comparison assembly_post_processor.xml @ 101:7ca8ab9a46e9 draft

Uploaded

100:e0db1f719af1

    #if str($options_type.dereplicate) == 'yes':
        && mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds'
        && mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep'
    #end if
#end if
    ]]></command>
    <inputs>
        <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>
        <conditional name="prediction_method_cond">
            <param name="prediction_method" type="select" label="Coding regions prediction method">

This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and
evolutionary analyses of genome-scale gene families and transcriptomes.  This tool post-processes de novo
assembled transcripts into putative coding sequences and their corresponding amino acid translations and
optionally assigns transcripts to circumscribed gene families ("orthogroups")[2].  After transcripts have been
assigned to gene families, overlapping contigs can be identified and merged to reduce fragmentation in the
de novo assembly.  

-----

**Required options**

101:7ca8ab9a46e9

    #if str($options_type.dereplicate) == 'yes':
        && mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds'
        && mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep'
    #end if
#end if
&& if [[ $? -ne 0 ]]; then
  cat proc.log >&2;
fi
    ]]></command>
    <inputs>
        <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>
        <conditional name="prediction_method_cond">
            <param name="prediction_method" type="select" label="Coding regions prediction method">

This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and
evolutionary analyses of genome-scale gene families and transcriptomes.  This tool post-processes de novo
assembled transcripts into putative coding sequences and their corresponding amino acid translations and
optionally assigns transcripts to circumscribed gene families ("orthogroups")[2].  After transcripts have been
assigned to gene families, overlapping contigs can be identified and merged to reduce fragmentation in the
de novo assembly.

-----

**Required options**