Mercurial > repos > iuc > art

changeset 1:a12ce5668966 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
author iuc
date Thu, 11 Jun 2015 13:50:36 -0400
parents b98d6fffd00b
children 7a12314c5b64
files art_454.xml art_illumina.xml art_solid.xml macros.xml tool_dependencies.xml
diffstat 5 files changed, 13 insertions(+), 34 deletions(-) [+]
line wrap: on
line diff
--- a/art_454.xml	Thu Jun 11 11:51:06 2015 -0400
+++ b/art_454.xml	Thu Jun 11 13:50:36 2015 -0400
@@ -3,6 +3,7 @@
   <macros>
       <import>macros.xml</import>
   </macros>
+  <expand macro="requirements"/>
   <expand macro="stdio" />
   <command><![CDATA[
 art_454 $t
--- a/art_illumina.xml	Thu Jun 11 11:51:06 2015 -0400
+++ b/art_illumina.xml	Thu Jun 11 13:50:36 2015 -0400
@@ -3,6 +3,7 @@
   <macros>
       <import>macros.xml</import>
   </macros>
+  <expand macro="requirements"/>
   <expand macro="stdio" />
   <command><![CDATA[
 art_illumina
--- a/art_solid.xml	Thu Jun 11 11:51:06 2015 -0400
+++ b/art_solid.xml	Thu Jun 11 13:50:36 2015 -0400
@@ -3,6 +3,7 @@
   <macros>
       <import>macros.xml</import>
   </macros>
+  <expand macro="requirements"/>
   <expand macro="stdio" />
   <command><![CDATA[
 art_SOLiD
--- a/macros.xml	Thu Jun 11 11:51:06 2015 -0400
+++ b/macros.xml	Thu Jun 11 13:50:36 2015 -0400
@@ -1,5 +1,13 @@
 <macros>
     <token name="@WRAPPER_VERSION@">2014.11.03.0</token>
+
+    <xml name="requirements">
+      <requirements>
+        <requirement type="package" version="2014.11.03">art</requirement>
+        <yield/>
+      </requirements>
+    </xml>
+
     <xml name="stdio">
         <stdio>
             <!-- Anything other than zero is an error -->
--- a/tool_dependencies.xml	Thu Jun 11 11:51:06 2015 -0400
+++ b/tool_dependencies.xml	Thu Jun 11 13:50:36 2015 -0400
@@ -1,38 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="package_gsl_1_16" version="1.16">
-    <repository changeset_revision="4391a79f86fa" name="package_gsl_1_16" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-  </package>
-  <package name="art" version="2014_11_03">
-    <install version="1.0">
-      <actions>
-        <action type="download_by_url">http://www.niehs.nih.gov/research/resources/assets/docs/artsrcvanillaicecream031114linuxtgz.tgz</action>
-        <action type="set_environment_for_install">
-          <repository changeset_revision="4391a79f86fa" name="package_gsl_1_16" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
-            <package name="gsl" version="1.16" />
-          </repository>
-        </action>
-        <action type="autoconf" />
-        <action type="set_environment">
-          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable>
-        </action>
-      </actions>
-    </install>
-    <readme>ART is a set of simulation tools to generate synthetic next-generation
-sequencing reads. ART simulates sequencing reads by mimicking real
-sequencing process with empirical error models or quality profiles summarized
-from large recalibrated sequencing data. ART can also simulate reads using user
-own read error model or quality profiles. ART supports simulation of
-single-end, paired-end/mate-pair reads of three major commercial
-next-generation sequencing platforms: Illumina's Solexa, Roche's 454 and
-Applied Biosystems' SOLiD. ART can be used to test or benchmark a variety
-of method or tools for next-generation sequencing data analysis, including
-read alignment, de novo assembly, SNP and structure variation discovery.
-ART was used as a primary tool for the simulation study of the 1000 Genomes
-Project . ART is implemented in C++ with optimized algorithms and is highly
-efficient in read simulation. ART outputs reads in the FASTQ format, and
-alignments in the ALN format. ART can also generate alignments in the SAM
-alignment or UCSC BED file format.
-</readme>
+  <package name="art" version="2014.11.03">
+    <repository changeset_revision="eaadf9edc5c1" name="package_art_2014_11_03" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
 </tool_dependency>