Mercurial > repos > devteam > bowtie2
changeset 1:aceaf1d94d2d draft
Uploaded new version from GH
| author | devteam |
|---|---|
| date | Mon, 10 Nov 2014 13:58:50 -0500 |
| parents | a03a7ee6cdff |
| children | 2a6cfe8997aa |
| files | bowtie2_wrapper.xml tool_data_table_conf.xml.sample tool_dependencies.xml |
| diffstat | 3 files changed, 5 insertions(+), 5 deletions(-) [+] |
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--- a/bowtie2_wrapper.xml Thu Jan 23 12:30:45 2014 -0500 +++ b/bowtie2_wrapper.xml Mon Nov 10 13:58:50 2014 -0500 @@ -263,7 +263,7 @@ <param name="source" value="history" /> <param name="input_1" value="bowtie2/phix_reads.fastq" ftype="fastqsanger"/> <param name="own_file" value="bowtie2/phix_genome.fasta" /> - <output name="output" file="bowtie2/phix_mapped.bam" /> + <output name="output" file="bowtie2/phix_mapped.bam" ftype="bam" lines_diff="2" /> </test> </tests>
--- a/tool_data_table_conf.xml.sample Thu Jan 23 12:30:45 2014 -0500 +++ b/tool_data_table_conf.xml.sample Mon Nov 10 13:58:50 2014 -0500 @@ -1,7 +1,7 @@ <!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> <tables> - <!-- Locations of indexes in the Bowtie2 mapper format for TopHat2 to use --> - <table name="tophat2_indexes" comment_char="#"> + <!-- Locations of indexes in the Bowtie2 mapper format --> + <table name="bowtie2_indexes" comment_char="#"> <columns>value, dbkey, name, path</columns> <file path="tool-data/bowtie2_indices.loc" /> </table>
--- a/tool_dependencies.xml Thu Jan 23 12:30:45 2014 -0500 +++ b/tool_dependencies.xml Mon Nov 10 13:58:50 2014 -0500 @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> <package name="bowtie2" version="2.1.0"> - <repository changeset_revision="606d435a57a4" name="package_bowtie2_2_1_0" owner="devteam" prior_installation_required="False" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="606d435a57a4" name="package_bowtie2_2_1_0" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="samtools" version="0.1.18"> - <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="False" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>