Mercurial > repos > iuc > stringtie
changeset 11:52f55ad3dee2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 46636ba3d63d34e9ee30a2e0ee28cca0213628c8
| author | iuc |
|---|---|
| date | Wed, 25 May 2016 15:04:16 -0400 |
| parents | ce5e12ebb972 |
| children | f70601406e0e |
| files | stringtie.xml tool_dependencies.xml |
| diffstat | 2 files changed, 27 insertions(+), 27 deletions(-) [+] |
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--- a/stringtie.xml Wed Oct 21 16:06:19 2015 -0400 +++ b/stringtie.xml Wed May 25 15:04:16 2016 -0400 @@ -4,31 +4,31 @@ <requirement type="package" version="1.1.0">stringtie</requirement> </requirements> <command><![CDATA[ -stringtie "$input_bam" --o "$output_gtf" --p "\${GALAXY_SLOTS:-1}" -#if str($guide.use_guide) == 'yes': - -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation - #if str($guide.output_ballgown) == '-b': - $guide.output_ballgown `pwd` - #end if -#end if -#if str($option_set.options) == 'advanced': - -l "$option_set.name_prefix" - -f "$option_set.fraction" - -m "$option_set.min_tlen" - -a "$option_set.min_anchor_len" - -j "$option_set.min_anchor_cov" - -c "$option_set.min_bundle_cov" - -g "$option_set.bdist" - -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming - #if $option_set.A: - -A "$gene_abundance_estimation" - #end if - #if str($option_set.x).strip() != "": - -x "$option_set.x" - #end if -#end if + stringtie "$input_bam" + -o "$output_gtf" + -p "\${GALAXY_SLOTS:-1}" + #if str($guide.use_guide) == 'yes': + -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation + #if str($guide.output_ballgown) == '-b': + $guide.output_ballgown `pwd` + #end if + #end if + #if str($option_set.options) == 'advanced': + -l "$option_set.name_prefix" + -f "$option_set.fraction" + -m "$option_set.min_tlen" + -a "$option_set.min_anchor_len" + -j "$option_set.min_anchor_cov" + -c "$option_set.min_bundle_cov" + -g "$option_set.bdist" + -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming + #if $option_set.A: + -A "$gene_abundance_estimation" + #end if + #if str($option_set.x).strip() != "": + -x "$option_set.x" + #end if + #end if ]]> </command> <inputs> @@ -194,6 +194,6 @@ ]]> </help> <citations> - <citation type="doi">doi:10.1038/nbt.3122</citation> + <citation type="doi">10.1038/nbt.3122</citation> </citations> </tool>
--- a/tool_dependencies.xml Wed Oct 21 16:06:19 2015 -0400 +++ b/tool_dependencies.xml Wed May 25 15:04:16 2016 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="stringtie" version="1.1.0"> - <repository changeset_revision="5469f0f9e590" name="package_stringtie_1_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="84784276cc2c" name="package_stringtie_1_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>