Mercurial > repos > trinity_ctat > ctat_lncrna
changeset 11:378e2e65edc5 draft
Uploaded
author | trinity_ctat |
---|---|
date | Thu, 12 Jul 2018 10:47:23 -0400 |
parents | f3f722c9dbf8 |
children | 68ad589338ef |
files | ctat_lncrna.xml |
diffstat | 1 files changed, 9 insertions(+), 9 deletions(-) [+] |
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--- a/ctat_lncrna.xml Mon Jul 09 12:24:27 2018 -0400 +++ b/ctat_lncrna.xml Thu Jul 12 10:47:23 2018 -0400 @@ -54,8 +54,8 @@ <param name="min_coding" type="float" value="0.1" label="Min exonic identity to filter out transcript that aligns to orthologous coding gene" help="default is set by learning coding alignment distribution from data"/> <param name="minMatch" type="float" value="0.1" label="Min match" help="Minimum match parameter for liftover" /> <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="gap_open" type="integer" 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="integer" 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"> <options from_data_table="ctat_lncrna_annotations" /> </param> @@ -63,14 +63,14 @@ <outputs> <data format="html" name="html_file" label="web_report" from_work_dir="slncky.EvolutionBrowser/browse.html"/> - <data format="text" name="canonical_to_lncs" label="canonical_to_lncs" from_work_dir="slncky.canonical_to_lncs.txt"/> - <data format="text" name="cluster_info" label="cluster_info" from_work_dir="slncky.cluster_info.txt"/> - <data format="text" name="filtered_info" label="filtered_info" from_work_dir="slncky.filtered_info.txt"/> + <data format="tabular" name="canonical_to_lncs" label="canonical_to_lncs" from_work_dir="slncky.canonical_to_lncs.txt"/> + <data format="tabular" name="cluster_info" label="cluster_info" from_work_dir="slncky.cluster_info.txt"/> + <data format="tabular" name="filtered_info" label="filtered_info" from_work_dir="slncky.filtered_info.txt"/> <data format="bed" name="lncs" label="lncs" from_work_dir="slncky.lncs.bed"/> - <data format="text" name="lncs_info" label="lncs.info" from_work_dir="slncky.lncs.info.txt"/> - <data format="text" name="orfs" label="orfs" from_work_dir="slncky.orfs.txt"/> - <data format="text" name="orthologs_top" label="orthologs.top" from_work_dir="slncky.orthologs.top.txt"/> - <data format="text" name="orthologs" label="orthologs" from_work_dir="slncky.orthologs.txt"/> + <data format="tabular" name="lncs_info" label="lncs.info" from_work_dir="slncky.lncs.info.txt"/> + <data format="tabular" name="orfs" label="orfs" from_work_dir="slncky.orfs.txt"/> + <data format="tabular" name="orthologs_top" label="orthologs.top" from_work_dir="slncky.orthologs.top.txt"/> + <data format="tabular" name="orthologs" label="orthologs" from_work_dir="slncky.orthologs.txt"/> </outputs> <stdio>