Mercurial > repos > trinity_ctat > ctat_lncrna
changeset 8:bddb36ef9fb3 draft
Updating tools requirements.
| author | trinity_ctat |
|---|---|
| date | Wed, 27 Jun 2018 14:09:46 -0400 |
| parents | 018041e308fe |
| children | f4fe52ab2ead |
| files | ctat_lncrna.xml |
| diffstat | 1 files changed, 3 insertions(+), 8 deletions(-) [+] |
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--- a/ctat_lncrna.xml Fri Jun 22 18:55:00 2018 -0400 +++ b/ctat_lncrna.xml Wed Jun 27 14:09:46 2018 -0400 @@ -3,21 +3,16 @@ <description>Filters a high-quality set of lncRNA from reconstructed RNA-seq data</description> <requirements> <requirement type="package">ctat-lncrna</requirement> - <requirement type="package">numpy</requirement> </requirements> <command detect_errors="default"> <![CDATA[ #if str($bedfile) != "": lncrna --bedfile $bedfile - --config "${assembly.fields.path}" + --config "${annotations.fields.path}" #end if - --bedtools "$__root_dir__/database/dependencies/_conda/envs/__ctat-lncrna@_uv_/bin" - --lastz "$__root_dir__/database/dependencies/_conda/envs/__ctat-lncrna@_uv_/bin" - --liftover "$__root_dir__/database/dependencies/_conda/envs/__ctat-lncrna@_uv_/bin" - #if str($assembly) != "": - --assembly "${assembly.fields.value}" + --assembly "$assembly" #end if #if $min_overlap != "": @@ -62,7 +57,7 @@ <param name="pad" type="integer" value="0" label="Pad" help="No. of basepairs to search up- and down-stream when lifting over lnc to ortholog" /> <param name="gap_open" type="text" value="200" label="Gap open penalty to pass to lastz" help="Decreasing this parameter will increase sensitivity of orthology search"/> <param name="gap_extend" type="text" value="40" label="Gap extend penalty to pass to lastz" help="Decreasing this parameter will increase sensitivity of orthology search."/> - <param name="assembly" type="select" label="Choose annotation:" help="Select annotation"> + <param name="annotations" type="select" label="Choose annotation:" help="Select annotation"> <options from_data_table="ctat_lncrna_annotations" /> </param> </inputs>