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comparison transdecoder.xml @ 7:ffd1300599a1 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 2147ee46c226f99d16899eb29b223f0f80db5491"
author iuc
date Fri, 22 Oct 2021 11:15:03 +0000
parents d0d4cef4f967
children
comparison
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6:d0d4cef4f967 7:ffd1300599a1
1 <tool id="transdecoder" name="TransDecoder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="transdecoder" name="TransDecoder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description>finds coding regions within transcripts</description> 2 <description>finds coding regions within transcripts</description>
3 <xrefs>
4 <xref type="bio.tools">TransDecoder</xref>
5 </xrefs>
3 <macros> 6 <macros>
4 <token name="@TOOL_VERSION@">5.5.0</token> 7 <token name="@TOOL_VERSION@">5.5.0</token>
5 <token name="@VERSION_SUFFIX@">1</token> 8 <token name="@VERSION_SUFFIX@">2</token>
6 </macros> 9 </macros>
7 <requirements> 10 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">transdecoder</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">transdecoder</requirement>
9 <requirement type="package" version="3.0">zip</requirement> 12 <requirement type="package" version="3.0">zip</requirement>
10 </requirements> 13 </requirements>
107 <when value="strict"> 110 <when value="strict">
108 <param argument="--retain_long_orfs_length" type="integer" value="1000000" min="0" label="Set long ORFs length" help="Retain all ORFs found that are equal or longer than these many nucleotides even if no other evidence marks it as coding."/> 111 <param argument="--retain_long_orfs_length" type="integer" value="1000000" min="0" label="Set long ORFs length" help="Retain all ORFs found that are equal or longer than these many nucleotides even if no other evidence marks it as coding."/>
109 </when> 112 </when>
110 </conditional> 113 </conditional>
111 <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)"/> 114 <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)"/>
112 <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)"/> 115 <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)"/>
113 <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."/> 116 <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."/>
114 <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?"/> 117 <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?"/>
115 <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."/> 118 <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."/>
116 </when> 119 </when>
117 <when value="no"/> 120 <when value="no"/>