diff gemini_load.xml @ 0:720cbfb4190d draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_load.xml	Mon Aug 25 17:15:54 2014 -0400
@@ -0,0 +1,80 @@
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+    <description>Loading a VCF file into GEMINI</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <macros>
+        <import>gemini_macros.xml</import>
+        <token name="@BINARY@">load</token>
+    </macros>
+    <command>
+<![CDATA[
+        gemini 
+            --annotation-dir ${annotation_databases.fields.path}
+            @BINARY@
+            -v "${ infile }"
+            -t $annotation_type
+
+            #if $ped:
+                -p $ped
+            #end if
+
+            $skip_gerp_bp
+            $skip_cadd
+            $skip_gene_tables
+            $no_load_genotypes
+            $no_genotypes
+            $passonly
+            --cores \${GALAXY_SLOTS:-4}
+
+            "${ outfile }"
+]]>
+    </command>
+    <expand macro="stdio" />
+    <inputs>
+        <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="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)" />
+        <expand macro="annotation_dir" />
+
+        <param name="skip_gerp_bp" type="boolean" truevalue="--skip-gerp-bp" falsevalue="" checked="False" 
+            label="Do not load GERP scores at base pair resolution" help="(--skip-gerp-bp)"/>
+
+        <param name="skip_cadd" type="boolean" truevalue="--skip-cadd" falsevalue="" checked="False" 
+            label="Do not load CADD scores" help="(--skip-cadd)"/>
+
+        <param name="skip_gene_tables" type="boolean" truevalue="--skip-gene-tables" falsevalue="" checked="False" 
+            label="Do not load gene tables" help="(--skip-gene-tables)"/>
+
+        <param name="no_load_genotypes" type="boolean" truevalue="--no-load-genotypes" falsevalue="" checked="False" 
+            label="Genotypes exist in the file, but should not be stored" help="(--no-load-genotypes)"/>
+
+        <param name="no_genotypes" type="boolean" truevalue="--no-load-genotypes" falsevalue="" checked="False" 
+            label="There are no genotypes in the file" help="e.g. some 1000G VCFs (--no-genotypes)"/>
+
+        <param name="passonly" type="boolean" truevalue="--passonly" falsevalue="" checked="False" 
+            label="Keep only variants that pass all filters" help="e.g. some 1000G VCFs (--passonly)"/>
+
+    </inputs>
+    <outputs>
+        <data name="outfile" format="sqlite" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Before we can use GEMINI to explore genetic variation, we must first load our VCF file into the GEMINI database framework.
+We expect you to have first annotated the functional consequence of each variant in your VCF using either VEP or snpEff.
+
+http://gemini.readthedocs.org/en/latest/content/loading.html
+
+@CITATION@
+    </help>
+    <expand macro="citations"/>
+</tool>