Mercurial > repos > devteam > bowtie_wrappers
changeset 2:ba29251df197 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit b2e1043bf4db38be490fec298a1829f8e4a1c48e
| author | devteam |
|---|---|
| date | Thu, 18 Aug 2016 10:19:58 -0400 |
| parents | 867a8c8e870e |
| children | 9326d6e6882a |
| files | bowtie_wrapper.py bowtie_wrapper.xml test-data/bowtie_indices.loc tool_data_table_conf.xml.test tool_dependencies.xml |
| diffstat | 5 files changed, 19 insertions(+), 7 deletions(-) [+] |
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--- a/bowtie_wrapper.py Fri Dec 18 18:50:53 2015 -0500 +++ b/bowtie_wrapper.py Thu Aug 18 10:19:58 2016 -0400 @@ -2,7 +2,6 @@ """ Runs Bowtie on single-end or paired-end data. -For use with Bowtie v. 0.12.7 usage: bowtie_wrapper.py [options] -t, --threads=t: The number of threads to run
--- a/bowtie_wrapper.xml Fri Dec 18 18:50:53 2015 -0500 +++ b/bowtie_wrapper.xml Thu Aug 18 10:19:58 2016 -0400 @@ -1,6 +1,6 @@ -<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.4"> +<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.5"> <requirements> - <requirement type="package" version="0.12.7">bowtie</requirement> + <requirement type="package" version="1.1.2">bowtie</requirement> </requirements> <description></description> <version_command>bowtie --version</version_command> @@ -552,7 +552,9 @@ <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" /> <param name="sSettingsType" value="preSet" /> <param name="suppressHeader" value="true" /> - <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True" /> + <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True"> + <metadata name="dbkey" value="equCab2" /> + </output> </test> <test> <!-- @@ -720,7 +722,9 @@ <param name="sOffrate" value="-1" /> <param name="sSeed" value="-1" /> <param name="suppressHeader" value="true" /> - <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True" /> + <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True"> + <metadata name="dbkey" value="equCab2" /> + </output> </test> <test> <!--
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_indices.loc Thu Aug 18 10:19:58 2016 -0400 @@ -0,0 +1,1 @@ +equCab2chrM equCab2 Horse (Equus caballus): equCab2 chrM ${__HERE__}/indexes/equCab2chrM/equCab2chrM
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Thu Aug 18 10:19:58 2016 -0400 @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of indexes in the Bowtie mapper format --> + <table name="bowtie_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/bowtie_indices.loc" /> + </table> +</tables>
--- a/tool_dependencies.xml Fri Dec 18 18:50:53 2015 -0500 +++ b/tool_dependencies.xml Thu Aug 18 10:19:58 2016 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="bowtie" version="0.12.7"> - <repository changeset_revision="f0faa5eea2eb" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="bowtie" version="1.1.2"> + <repository changeset_revision="8584a4574ab1" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>