annotate translate_bed_sequences.xml @ 2:4221664a2bd0 draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"

<tool id="translate_bed_sequences" name="Translate BED Sequences" version="0.2.0">
    <description>3 frame translation of BED augmented with a sequence column</description>
    <requirements>
        <requirement type="package" version="1.76">biopython</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Error" />
    </stdio>
    <command>
    python '$__tool_directory__/translate_bed_sequences.py' 
        --input '$input'
          #if $fa_db:
           --fa_db='$fa_db'
          #end if
          #if $fa_sep:
           --fa_sep='$fa_sep'
          #end if
          #if $id_prefix:
           --id_prefix='$id_prefix'
          #end if
          #if $reference:
           --reference $reference
          #else:
           --reference ${input.metadata.dbkey}
          #end if
          #if $refsource:
           --refsource $refsource
          #end if
          #if $seqtype:
            --seqtype $seqtype
          #end if
          #if $score_name:
            --score_name $score_name
          #end if
          #if $filter.filterseqs == 'yes':
            #if $filter.leading_bp:
              --leading_bp $filter.leading_bp
            #end if
            #if $filter.trailing_bp:
              --trailing_bp $filter.trailing_bp
            #end if
          #else:
            --unfiltered
          #end if
          #if $trim.trimseqs == 'no':
            --untrimmed
            #if str($trim.max_stop_codons) != '':
              --max_stop_codons $trim.max_stop_codons
            #end if
          #end if
          #if str($min_length) != '':
           --min_length $min_length     
          #end if
          --bed $translated_bed
          --output '$output'
    </command>
    <inputs>
        <param name="input" type="data" format="bed" label="BED file with added sequence column" 
               help="Output from 'Extract Genomic DNA' run on tophat junctions.bed "/> 
        <param name="fa_db" type="text" value="" optional="true" label="fasta ID source, e.g. generic"
               help="Any Compomics application such as PeptideShaker, requires a source">
        </param>
        <param name="fa_sep" type="text" value="" optional="true" label="fasta ID line separator character"
               help="Only used when a fasta ID source is given, defaults to the pipe character">
        </param>
        <param name="id_prefix" type="text" value="" optional="true" label="ID prefix for generated IDs"
               help="Can be used to distinguish samples">
            <validator type="regex" message="Allowed chars:a-z A-Z 0-9 _ - |">^[a-zA-Z0-9_-|]*$</validator>
        </param>
        <param name="refsource" type="text" value="Ensembl" optional="true" label="Genome reference source"
               help=""/>
        <param name="reference" type="text" value="" optional="true" label="Genome reference name"
               help="By default, the database metadata will be used."/>
        <param name="seqtype" type="text" value="" optional="true" label="The SEQTYPE:STATUS to include in the fasta ID lines"
               help="For example:  pep:splice"/>
        <param name="score_name" type="text" value="" optional="true" label="Add the bed score field fasta ID line with this tag name"
               help="For example:  with the tag name 'depth' and bed score 12:   depth:12"/>
        <conditional name="filter">
          <param name="filterseqs" type="select" label="Filter out translations with stop codons before the splice site">
            <option value="yes" selected="true">Yes</option>
            <option value="no">No</option>
          </param>
          <when value="yes">
            <param name="leading_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering start position base pairs" 
                   help="Do not reject translation is stop_codons are within base pairs of the BED start position for positive strand"/>
            <param name="trailing_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering end position base pairs" 
                   help="Do not reject translation is stop_codons are within base pairs of the BED end position for negative strand"/>
          </when>
          <when value="no"/>
        </conditional>
        <conditional name="trim">
          <param name="trimseqs" type="select" label="Trim translations to stop codons">
            <option value="yes" selected="true">Yes</option>
            <option value="no">No</option>
          </param>
          <when value="no">
            <param name="max_stop_codons" type="integer" value="" min="0" optional="true" label="Maximum number of stop codons allowed in a translation to be reported"/>
          </when>
        </conditional>
        <param name="min_length" type="integer" value="" min="0" optional="true" label="Minimum length of a translation to be reported"/>
    </inputs>
    <outputs>
        <data name="translated_bed" metadata_source="input" format="bed" label="${tool.name} on ${on_string} bed" />
        <data name="output" metadata_source="input" format="fasta" label="${tool.name} on ${on_string} fasta" />
    </outputs>
    <tests>
        <test>
          <param name="input" value="Extract_Genomic_DNA.bed" ftype="bed" dbkey="hg19"/>
          <param name="reference" value="GRCh37"/>
          <param name="seqtype" value="pep:novel"/>
          <param name="score_name" value="depth"/>
          <output name="output" file="translated_bed_sequences.fa"/>
        </test>
    </tests>
    <help>
**Translate BED Sequences**

This tool takes a BED input file that has been processed 
by the Galaxy tool "Extract Genomic DNA" to add a 13th column with the transcript sequence.

It generates a peptide fasta file with the 3-frame translations of the spliced sequence 
defined by each entry in the input BED file.

    </help>
</tool>