Commit f7ad074e authored by JCabral's avatar JCabral

adding wombac package and wombac_shred

parent 828180a1
<?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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