diff gemini_load.xml @ 17:65f742e605ec draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a

--- a/gemini_load.xml	Tue Apr 28 22:55:56 2015 -0400
+++ b/gemini_load.xml	Mon May 04 22:46:38 2015 -0400
@@ -1,16 +1,17 @@
 <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>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
     <command>
 <![CDATA[
         ln -s "${ infile }" input.vcf &&
 
-        gemini 
+        gemini
             --annotation-dir ${annotation_databases.fields.path}
             @BINARY@
             -v input.vcf
@@ -33,7 +34,6 @@
             "${ outfile }"
 ]]>
     </command>
-    <expand macro="stdio" />
     <inputs>
         <param name="infile" type="data" format="vcf" label="VCF file to be loaded in the GEMINI database" help="Only build 37 (aka hg19) of the human genome is supported.">
             <options>
@@ -51,22 +51,22 @@
         <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" 
+        <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" 
+        <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" 
+        <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" 
+        <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" 
+        <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" 
+        <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>