diff gemini_lof_sieve.xml @ 0:be7ac09bc2fa 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_lof_sieve.xml	Thu Feb 18 08:53:32 2016 -0500
@@ -0,0 +1,52 @@
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+    <description>Filter LoF variants by transcript position and type</description>
+    <macros>
+        <import>gemini_macros.xml</import>
+        <token name="@BINARY@">lof_sieve</token>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+<![CDATA[
+        gemini @BINARY@
+            "${ infile }"
+            > "${ outfile }"
+]]>
+    </command>
+    <inputs>
+        <expand macro="infile" />
+    </inputs>
+    <outputs>
+        <data name="outfile" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="gemini_burden_input.db" ftype="gemini.sqlite" />
+            <output name="outfile" file="gemini_lofsieve_result.tabular" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+*Filter LoF variants by transcript position and type*
+
+Not all candidate LoF variants are created equal. For e.g, a nonsense (stop gain) variant impacting the first 5% of a polypeptide is far
+more likely to be deleterious than one affecting the last 5%. Assuming you’ve annotated your VCF with snpEff v3.0+, the lof_sieve tool
+reports the fractional position (e.g. 0.05 for the first 5%) of the mutation in the amino acid sequence.
+In addition, it also reports the predicted function of the transcript so that one can segregate candidate
+LoF variants that affect protein_coding transcripts from processed RNA, etc.
+
+**Example**
+
+Output with default settings::
+
+ chrom   start       end        ref  alt  highest_impact  aa_change   var_trans_pos   trans_aa_length var_trans_pct   sample   genotype    gene    transcript       trans_type
+ chr22   17072346    17072347   C    T    stop_gain       W365*       365             557             0.655296229803  NA19327  C|T         CCT8L2  ENST00000359963  protein_coding
+ chr22   17072346    17072347   C    T    stop_gain       W365*       365             557             0.655296229803  NA19375  T|C         CCT8L2  ENST00000359963  protein_coding
+ chr22   17129539    17129540   C    T    splice_donor    None        None            None            None            NA18964  T|C         TPTEP1  ENST00000383140  lincRNA
+ chr22   17129539    17129540   C    T    splice_donor    None        None            None            None            NA19675  T|C         TPTEP1  ENST00000383140  lincRNA
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>