Mercurial > repos > malbuquerque > factera
changeset 1:c2e36f5b53c7 draft
Uploaded
| author | malbuquerque |
|---|---|
| date | Thu, 15 Jan 2015 18:28:18 -0500 |
| parents | 46672ba5e1e8 |
| children | 97973e7ca771 |
| files | factera/factera.xml factera/tool_dependencies.xml |
| diffstat | 2 files changed, 0 insertions(+), 108 deletions(-) [+] |
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--- a/factera/factera.xml Thu Jan 15 17:47:37 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,54 +0,0 @@ -<tool id="factera" name="FACTERA"> - - <description>Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm</description> - - <command> - - <!-- Run commands using Galaxy perl --> - #if $cond.additionalOpt.value == "no" - perl $FACTERA_DIR/factera.pl -o ./ $sortedBam $exonBed $genome2Bit - #else - perl $FACTERA_DIR/factera.pl -r $cond.r -m $cond.m -x $cond.x -s $cond.s -f $cond.f -S $cond.S - -k $cond.k -c $cond.c -b $cond.b -p $cond.p -a $cond.a -o ./ $sortedBam $exonBed $genome2Bit - #end if - - <!-- Keep only the fusion file --> - cat *fusions.txt > $outfile; - - </command> - - <inputs> - <param format="bam" name="sortedBam" type="data" label="Alignment in BAM format" /> - <param format="bed" name="exonBed" type="data" label="Genomic coordinates with gene/exon names in fourth column" /> - <param format="2bit" name="genome2Bit" type="data" label="Two bit reference sequence" /> - <conditional name="cond"> - - <param type="select" name="additionalOpt" label="Additional Options"> - <option value="yes">Yes</option> - <option value="no" selected="True">No</option> - </param> - - <when value="yes"> - <!-- Names follow command line flags in factera.pl --> - <param type="integer" name="r" label="Minimum number of breakpoint-scanning reads required for output" value="5"/> - <param type="integer" name="m" label="Minimum number of discordant reads required for each candidate fusion" value="2"/> - <param type="integer" name="x" label="Maximum number of breakpoints to examine for each pair of genomic regions" value="5"/> - <param type="integer" name="s" label="Minimum number of reads with the same breakpoint" value="1"/> - <param type="float" name="f" min="0" max="1" label="Minimum fraction of read bases required for alignment to fusion template" value=".9"/> - <param type="float" name="S" min="0" max="1" label="Minimum similarity required for read to match fusion template" value=".95"/> - <param type="integer" name="k" label="K-mer size (number of bases) for fragment comparison" value="10"/> - <param type="integer" name="c" label="Minimum size of soft-clipped region to consider" value="16"/> - <param type="integer" name="b" label="Number of bases flanking breakpoint for fusion template" value="500"/> - <param type="integer" name="p" label="Number of threads for blastn search" value="4"/> - <param type="integer" name="a" label="Number of bases flanking breakpoint to provide in output" value="50"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="outfile" /> - </outputs> - - <help>This tool does Factera</help> - -</tool>
--- a/factera/tool_dependencies.xml Thu Jan 15 17:47:37 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,54 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - - <package name="blast_plus" version="2.2.26"> - <repository changeset_revision="85e43fb3f363" name="package_blast_plus_2_2_26" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - - <package name="samtools" version="0.1.19"> - <repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - - <package name="twoBitToFa" version="1.0.0"> - <repository changeset_revision="0f4127c3c51f" name="ucsc_user_apps" owner="malbuquerque" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - - <package name="factera_perl_dependency" version="1.4.3"> - <install version="1.0"> - <actions> - - <action type="download_by_url">http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/Statistics-Descriptive-3.0608.tar.gz</action> - <action type="shell_command">perl Makefile.PL PREFIX=$INSTALL_DIR</action> - <action type="shell_command">make</action> - <action type="shell_command">make install</action> - - <action type="set_environment"> - <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/site_perl</environment_variable> - </action> - - </actions> - </install> - </package> - - <package name="package_factera_1_4_3" version="1.4.3"> - <install version="1.0"> - <actions> - - <action type="download_by_url">http://factera.stanford.edu/files/factera-v1.4.3.pl</action> - - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - - <action type="set_environment"> - <environment_variable action="set_to" name="FACTERA_DIR">$INSTALL_DIR</environment_variable> - </action> - - </actions> - </install> - <readme> - </readme> - </package> - -</tool_dependency>