Commit 14cfc3c5 authored by Philip Mabon's avatar Philip Mabon

Merge branch 'galtooldev' into 'development'

Galtooldev

Adding the package for Wombac and the wombac shred tool.

See merge request !2
parents 43fe2f60 f7ad074e
<?xml version="1.0"?>
<tool_dependency>
<package name="perl" version="5.18.1">
<repository name="package_perl_5_18" owner="iuc" prior_installation_required="True" />
</package>
<package name="wombac" version="2.1">
<install version="1.0">
<actions>
<action type="setup_perl_environment">
<repository name="package_perl_5_18" owner="iuc">
<package name="perl" version="5.18.1" />
</repository>
<package>Time::Piece</package>
<package>https://cpan.metacpan.org/authors/id/D/DL/DLAND/File-Path-2.09.tar.gz</package>
<package>https://cpan.metacpan.org/authors/id/S/SM/SMUELLER/PathTools-3.47.tar.gz</package>
<package>https://cpan.metacpan.org/authors/id/P/PE/PEVANS/Scalar-List-Utils-1.42.tar.gz</package>
<package>https://cpan.metacpan.org/authors/id/S/SM/SMUELLER/Data-Dumper-2.154.tar.gz</package>
<package>https://cpan.metacpan.org/authors/id/R/RE/REHSACK/List-MoreUtils-0.410.tar.gz</package>
</action>
<action type="change_directory">../</action>
<action type="shell_command">git clone https://github.com/tseemann/wombac.git</action>
<action type="change_directory">wombac/bin/</action>
<action type="move_directory_files">
<source_directory>.</source_directory>
<destination_directory>$INSTALL_DIR/wombac</destination_directory>
</action>
<action type="set_environment">
<environment_variable action="set_to" name="WOMBACLIB">$INSTALL_DIR/wombac</environment_variable>
<environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
</action>
</actions>
</install>
<readme>
</readme>
</package>
</tool_dependency>
<?xml version="1.0"?>
<tool_dependency>
<package name="perl" version="5.18.1">
<repository name="package_perl_5_18" owner="iuc" />
</package>
<package name="wombac" version="2.1">
<repository name="package_wombac_2_1" owner="jen-cabral" />
</package>
</tool_dependency>
<tool id="wombac_shred" name="Wombac Shred" version ="0.0.1">
<description>Shred a Fasta file </description>
<requirements>
<requirement type="package" version="5.18.1">perl</requirement>
<requirement type="package" version="2.1">wombac</requirement>
</requirements>
<command interpreter="perl">
/\$WOMBACLIB/wombac-shred_fasta $fastq --fastq --coverage=$coverage --readlen=$readlen > $output
</command>
<inputs>
<param name="fastq" type="data" label="File to shred" format="fastqsanger" />
<param name="readlen" type="integer" label="Read Length" value="100" />
<param name="coverage" type="integer" label="Depth of Coverage" value="50" />
</inputs>
<outputs>
<data format="fastqsanger" name="output" label=""/>
</outputs>
<stdio>
</stdio>
<tests>
<test>
</test>
</tests>
<help>
What it does
============
Usage
=====
</help>
</tool>
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