| Previous changeset 6:d0d4cef4f967 (2021-02-01) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 2147ee46c226f99d16899eb29b223f0f80db5491" |
|
modified:
transdecoder.xml |
| b |
| diff -r d0d4cef4f967 -r ffd1300599a1 transdecoder.xml --- a/transdecoder.xml Mon Feb 01 20:51:40 2021 +0000 +++ b/transdecoder.xml Fri Oct 22 11:15:03 2021 +0000 |
| b |
| @@ -1,8 +1,11 @@ -<tool id="transdecoder" name="TransDecoder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> +<tool id="transdecoder" name="TransDecoder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> <description>finds coding regions within transcripts</description> + <xrefs> + <xref type="bio.tools">TransDecoder</xref> + </xrefs> <macros> <token name="@TOOL_VERSION@">5.5.0</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">transdecoder</requirement> @@ -109,7 +112,7 @@ </when> </conditional> <param argument="--retain_blastp_hits" type="data" format="tabular" optional="true" label="Select BlastP result file" help="Any ORF with a blast match will be retained in the final output. (tabular outfmt6 file)"/> - <param argument="--retain_pfam_hits" type="data" format="tabular" optional="true" label="Select Pfam result file" help="Domain table output file from running hmmscan to search Pfam. Any ORF with a pfam domain hit will be retained in the final output. (tabular domtblout file)"/> + <param argument="--retain_pfam_hits" type="data" format="txt" optional="true" label="Select Pfam result file" help="Domain table output file from running hmmscan to search Pfam. Any ORF with a pfam domain hit will be retained in the final output. (tabular domtblout file)"/> <param argument="--single_best_only" type="boolean" truevalue="--single_best_only" falsevalue="" label="Retain only the single best ORF per transcript?" help="Prioritized by homology than ORF length."/> <param argument="--no_refine_starts" type="boolean" truevalue="--no_refine_starts" falsevalue="" label="Start refinement that identifies potential start codons for 5' partial ORFs using a PWM?"/> <param argument="-T" type="integer" value="500" min="1" label="Set top longest ORFs to train Markov Model" help="The first (10*value) elements are selected for removing redundancies. Then number of longst ORFs of this value are selected from the non-redundant set."/> |