diff gemini_region.xml @ 0:bb4a5f979906 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_region.xml	Thu Feb 18 08:51:44 2016 -0500
@@ -0,0 +1,80 @@
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+    <description>Extracting variants from specific regions or genes</description>
+    <macros>
+        <import>gemini_macros.xml</import>
+        <token name="@BINARY@">region</token>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+<![CDATA[
+        gemini @BINARY@
+
+            #if $region.region_selector == '--reg':
+                #if str($region.region).strip():
+                    --reg "${region.region}"
+                #end if
+            #else:
+                #if str($region.gene).strip():
+                    --gene "${region.gene}"
+                #end if
+            #end if
+
+            #if $report.report_selector != 'all':
+                --columns "${report.columns}"
+            #end if
+
+            @CMDLN_SQL_FILTER_FILTER_OPTION@
+
+            $show_samples
+
+
+            $header
+            "${ infile }"
+            > "${ outfile }"
+]]>
+    </command>
+    <inputs>
+        <expand macro="infile" />
+
+        <conditional name="region">
+            <param name="region_selector" type="select" label="Select by ...?" help="">
+                <option value="--reg">genomic coordinates</option>
+                <option value="--gene">gene name</option>
+            </param>
+            <when value="--reg">
+                <param name="region" type="text" label="Specify genomic region" help="e.g. chr1:100-200 (--reg)"/>
+            </when>
+            <when value="--gene">
+                <param name="gene" type="text" label="Specify gene name" help="e.g. PTPN22 (--gene)" />
+            </when>
+        </conditional>
+
+        <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)"/>
+
+        <expand macro="column_filter" />
+        <expand macro="filter" />
+        <expand macro="add_header_column" />
+
+    </inputs>
+    <outputs>
+        <data name="outfile" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="gemini_burden_input.db" ftype="gemini.sqlite" />
+            <param name="region_selector" value="--reg" />
+            <param name="region" value="chr10:48000000-49000000" />
+            <param name="columns" value="chrom,start,gene" />
+            <output name="outfile" file="gemini_region_result.tabular" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+One often is concerned with variants found solely in a particular gene or genomic region.
+
+    </help>
+    <expand macro="citations"/>
+</tool>