diff gemini_mendel_errors.xml @ 0:dd963f00f297 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_mendel_errors.xml	Thu Feb 18 08:54:21 2016 -0500
@@ -0,0 +1,80 @@
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+    <description>Identify candidate violations of Mendelian inheritance</description>
+    <macros>
+        <import>gemini_macros.xml</import>
+        <token name="@BINARY@">mendel_errors</token>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+<![CDATA[
+        gemini @BINARY@
+
+            #if $report.report_selector != 'all':
+                --columns "${report.columns}"
+            #end if
+
+            @CMDLN_SQL_FILTER_FILTER_OPTION@
+
+            #if int($min_kindreds) > 0:
+                --min-kindreds $min_kindreds
+            #end if
+
+            #if str($families).strip():
+                --families "$families"
+            #end if
+
+            $lenient
+            $only_affected
+
+            -d $d
+
+            #if int($min_gq) > 0:
+                --min-gq $min_gq
+            #end if
+
+            #if int($gt_pl_max) > -1:
+                --gt-pl-max $gt_pl_max
+            #end if
+
+
+            "${ infile }"
+            > "${ outfile }"
+]]>
+    </command>
+    <inputs>
+        <expand macro="infile" />
+        <expand macro="column_filter" />
+        <expand macro="filter" />
+        <expand macro="min_kindreds" />
+        <expand macro="family" />
+        <expand macro="lenient" />
+        <!-- this parameter should be allow-unaffected, but unfortunately it is not. -->
+        <param name="only_affected" type="boolean" truevalue="--only-affected" falsevalue="" checked="False" label="Only consider candidates from affected samples." help="(--only-affected)"/>
+        <expand macro="min_sequence_depth" />
+        <expand macro="min_gq" />
+        <expand macro="gt_pl_max" />
+    </inputs>
+    <outputs>
+        <data name="outfile" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
+            <param name="columns" value="gene,ref,alt,impact" />
+            <output name="outfile" file="gemini_mendel_errors_result.tabular" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+**What it does**
+
+Assuming you have defined the familial relationships between samples when loading your VCF into GEMINI,
+you can use this tool for identifying mutations that violate the Mendelian inheritance scheme.
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>