+        <param argument="-s" name="s" type="integer" value="1000" min="0"
+        label="Step size for sliding the window in bp" help="Specify 0 here for sliding by one full window size" />
     </inputs>
-
     <outputs>
         <data name="outfile" format="tabular" />
     </outputs>
@@ -62,27 +57,28 @@
     <help><![CDATA[
 **What it does**
 
-It computs variation metrics across genomic windows (both fixed and sliding).
+Compute variation metrics across genomic windows.
 
 **Examples**
 
-Compute the average nucleotide diversity for all variants found in non-overlapping, 50Kb windows with following settings::
+Compute the average nucleotide diversity for all variants found in non-overlapping, 50Kb windows::
 
  -w 50000 
  -s 0 
  -t nucl_div 
  -o mean
 
-Compute the average nucleotide diversity for all variants found in 50Kb windows that overlap by 10kb with following settings::
+Compute the average nucleotide diversity for all variants found in 50Kb windows that overlap by 40kb::
 
  -w 50000
  -s 10000
  -t nucl_div
  -o mean 
 
-Compute the max value for HWE statistic for all variants in a window of size 10kb with following settings::
+Compute the max value for HWE statistics for all variants in 10kb windows every 100kb along the genome::
 
- -w 10000 
+ -w 10000
+ -s 100000
  -t hwe
  -o max
 
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 repository_dependencies.xml
--- a/repository_dependencies.xml Fri Dec 14 12:41:48 2018 -0500
+++ b/repository_dependencies.xml Fri Jan 11 17:38:04 2019 -0500
b
@@ -1,4 +1,4 @@
 <?xml version="1.0" ?>
 <repositories description="This requires the GEMINI data manager definition to install all required annotation databases.">
-    <repository changeset_revision="fe5a9a7d95b0" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/>
+    <repository changeset_revision="f57426daa04d" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/>
 </repositories>
\ No newline at end of file
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 test-data/gemini_amend_input.db
b
Binary file test-data/gemini_amend_input.db has changed
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 test-data/gemini_annotate_result.db
b
Binary file test-data/gemini_annotate_result.db has changed
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 test-data/gemini_auto_dom_input.db
b
Binary file test-data/gemini_auto_dom_input.db has changed
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 test-data/gemini_auto_rec_input.db
b
Binary file test-data/gemini_auto_rec_input.db has changed
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 test-data/gemini_comphets_input.db
b
Binary file test-data/gemini_comphets_input.db has changed
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 test-data/gemini_de_novo_input.db
b
Binary file test-data/gemini_de_novo_input.db has changed
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 test-data/gemini_is_somatic_result.db
b
Binary file test-data/gemini_is_somatic_result.db has changed
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 test-data/gemini_load_result1.db
b
Binary file test-data/gemini_load_result1.db has changed
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 test-data/gemini_load_result2.db
b
Binary file test-data/gemini_load_result2.db has changed
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 test-data/gemini_versioned_databases.loc
--- a/test-data/gemini_versioned_databases.loc Fri Dec 14 12:41:48 2018 -0500
+++ b/test-data/gemini_versioned_databases.loc Fri Jan 11 17:38:04 2019 -0500
b
@@ -1,3 +1,3 @@
 ## GEMINI versioned databases
 #DownloadDate dbkey DBversion Description Path
-1999-01-01 hg19 181 GEMINI annotations (test snapshot) ${__HERE__}/test-cache
+1999-01-01 hg19 200 GEMINI annotations (test snapshot) ${__HERE__}/test-cache
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 test-data/test-cache/gemini-config.yaml
--- a/test-data/test-cache/gemini-config.yaml Fri Dec 14 12:41:48 2018 -0500
+++ b/test-data/test-cache/gemini-config.yaml Fri Jan 11 17:38:04 2019 -0500
b
@@ -2,12 +2,14 @@
 versions:
   ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.tidy.vcf.gz: 4
   ESP6500SI.all.snps_indels.tidy.v2.vcf.gz: 2
-  ExAC.r0.3.sites.vep.tidy.vcf.gz: 3
+  ExAC.r0.3.sites.vep.tidy.vcf.gz: 4
   GRCh37-gms-mappability.vcf.gz: 2
-  clinvar_20160203.tidy.vcf.gz: 5
+  clinvar_20170130.tidy.vcf.gz: 5
   cosmic-v68-GRCh37.tidy.vcf.gz: 3
-  dbsnp.b141.20140813.hg19.tidy.vcf.gz: 4
+  dbsnp.b147.20160601.tidy.vcf.gz: 1
   detailed_gene_table_v75: 2
   geno2mp.variants.tidy.vcf.gz: 1
+  gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz: 2
   hg19.rmsk.bed.gz: 2
   summary_gene_table_v75: 2
+  whole_genome_SNVs.tsv.compressed.gz: 2
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz
b
Binary file test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz has changed
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz.tbi
b
Binary file test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz.tbi has changed
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz
b
Binary file test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz has changed
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz.tbi
b
Binary file test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz.tbi has changed
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz
b
Binary file test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz has changed
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz.tbi
b
Binary file test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz.tbi has changed
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz
b
Binary file test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz has changed
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz.tbi
b
Binary file test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz.tbi has changed
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz
b
Binary file test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz has changed
b
diff -r 9aad9ef0502c -r 3b5b1ebc8423 test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz.tbi
b
Binary file test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz.tbi has changed