Mercurial > repos > iuc > gemini_dump

diff gemini_dump.xml @ 4:7b24461e6bc3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 85a2af25c79df4758afe9f846e11ef0af16b1c1f
author iuc
date Mon, 17 Dec 2018 12:21:48 -0500
parents a48f00c341dc
children
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--- a/gemini_dump.xml	Fri Dec 14 12:35:04 2018 -0500
+++ b/gemini_dump.xml	Mon Dec 17 12:21:48 2018 -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>Extract data from the Gemini DB</description>
     <macros>
         <import>gemini_macros.xml</import>
@@ -23,7 +23,11 @@
 
         <param name="report" type="select" label="The information to be reported" help="(-t)">
             <option value="--variants">All rows/columns from the variants table (--variants)</option>
-            <option value="--genotypes">All rows/columns from the variants table with one line per sample/genotype (--genotypes)</option>
+            <!-- The genotypes option is broken in gemini v0.20.1.
+            Add this option back in once there is an upstream fix!
+            Remember then to replace all underscores with dashes on the following line. They are only there to not break this comment!
+            <option value="__genotypes">All rows/columns from the variants table with one line per sample/genotype (__genotypes)</option>
+            -->
             <option value="--samples">All rows/columns from the samples table (--samples)</option>
         </param>
         <param argument="--header" type="boolean" label="Include a header of column names" truevalue="--header" falsevalue="" checked="False" />
@@ -34,12 +38,12 @@
     </outputs>
     <tests>
         <test>
-            <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
+            <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
             <param name="header" value="True" />
-            <param name="report" value="--genotypes" />
+            <param name="report" value="--samples" />
             <output name="outfile">
                 <assert_contents>
-                    <has_line_matching expression="chrom&#009;start&#009;end&#009;.*sample&#009;.*genotype.*" />
+                    <has_line_matching expression="sample_id&#009;family_id&#009;name&#009;paternal_id&#009;maternal_id&#009;sex&#009;phenotype" />
                 </assert_contents>
             </output>
         </test>