Mercurial > repos > iuc > crossmap_vcf

changeset 3:9db73ff23c9f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622
author iuc
date Thu, 24 May 2018 19:09:50 -0400
parents 7a3c34157901
children 9d61d74f03a4
files crossmap_vcf.xml macros.xml
diffstat 2 files changed, 6 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/crossmap_vcf.xml	Fri Oct 20 11:34:06 2017 -0400
+++ b/crossmap_vcf.xml	Thu May 24 19:09:50 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="crossmap_vcf" name="CrossMap VCF" version="@WRAPPER_VERSION@-0">
+<tool id="crossmap_vcf" name="CrossMap VCF" version="@WRAPPER_VERSION@">
     <description>Convert genome coordinates or annotation files between genome assemblies</description>
     <macros>
         <import>macros.xml</import>
@@ -22,9 +22,7 @@
 '${input_file}'
 '${seq_source.input_fasta}'
 
-'${output}'
-
-&& mv '${output}.unmap' '$output_unmapped'
+output
     ]]></command>
 
     <inputs>
@@ -59,8 +57,8 @@
     </inputs>
 
     <outputs>
-        <data name="output" format="vcf" label="${tool.name} on ${on_string}" />
-        <data name="output_unmapped" format="vcf" label="${tool.name} (unmapped) on ${on_string}" />
+        <data name="output" format="vcf" label="${tool.name} on ${on_string}" from_work_dir="output" />
+        <data name="output_unmapped" format="vcf" label="${tool.name} (unmapped) on ${on_string}" from_work_dir="output.unmap" />
     </outputs>
 
     <tests>
@@ -107,7 +105,6 @@
   you run CrossMap).
 - In the output VCF file, whether the chromosome IDs contain “chr” or not
   depends on the format of the input VCF file.
-
     ]]></help>
 
     <citations>
--- a/macros.xml	Fri Oct 20 11:34:06 2017 -0400
+++ b/macros.xml	Thu May 24 19:09:50 2018 -0400
@@ -2,11 +2,11 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="0.2.5">crossmap</requirement>
+            <requirement type="package" version="0.2.7">crossmap</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@WRAPPER_VERSION@">0.2.5</token>
+    <token name="@WRAPPER_VERSION@">0.2.7</token>
     <xml name="stdio">
         <stdio>
             <regex match="Aborted (core dumped)" source="stdout" level="fatal"/>