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<tool id="ArmDB" name="ArmDB: Generation of Pre-miRNA arm reference DB (5p and 3p arms)" version="0.1.0">
  <requirements>
    <requirement type="package" version="2.28.0">Bedtools</requirement>
     <requirement type="package" version="3.7.4">python</requirement>
  </requirements>
  <command>
    #if $mir_input.analysis == "1":
     #set path=$mir_input.genome1.fields.dbkey
     python $__tool_directory__/pre_mirbase.py -pos $positions -tool_dir $__tool_directory__ -gff3 "$path" -gen $mir_input.genome1.fields.value
    #end if    
    #if $mir_input.analysis == "2":
     #set path=$mir_input.genome2.fields.value
     python $__tool_directory__/pre_mirgene.py -pos $positions -tool_dir $__tool_directory__ -sym "$path"
    #end if
  </command>
  <inputs>
   <conditional name="mir_input">
    <param name="analysis" type="select" label="Choose reference Mir database" help="Choose which database prefer to be used.">
      <option value="1" selected="true">MirBase</option>
      <option value="2">MirGene</option>
    </param>
    <when value="1">
        <param name="genome1" type="select" label="Choose organism" help="If your genome coordinates of interest is not listed, contact the Galaxy team">
          <options from_data_table="mirbase" />
        </param> 
    </when>
    <when value="2">
      <param name="genome2" type="select" label="Choose organism" help="If your genome coordinates of interest is not listed, contact the" >
        <options from_data_table="mirgene" />
      </param>
    </when>
   </conditional>
   <param name="positions" type="integer" min="0" max="8" value="1" label="Custom Arm length" help="Choose how many nucleotides you want to extend the 5p and 3p mature sequences to create the refernce arms" />
  </inputs>
  <outputs>
    <data name="shifted_gff1" format="txt" label="Custom Bed file" from_work_dir="$__tool_directory__/shifted_mirnas.bed">
         <filter>mir_input['analysis']== "1" </filter>
    </data>
    <data name="normal_gff1" format="fasta" label="Official Bed file" from_work_dir="$__tool_directory__/original_mirnas.bed" >
       	 <filter>mir_input['analysis']== "1" </filter>
    </data>
    <data name="custom reference genome1" format="fasta" label="Custom reference arms" from_work_dir="$__tool_directory__/new_ref.fa" >
       	 <filter>mir_input['analysis']== "1" </filter>
    </data>

    <data name="shifted_gff" format="txt" label="Mature and star miRNA sequences" from_work_dir="$__tool_directory__/shifted_mirnas.bed">
       	 <filter>mir_input['analysis']== "2" </filter>
    </data>
    <data name="normal_gff" format="fasta" label="Primary transcripts with flanks" from_work_dir="$__tool_directory__/original_mirnas.bed" >
         <filter>mir_input['analysis']== "2" </filter>
    </data>
    <data name="custom reference genome" format="fasta" label="Custom reference arms" from_work_dir="$__tool_directory__/new_ref.fa" >
    	 <filter>mir_input['analysis']== "2" </filter>
    </data>

  </outputs>
  <help><![CDATA[
.. class:: infomark

**What it does**

-----

**Inputs**

- Genome coordinates in General Feature Format (GFF3) or FASTA files of RefSeq miRNAs

ArmDB takes genome coordinates (GFF3) files from MirBase or FASTA files from MirGene as input. GFF3 files and FASTA files are downloaded directly from the databases.

.. image:: armdb.png

**Outputs**

- ArmDB generates FASTA files containing the custom reference arms that are produced with the user-defined nucleotides extension of the RefSeq sequences (up to 8 nt)

 ]]></help>
  <citations>
     <citation type="doi">10.3390/cancers13225663</citation>
  </citations>
</tool>