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changeset 2:8fb92fcd20ae draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
author devteam
date Thu, 15 Sep 2016 16:06:22 -0400
parents d6c944f1581a
children e92b3c0f9224
files macros.xml test-data/vcf2tsv-test1.tab tool_dependencies.xml vcf2tsv.xml
diffstat 4 files changed, 48 insertions(+), 53 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Mar 19 12:19:17 2015 -0400
+++ b/macros.xml	Thu Sep 15 16:06:22 2016 -0400
@@ -1,7 +1,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="8a5602bf07">vcflib</requirement>
+            <requirement type="package" version="1.0.0_rc1">vcflib</requirement>
             <yield/>
         </requirements>
     </xml>
@@ -10,6 +10,7 @@
             <exit_code range="1:" level="fatal" />
         </stdio>
     </xml>
+   <token name="@WRAPPER_VERSION@">1.0.0_rc1</token>
    	<xml name="citations">
    	     <citations>
              <citation type="bibtex">
--- a/test-data/vcf2tsv-test1.tab	Thu Mar 19 12:19:17 2015 -0400
+++ b/test-data/vcf2tsv-test1.tab	Thu Sep 15 16:06:22 2016 -0400
@@ -22,6 +22,7 @@
 20	1234567	microsat1	G	GA,GAC	50	PASS	G	3,1	.	6	9	3	0	0	NA00003	3	40	1/1	.
 20	1235237	.	T	.	0	.	.	.	.	.	.	.	0	0	NA00001	.	.	0/0	.
 20	1235237	.	T	.	0	.	.	.	.	.	.	.	0	0	NA00002	.	.	0|0	.
+20	1235237	.	T	.	0	.	.	.	.	.	.	.	0	0	NA00003	.	.	./.	.
 X	10	rsTest	AC	A,ATG	10	PASS	.	.	.	.	.	.	0	0	NA00001	.	.	0	.
 X	10	rsTest	AC	A,ATG	10	PASS	.	.	.	.	.	.	0	0	NA00002	.	.	0/1	.
 X	10	rsTest	AC	A,ATG	10	PASS	.	.	.	.	.	.	0	0	NA00003	.	.	0|2	.
--- a/tool_dependencies.xml	Thu Mar 19 12:19:17 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="vcflib" version="8a5602bf07">
-        <repository changeset_revision="7e67466b033e" name="package_vcflib_8a5602bf07" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>
--- a/vcf2tsv.xml	Thu Mar 19 12:19:17 2015 -0400
+++ b/vcf2tsv.xml	Thu Sep 15 16:06:22 2016 -0400
@@ -1,46 +1,45 @@
-<tool id="vcf2tsv" name="VCFtoTab-delimited:" version="0.0.3">
-  <description>Convert VCF data into TAB-delimited format</description>
-  <macros>
-      <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"></expand>
-  <expand macro="stdio" />
-  <command>vcf2tsv ${g_option} -n "${null_filler}" "${input}" > "${out_file1}"</command>
-  <inputs>
-    <param format="vcf" name="input" type="data" label="Select VCF dataset to convert"/>
-    <param name="g_option" type="boolean" checked="true" truevalue="-g" falsevalue="" label="Report data per sample" help="-g option"/>
-    <param name="null_filler" type="select" label="Fill empty fields with" help="-n option" >
-      <option value="">Nothing</option>
-      <option value=".">.</option>
-      <option value="*">*</option>
-      <option value="NULL">NULL</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="tabular" name="out_file1" />
-  </outputs>
-  <tests>
-    <test>
-      <param name="g_option" value="true"/>
-      <param name="null_filler" value="."/>
-      <param name="input" value="vcflib.vcf"/>
-      <output name="out_file1" file="vcf2tsv-test1.tab"/>
-    </test>
-   <test>
-      <param name="g_option" value="false"/>
-      <param name="null_filler" value="."/>
-      <param name="input" value="vcflib.vcf"/>
-      <output name="out_file1" file="vcf2tsv-test2.tab"/>
-    </test>
-    </tests>
-  <help>
-
-Converts VCF dataset to tab-delimited format, using null string to replace empty values in the table.
-Specifying "**Report data per sample**" (-g) will output one line per sample with genotype information.
-
-----
-
-Vcf2Tsv @IS_PART_OF_VCFLIB@
-</help>
-  <expand macro="citations" />
-</tool>
+<tool id="vcf2tsv" name="VCFtoTab-delimited:" version="@WRAPPER_VERSION@.0">
+  <description>Convert VCF data into TAB-delimited format</description>
+  <macros>
+      <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio" />
+  <command>vcf2tsv ${g_option} -n '${null_filler}' '${input}' > '${out_file1}'</command>
+  <inputs>
+    <param format="vcf" name="input" type="data" label="Select VCF dataset to convert"/>
+    <param name="g_option" type="boolean" checked="true" truevalue="-g" falsevalue="" label="Report data per sample" help="-g option"/>
+    <param name="null_filler" type="select" label="Fill empty fields with" help="-n option" >
+      <option value="">Nothing</option>
+      <option value=".">.</option>
+      <option value="*">*</option>
+      <option value="NULL">NULL</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="g_option" value="true"/>
+      <param name="null_filler" value="."/>
+      <param name="input" value="vcflib.vcf"/>
+      <output name="out_file1" file="vcf2tsv-test1.tab"/>
+    </test>
+   <test>
+      <param name="g_option" value="false"/>
+      <param name="null_filler" value="."/>
+      <param name="input" value="vcflib.vcf"/>
+      <output name="out_file1" file="vcf2tsv-test2.tab"/>
+    </test>
+    </tests>
+  <help>
+Converts VCF dataset to tab-delimited format, using null string to replace empty values in the table.
+Specifying "**Report data per sample**" (-g) will output one line per sample with genotype information.
+
+----
+
+Vcf2Tsv @IS_PART_OF_VCFLIB@
+  </help>
+  <expand macro="citations" />
+</tool>