Mercurial > repos > fubar > genomic_association_tester
changeset 15:97e86bb663f2 draft
Uploaded
| author | fubar |
|---|---|
| date | Thu, 29 Aug 2013 03:44:40 -0400 |
| parents | 08cb01b2b9d7 |
| children | f1cc3297dce7 |
| files | rlGAT/rlGAT.xml rlGAT/tool_dependencies.xml |
| diffstat | 2 files changed, 13 insertions(+), 14 deletions(-) [+] |
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--- a/rlGAT/rlGAT.xml Thu Aug 29 02:47:08 2013 -0400 +++ b/rlGAT/rlGAT.xml Thu Aug 29 03:44:40 2013 -0400 @@ -1,4 +1,4 @@ -<tool id="rlGAT" name="Genomic association tests" version="0.1.3"> +<tool id="rlGAT" name="Genomic association tests" version="0.1.4"> <description>using the GAT package</description> <stdio> <regex match=".*" source="both" level="warning" description="stdout/err chatter from gat-run.py"/> @@ -76,17 +76,15 @@ </outputs> <tests> <test> - <param name="feature_type" value="exon" /> - <param name="gfffile" value="rn4_chr20_100k.gtf" /> - <param name="firstsamf" value="rn4chr20test1.bam" ftype="bam"/> - <param name="secondsamf" value="rn4chr20test2.bam" ftype="bam"/> - <param name="id_attr" value="gene_name" /> - <param name="model" value="union" /> - <param name="stranded" value="no" /> - <param name="title" value="htseqtest" /> - <param name="mapqMin" value="0" /> - - <output name="outfile" file="htseqsams2mx_test1_out.xls" lines_diff="1"/> + <param name="sf" value="GATsrf.bed" /> + <param name="anno" value="GATjurkat.bed" /> + <param name="wsf" value="GATcontig.bed"/> + <param name="ignore_segments" value="--ignore-segment-tracks" /> + <param name="counter" value="nucleotide-overlap" /> + <param name="title" value="GATtest" /> + <param name="numsamp" value="1000" /> + <output name="logfile" file="gat_test1_out.log" lines_diff="20"/> + <output name="outfile" file="gat_test1_out.tsv"/> </test> </tests> <help>
--- a/rlGAT/tool_dependencies.xml Thu Aug 29 02:47:08 2013 -0400 +++ b/rlGAT/tool_dependencies.xml Thu Aug 29 03:44:40 2013 -0400 @@ -12,8 +12,9 @@ <package name="gat" version="0.1"> <install version="1.0"> <actions> - <!--<action type="download_by_url">https://genomic-association-tester.googlecode.com/files/genomic-association-tester-0.1.tar.gz</action> --> - <action type="download_by_url" target_filename="genomic-association-tester-0.1.tar.gz">https://dl.dropboxusercontent.com/u/7144491/gat_galaxysetup_tar.gz</action> + <!--<action type="download_by_url">https://genomic-association-tester.googlecode.com/files/genomic-association-tester-0.1.tar.gz</action> + <action type="download_by_url" target_filename="genomic-association-tester-0.1.tar.gz">https://dl.dropboxusercontent.com/u/7144491/gat_galaxysetup_tar.gz</action> --> + <action type="download_by_url" >http://www.cgat.org/~andreas/gat/gat-1.1.tar.gz</action> <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise --> <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise --> <action type="set_environment_for_install">