Mercurial > repos > iuc > gemini_load

diff gemini_load.xml @ 9:2270a8b83c12 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
author iuc
date Wed, 13 Jul 2022 15:38:57 +0000
parents 64132aa2d62a
children
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line diff
--- a/gemini_load.xml	Tue Mar 10 06:16:34 2020 -0400
+++ b/gemini_load.xml	Wed Jul 13 15:38:57 2022 +0000
@@ -1,5 +1,6 @@
 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@+galaxy2">
     <description>Loading a VCF file into GEMINI</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>gemini_macros.xml</import>
         <token name="@BINARY@">load</token>
@@ -105,7 +106,7 @@
             <param name="annotation_databases" value="1999-01-01" />
             <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
             <param name="opt_content" value="gene_tables,genotypes,gt_pl" />
-            <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
+            <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="10000" />
             <assert_command>
                 <has_text text="--skip-gerp-bp" />
                 <has_text text="--skip-cadd" />
@@ -122,7 +123,7 @@
             <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
             <param name="opt_content" value="gerp_bp,cadd,gene_tables,genotypes,gt_pl" />
             <param name="has_genotypes" value="True" />
-            <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
+            <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="10000" />
             <assert_stderr>
                 <has_text text="CADD scores are not being loaded because the annotation file could not be found." />
                 <has_text text="GERP per bp is not being loaded because the annotation file could not be found." />
@@ -143,7 +144,7 @@
             <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
             <param name="opt_content" value="genotypes,gt_pl" />
             <param name="has_genotypes" value="False" />
-            <output name="outfile" file="gemini_load_result2.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
+            <output name="outfile" file="gemini_load_result2.db" ftype="gemini.sqlite" compare="sim_size" delta="10000" />
             <assert_command>
                 <has_text text="--skip-gerp-bp" />
                 <has_text text="--skip-cadd" />
@@ -161,7 +162,7 @@
             <param name="opt_content" value="gene_tables,genotypes,gt_pl" />
             <param name="has_genotypes" value="True" />
             <param name="ped" value="gemini_amend.ped" ftype="tabular" />
-            <output name="outfile" file="gemini_auto_rec_input.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
+            <output name="outfile" file="gemini_auto_rec_input.db" ftype="gemini.sqlite" compare="sim_size" delta="20000" />
         </test>
         <test>
             <param name="annotation_databases" value="1999-01-01" />
@@ -169,7 +170,7 @@
             <param name="opt_content" value="gene_tables,genotypes,gt_pl" />
             <param name="has_genotypes" value="True" />
             <param name="ped" value="gemini_amend.ped" ftype="tabular" />
-            <output name="outfile" file="gemini_auto_rec_input.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
+            <output name="outfile" file="gemini_auto_rec_input.db" ftype="gemini.sqlite" compare="sim_size" delta="20000" />
         </test>
     </tests>
     <help><![CDATA[