Mercurial > repos > yhoogstrate > featurecounts
changeset 1:63bd455ed299 draft
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
| author | yhoogstrate |
|---|---|
| date | Mon, 01 Jun 2015 07:18:31 -0400 |
| parents | ab0323782bb5 |
| children | b5c93611d2c5 |
| files | README.rst featurecounts.xml tool_dependencies.xml |
| diffstat | 3 files changed, 4 insertions(+), 25 deletions(-) [+] |
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--- a/README.rst Mon May 18 04:49:19 2015 -0400 +++ b/README.rst Mon Jun 01 07:18:31 2015 -0400 @@ -21,10 +21,6 @@ http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch -More tools by the Translational Research IT (TraIT) project can be found in the following repository: - -http://toolshed.dtls.nl/ - License -------
--- a/featurecounts.xml Mon May 18 04:49:19 2015 -0400 +++ b/featurecounts.xml Mon Jun 01 07:18:31 2015 -0400 @@ -39,7 +39,7 @@ #end if -o "$output" - -T $threads + -T \${GALAXY_SLOTS:-2} #if $extended_parameters.parameters == "extended" -t $extended_parameters.gff_feature_type @@ -148,8 +148,6 @@ <option value="bed">BED format (line per exon): chr "\t" start "\t" stop "\t" description "\t" readcount (tab-delimited)</option> </param> - <param name="threads" type="integer" value="2" min="1" label="Number of the CPU threads. Higher numbers only make sense with a higher number of samples." /> - <conditional name="extended_parameters"> <param name="parameters" type="select" label="featureCounts parameters" help="For more advanced featureCounts settings."> <option value="default">Default settings</option>
--- a/tool_dependencies.xml Mon May 18 04:49:19 2015 -0400 +++ b/tool_dependencies.xml Mon Jun 01 07:18:31 2015 -0400 @@ -1,22 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <package name="featurecounts" version="1.4.6.p1"> - <install version="1.0"> - <actions> - <action type="shell_command">wget http://garr.dl.sourceforge.net/project/subread/subread-1.4.6-p1/subread-1.4.6-p1-source.tar.gz && tar -zxvf subread-1.4.6-p1-source.tar.gz && cd subread-1.4.6-p1-source/src/ && make -f Makefile.Linux && cd ../../</action> - <action type="move_file"> - <source>../subread-1.4.6-p1-source/bin/featureCounts</source> - <destination>$INSTALL_DIR/bin/</destination> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - <!--<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>--> - </action> - </actions> - </install> - <readme> - Downloads and installs featureCounts; requires WGET, GNU AUTOTOOLS and TAR to be installed. - </readme> + <repository changeset_revision="a4c247fdd71b" name="package_featurecounts_1_4_6" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="featurecounts2bed" version="1.0.0"> @@ -27,8 +12,8 @@ <file mode="755">$INSTALL_DIR/bin/featurecounts2bed.sh</file> </action> <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable> </action> </actions> </install>