Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 101:7ca8ab9a46e9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Thu, 07 Dec 2017 10:28:43 -0500
parents 01ef9d05d455
children 62df33ce7eaa
comparison
equal deleted inserted replaced
100:e0db1f719af1 101:7ca8ab9a46e9
46 #if str($options_type.dereplicate) == 'yes': 46 #if str($options_type.dereplicate) == 'yes':
47 && mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds' 47 && mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds'
48 && mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep' 48 && mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep'
49 #end if 49 #end if
50 #end if 50 #end if
51 && if [[ $? -ne 0 ]]; then
52 cat proc.log >&2;
53 fi
51 ]]></command> 54 ]]></command>
52 <inputs> 55 <inputs>
53 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/> 56 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>
54 <conditional name="prediction_method_cond"> 57 <conditional name="prediction_method_cond">
55 <param name="prediction_method" type="select" label="Coding regions prediction method"> 58 <param name="prediction_method" type="select" label="Coding regions prediction method">
166 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and 169 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and
167 evolutionary analyses of genome-scale gene families and transcriptomes. This tool post-processes de novo 170 evolutionary analyses of genome-scale gene families and transcriptomes. This tool post-processes de novo
168 assembled transcripts into putative coding sequences and their corresponding amino acid translations and 171 assembled transcripts into putative coding sequences and their corresponding amino acid translations and
169 optionally assigns transcripts to circumscribed gene families ("orthogroups")[2]. After transcripts have been 172 optionally assigns transcripts to circumscribed gene families ("orthogroups")[2]. After transcripts have been
170 assigned to gene families, overlapping contigs can be identified and merged to reduce fragmentation in the 173 assigned to gene families, overlapping contigs can be identified and merged to reduce fragmentation in the
171 de novo assembly. 174 de novo assembly.
172 175
173 ----- 176 -----
174 177
175 **Required options** 178 **Required options**
176 179