# HG changeset patch
# User iuc
# Date 1547247169 18000
# Node ID d65ca2fa673b102d3469405041fbf52b517db5c6
# Parent  ce54eb6fd5f9e279f1de6eb3658291ee667b069a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59

diff -r ce54eb6fd5f9 -r d65ca2fa673b gemini_macros.xml
--- a/gemini_macros.xml	Fri Dec 14 13:04:54 2018 -0500
+++ b/gemini_macros.xml	Fri Jan 11 17:52:49 2019 -0500
@@ -1,15 +1,12 @@
 <macros>
     <!-- gemini version to be used -->
-    <token name="@VERSION@">0.18.1</token>
+    <token name="@VERSION@">0.20.1</token>
     <!-- minimal annotation files version required by this version of gemini -->
-    <token name="@DB_VERSION@">181</token>
+    <token name="@DB_VERSION@">200</token>
 
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">gemini</requirement>
-            <requirement type="package" version="0.2.6">tabix</requirement>
-            <!-- for conda useage -->
-            <!--requirement type="package" version="1.3.1">htslib</requirement-->
             <yield />
         </requirements>
     </xml>
@@ -24,9 +21,17 @@
             <exit_code range=":-1" />
             <regex match="Error:" />
             <regex match="Exception:" />
+            <yield />
         </stdio>
     </xml>
 
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1371/journal.pcbi.1003153</citation>
+            <yield />
+        </citations>
+    </xml>
+
     <xml name="annotation_dir">
         <param name="annotation_databases" type="select" label="Choose a gemini annotation source">
             <options from_data_table="gemini_versioned_databases">
@@ -36,31 +41,36 @@
         </param>
     </xml>
 
-    <xml name="add_header_column">
-        <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" 
-            label="Add a header of column names to the output" help="(--header)"/>
-    </xml>
-
-    <xml name="radius">
-        <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"/>
+    <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>
         </param>
     </xml>
-    <xml name="variant_mode">
-        <param name="variant_mode" type="boolean" truevalue="--var" falsevalue="" checked="False" 
-            label="Returns variant info (e.g. impact, biotype) for interacting genes" help="(--var)"/>
+
+    <xml name="add_header_column">
+        <param argument="--header" name="header" type="boolean" truevalue="--header" falsevalue="" checked="True" 
+        label="Add a header of column names to the output" />
     </xml>
 
-    <xml name="column_filter">
+    <xml name="column_filter" token_help="" token_minimalset="variant_id, gene">
         <conditional name="report">
-            <param name="report_selector" type="select" label="Columns to include in the report"
-                help="By default, this tool reports all columns in the variants table. One may choose to report only a subset of the columns.">
-                <option value="all" selected="True">all</option>
-                <option value="column_filter">User given columns</option>
+            <param name="report_selector" type="select"
+            label="Set of columns to include in the variant report table"
+            help="@HELP@">
+                <option value="minimal">Minimal (report only a preconfigured minimal set of columns)</option>
+                <option value="full">Full (report all columns defined in the GEMINI database variants table)</option>
+                <option value="custom">Custom (report user-specified columns)</option>
             </param>
-            <when value="all"/>
-            <when value="column_filter">
-                <param name="columns" type="select" display="checkboxes" multiple="True" label="Choose columns to include in the report" help="(--columns)">
+            <when value="full" />
+            <when value="minimal">
+                <param name="columns" type="hidden" value="@MINIMALSET@" />
+                <param name="extra_cols" type="hidden" value="" />
+            </when>
+            <when value="custom">
+                <param name="columns" type="select" display="checkboxes" multiple="true" optional="true"
+                label="Choose columns to include in the report" help="(--columns)">
                     <option value="gene">gene</option>
                     <option value="chrom">chrom</option>
                     <option value="start">start</option>
@@ -69,27 +79,23 @@
                     <option value="alt">alt</option>
                     <option value="impact">impact</option>
                     <option value="impact_severity">impact_severity</option>
-                    <option value="max_aaf_all">alternative allele frequency</option>
+                    <option value="max_aaf_all">alternative allele frequency (max_aaf_all)</option>
                 </param>
-                <param name="extra_cols" type="text" label="Additional columns." help="Separate by whitespace"/>
+                <param name="extra_cols" type="text"
+                label="Additional columns (comma-separated)"
+                help="Column must be specified by the exact name they have in the GEMINI database, e.g., is_exonic or num_hom_alt, but, for genotype columns, GEMINI wildcard syntax is supported. The order of columns in the list is maintained in the output.">
+                    <expand macro="sanitize_query" />
+                </param>
             </when>
         </conditional>
     </xml>
 
-    <xml name="filter">
-        <conditional name="filter">
-            <param name="filter_selector" type="select" label="Apply additional constraints"
-                help="By default, this tool will report all variants regardless of their putative functional impact. In order to apply additional constraints on the variants returned, you can this optional filter.">
-                <option value="no">No additional constraints</option>
-                <option value="yes">Apply additional constraints</option>
-            </param>
-            <when value="no"/>
-            <when value="yes">
-                <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>
-        </conditional>
+    <xml name="filter" token_argument="--filter">
+        <param argument="@ARGUMENT@" name="filter" type="text"
+        label="Additional constraints expressed in SQL syntax"
+        help="Constraints defined here will become the WHERE clause of the SQL query issued to the GEMINI database. E.g. alt='G' or impact_severity = 'HIGH'.">
+            <expand macro="sanitize_query" />
+        </param>
     </xml>
 
     <xml name="sanitize_query">
@@ -103,10 +109,90 @@
        </sanitizer>
     </xml>
 
+    <xml name="lenient" token_argument="--lenient" token_truevalue="--lenient" token_help="The exact consequence of this setting depends on the type of inheritance pattern you are looking for (see the tool help below).">
+        <param argument="@ARGUMENT@" name="lenient" type="boolean" truevalue="@TRUEVALUE@" falsevalue="" checked="False"
+        label="Include hits with less convincing inheritance patterns"
+        help= "@HELP@" />
+    </xml>
+
+    <xml name="unaffected">
+        <param argument="--allow-unaffected" name="allow_unaffected" type="boolean" truevalue="--allow-unaffected" falsevalue="" checked="False"
+        label="Report candidates shared by unaffected samples"
+        help="Activating this option will enable the reporting of variants as candidate causative even if they are shared by unaffected samples in the family tree. The default will only report variants that are unique to affected samples."/>
+    </xml>
+
+    <xml name="min_kindreds" token_label="Minimum number of families with a candidate variant for a gene to be reported" token_help="This is the number of families required to have a variant fitting the inheritance model in the same gene in order for the gene and its variants to be reported. For example, we may only be interested in candidates where at least 4 families have a variant (with a fitting inheritance pattern) in that gene.">
+        <param argument="--min-kindreds" name="min_kindreds" type="integer" value="1" min="1"
+        label="@LABEL@"
+        help="@HELP@" />
+    </xml>
+
+    <xml name="insert_constraint" token_max_repeat="1">
+        <repeat name="constraint" title="Additional constraints on variants" default="0" max="@MAX_REPEAT@">
+            <expand macro="filter" />
+            <yield />
+        </repeat>
+    </xml>
+
+    <xml name="overwritable_where_default" token_default_where="">
+        <param name="overwrite_default_filter" type="boolean" checked="false"
+        label="Overwrite the default constraint of this tool"
+        help="By default, this tool restricts its analysis to @DEFAULT_WHERE@ and this constraint is applied on top of any constraint expressed above. With this option here selected, your custom constraint, if given, will overwrite the default instead." />
+    </xml>
+
+    <xml name="gt_filter" token_default_repeat="0" token_min_repeat="0" token_max_repeat="1">
+        <repeat name="filter_by_genotype" title="Genotype filter expression" default="@DEFAULT_REPEAT@" min="@MIN_REPEAT@" max="@MAX_REPEAT@">
+            <param argument="--gt-filter" name="gt_filter" type="text" value="" area="True" size="5x50"
+            label="Restrictions to apply to genotype values" help="">
+                <expand macro="sanitize_query" />
+                <validator type="expression" message="Genotype filter expression cannot be empty">value.strip()</validator>
+            </param>
+            <yield />
+        </repeat>
+    </xml>
+
+    <xml name="sample_filter">
+        <repeat name="filter_by_sample" title="Sample filter expression" default="0" max="1">
+            <param argument="--sample-filter" name="sample_filter" type="text" area="True" size="5x50"
+            label="SQL filter to use to filter the sample table" help="">
+                <expand macro="sanitize_query" />
+                <validator type="expression" message="Sample filter expression cannot be empty">value.strip()</validator>
+            </param>
+            <param argument="--in" name="in" type="select"
+            label="A variant must be in either all, none or any samples passing the sample-query filter"
+            help="">
+                <option value="">Return a variant if it is found in any sample passing the sample filter. (default) </option>
+                <option value="--in all">Return a variant if it is found in ALL samples passing the sample filter. (all)</option>
+                <option value="--in none">Return a variant if it is found in NO sample passing the sample filter. (none)</option>
+                <option value="--in only">Return a variant if it is found in any sample passing the sample filter, and in NO sample NOT passing it. (only)</option>
+                <option value="--in only all">Return a variant if is found in ALL samples passing the sample filter, and in NO sample NOT passing it. (only all)</option>
+            </param>
+            <expand macro="min_kindreds"
+            label="Minimum number of families in which a variant must pass the sample filter" help=""/>
+            <param argument="--family-wise" name="family_wise" type="boolean" truevalue="--family-wise" falsevalue="" checked="False"
+            label="Apply the sample-filter on a family-wise basis" help="If a variant passes the sample filter in at least the minimum number of families specified above it is retained." />
+        </repeat>
+    </xml>
+
+    <xml name="region_filter">
+        <repeat name="regions" title="Region Filter" default="0" min="0"
+        help="Filter variant sites by their position in the genome. If multiple Region Filters are specified, all variants that fall in ONE of the regions are reported.">
+            <param name="chrom" type="text" label="Chromosome">
+                <validator type="expression" message="A chromosome identifier is required when specifying a region filter">value.strip()</validator>
+            </param>
+            <param name="start" type="text" label="Region Start">
+                <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
+            </param>
+            <param name="stop" type="text" label="Region End">
+                <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
+            </param>
+        </repeat>
+    </xml>
+
     <token name="@PROVIDE_ANNO_DATA@"><![CDATA[
         mkdir gemini &&
-        ln -s "${annotation_databases.fields.path}/gemini/data" gemini/data &&
-        export GEMINI_CONFIG="${annotation_databases.fields.path}" &&
+        ln -s '${annotation_databases.fields.path}/gemini/data' gemini/data &&
+        export GEMINI_CONFIG='${annotation_databases.fields.path}' &&
     ]]></token>
 
     <token name="@MULTILN_SQL_EXPR_TO_CMDLN@">
@@ -119,67 +205,50 @@
         #end if
     </token>
 
-    <token name="@CMDLN_SQL_FILTER_FILTER_OPTION@">
-        #if str($filter.filter_selector) == 'yes' and $filter.filter:
-            --filter '${ str( $filter.filter ) }'
+    <token name="@SET_COLS@">
+        #if str($report.report_selector) == 'full':
+            #set cols = "*"
+        #else:
+            #if $report.columns and str($report.columns) != '':
+                #set $cols = str($report.columns)
+            #else
+                #set $cols = ''
+            #end if
+            #if str($report.extra_cols).strip():
+                #if $cols:
+                    #set $cols = $cols + ', ' + str($report.extra_cols)
+                #else:
+                    #set $cols = str($report.extra_cols)
+                #end if
+            #end if
+            #if not $cols:
+                #set $cols = "variant_id, gene"
+            #end if
         #end if
     </token>
 
     <token name="@COLUMN_SELECT@">
-        #if $report.report_selector != 'all':
-            --columns "${report.columns}
-            #if str($report.extra_cols).strip()
-                #echo ','+','.join(str($report.extra_cols).split()) 
-            #end if
-            "
+        @SET_COLS@
+        #if $cols != "*"
+            --columns '$cols'
         #end if
     </token>
 
-    <xml name="family">
-        <param name="families" type="text" value="" label="Comma seperated list of families to restrict the analysis to." help="e.g. Family1,Family3 (--families)"/>
-    </xml>
-
-    <xml name="lenient">
-        <param name="lenient" type="boolean" truevalue="--lenient" falsevalue="" checked="False" label="Loosen the restrictions on family structure"/>
-    </xml>
-
-    <xml name="unaffected">
-        <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)"/>
-    </xml>
-
-    <xml name="min_kindreds">
-        <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)" />
-    </xml>
-
-    <xml name="min_sequence_depth">
-        <param name="d" type="integer" value="0" min="0" label="The minimum aligned sequence depth (genotype DP) required for each sample"
-                help="default: 0 (-d)" />
-    </xml>
-
-    <xml name="min_gq">
-        <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)">
-            <validator type="in_range" min="0"/>
-        </param>
-    </xml>
-
-    <xml name="gt_pl_max">
-        <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)" />
-    </xml>
-
-    <xml name="citations">
-        <citations>
-            <citation type="doi">10.1371/journal.pcbi.1003153</citation>
-            <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>
-
+    <token name="@PARSE_REGION_ELEMENTS@"><![CDATA[
+        #set $region_elements = []
+        #for $r in $regions:
+            ## The actual chromosome name needs to be single-quoted
+            ## in SQL, so we need to quote the single quotes like the
+            ## sanitize_query macro would if the whole was a parameter.
+            #set $r_elements = ["chrom = '\"'\"'%s'\"'\"'" % str($r.chrom).strip()]
+            #if str($r.start).strip():
+                #silent $r_elements.append("start >= %d" % int($r.start))
+            #end if
+            #if str($r.stop).strip():
+                #silent $r_elements.append("end <= %d" % int($r.stop))
+            #end if
+            #silent $region_elements.append("(%s)" % " AND ".join($r_elements))
+        #end for
+    ]]>
+    </token>
 </macros>
diff -r ce54eb6fd5f9 -r d65ca2fa673b gemini_roh.xml
--- a/gemini_roh.xml	Fri Dec 14 13:04:54 2018 -0500
+++ b/gemini_roh.xml	Fri Jan 11 17:52:49 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
     <description>Identifying runs of homozygosity</description>
     <macros>
         <import>gemini_macros.xml</import>
@@ -17,39 +17,34 @@
             --max-hets $max_hets
             --max-unknowns $max_unknowns
             #if $samples.strip():
-                -s "${samples}"
+                #set $samples = ','.join([f.strip() for f in $samples.split(',')])
+                -s '$samples'
             #end if
-            "${ infile }"
-            > "${ outfile }"
+            '$infile'
+            > '$outfile'
 ]]>
     </command>
     <inputs>
         <expand macro="infile" />
-
-        <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" 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" 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" 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" 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" label="Maximum number of allowed unknowns in the run" help="default: 3 (-max-unknowns)">
-            <validator type="in_range" min="0"/>
-        </param>
-
-        <param name="samples" type="text" value="" label="Comma separated list of samples to screen for ROHs" help="e.g S120,S450 (-s)"/>
-
+        <param argument="--min-snps" name="min_snps" type="integer" value="25" min="0"
+        label="Minimum number of expected homozygous SNPs"
+        help="default: 25" />
+        <param argument="--min-total-depth" name="min_total_depth" type="integer" value="20" min="0"
+        label="The minimum overall sequencing depth required for a SNP to be considered"
+        help="default: 20" />
+        <param argument="--min-gt-depth" name="min_gt_depth" type="integer" value="0" min="0"
+        label="The minimum required sequencing depth underlying a given sample's genotype for a SNP to be considered"
+        help="default: 0" />
+        <param argument="--min-size" name="min_size" type="integer" value="100000" min="1"
+        label="Minimum run size in base pairs" help="default: 100000" />
+        <param argument="--max-hets" name="max_hets" type="integer" value="1" min="0"
+        label="Maximum number of allowed hets in the run" help="default: 1" />
+        <param argument="--max-unknowns" name="max_unknowns" type="integer" value="3" min="0"
+        label="Maximum number of allowed unknowns in the run"
+        help="default: 3" />
+        <param argument="-s" name="samples" type="text" value=""
+        label="Comma separated list of samples to screen for ROHs" help="e.g. S120,S450"/>
     </inputs>
-
     <outputs>
         <data name="outfile" format="tabular" />
     </outputs>
@@ -70,9 +65,6 @@
 
 **What it does**
 
-===========================================================================
-``ROH``: Identifying runs of homozygosity
-===========================================================================
 Runs of homozygosity are long stretches of homozygous genotypes that reflect
 segments shared identically by descent and are a result of consanguinity or
 natural selection. Consanguinity elevates the occurrence of rare recessive
diff -r ce54eb6fd5f9 -r d65ca2fa673b repository_dependencies.xml
--- a/repository_dependencies.xml	Fri Dec 14 13:04:54 2018 -0500
+++ b/repository_dependencies.xml	Fri Jan 11 17:52:49 2019 -0500
@@ -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
diff -r ce54eb6fd5f9 -r d65ca2fa673b test-data/gemini_amend_input.db
Binary file test-data/gemini_amend_input.db has changed
diff -r ce54eb6fd5f9 -r d65ca2fa673b test-data/gemini_annotate_result.db
Binary file test-data/gemini_annotate_result.db has changed
diff -r ce54eb6fd5f9 -r d65ca2fa673b test-data/gemini_auto_dom_input.db
Binary file test-data/gemini_auto_dom_input.db has changed
diff -r ce54eb6fd5f9 -r d65ca2fa673b test-data/gemini_auto_rec_input.db
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diff -r ce54eb6fd5f9 -r d65ca2fa673b test-data/gemini_comphets_input.db
Binary file test-data/gemini_comphets_input.db has changed
diff -r ce54eb6fd5f9 -r d65ca2fa673b test-data/gemini_de_novo_input.db
Binary file test-data/gemini_de_novo_input.db has changed
diff -r ce54eb6fd5f9 -r d65ca2fa673b test-data/gemini_is_somatic_result.db
Binary file test-data/gemini_is_somatic_result.db has changed
diff -r ce54eb6fd5f9 -r d65ca2fa673b test-data/gemini_load_result1.db
Binary file test-data/gemini_load_result1.db has changed
diff -r ce54eb6fd5f9 -r d65ca2fa673b test-data/gemini_load_result2.db
Binary file test-data/gemini_load_result2.db has changed
diff -r ce54eb6fd5f9 -r d65ca2fa673b test-data/gemini_versioned_databases.loc
--- a/test-data/gemini_versioned_databases.loc	Fri Dec 14 13:04:54 2018 -0500
+++ b/test-data/gemini_versioned_databases.loc	Fri Jan 11 17:52:49 2019 -0500
@@ -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
diff -r ce54eb6fd5f9 -r d65ca2fa673b test-data/test-cache/gemini-config.yaml
--- a/test-data/test-cache/gemini-config.yaml	Fri Dec 14 13:04:54 2018 -0500
+++ b/test-data/test-cache/gemini-config.yaml	Fri Jan 11 17:52:49 2019 -0500
@@ -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
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