comparison emboss_vectorstrip.xml @ 11:0e2484b6829b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68

10:9b98d3d903c6

<tool id="EMBOSS: vectorstrip106" name="vectorstrip" version="5.0.0">
  <description>Strips out DNA between a pair of vector sequences</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>vectorstrip -sequence $input1 -vectorsfile $input2 -outseq $ofile1 -outfile $ofile2 -vectorfile yes -mismatch "$mismatch" -besthits $besthits -linkera "$linkera" -linkerb
  "$linkerb" -osformat4 $out_format1 -auto</command>
  <inputs>
    <param format="fasta" name="input1" type="data">
      <label>Sequences</label>
    </param>
    <param format="data" name="input2" type="data">
      <label>Vector file</label>
    </param>
    <param name="mismatch" type="text" value="10">
      <label>Max allowed percent mismatch</label>
    </param>
    <param name="besthits" type="select">
      <label>Show only the best hits (minimize mismatches)</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="linkera" type="text" value="">
      <label>The 5' sequence</label>
    </param>
    <param name="linkerb" type="text" value="">
      <label>The 3' sequence</label>
    </param>
    <param name="out_format1" type="select">
      <label>Output Sequence File Format</label>
      <option value="fasta">FASTA (m)</option>
      <option value="acedb">ACeDB (m)</option>
      <option value="asn1">ASN.1 (m)</option>
      <option value="clustal">Clustal (m)</option>
      <option value="codata">CODATA (m)</option>

      <option value="text">Plain sequence (s)</option>
      <option value="treecon">Treecon (m)</option>
    </param>
  </inputs>
  <outputs>
    <data format="fasta" name="ofile1" />
    <data format="vectorstrip" name="ofile2" />
  </outputs>
  <!--  <tests>
    <test>
      <param name="input1" value="1.fasta"/>
      <param name="input2" value="2.fasta"/>

      <param name="linkerb" value=""/>
      <param name="out_format1" value="fasta"/>
      <output name="ofile1" file="emboss_vectorstrip_out.fasta"/>
    </test>
  </tests> -->
  <code file="emboss_format_corrector.py" />
  <help>
    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/vectorstrip.html

------

**Citation**

For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_

If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
  </help>
</tool>

11:0e2484b6829b

<tool id="EMBOSS: vectorstrip106" name="vectorstrip" version="5.0.0.1">
  <description>Strips out DNA between a pair of vector sequences</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>vectorstrip -sequence '$input1' -vectorsfile '$input2' -outseq '$ofile1' -outfile '$ofile2' -vectorfile yes -mismatch $mismatch -besthits $besthits -linkera '$linkera' -linkerb
  '$linkerb' -osformat4 $out_format1 -auto</command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="Sequences" />
    <param name="input2" type="data" format="data" label="Vector file" />
    <param name="mismatch" type="integer" value="10" label="Max allowed percent mismatch" />
    <param name="besthits" type="select" label="Show only the best hits (minimize mismatches)">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="linkera" type="text" value="" label="The 5' sequence" />
    <param name="linkerb" type="text" value="" label="The 3' sequence" />
    <param name="out_format1" type="select" label="Output sequence file format">
      <option value="fasta">FASTA (m)</option>
      <option value="acedb">ACeDB (m)</option>
      <option value="asn1">ASN.1 (m)</option>
      <option value="clustal">Clustal (m)</option>
      <option value="codata">CODATA (m)</option>

      <option value="text">Plain sequence (s)</option>
      <option value="treecon">Treecon (m)</option>
    </param>
  </inputs>
  <outputs>
    <data name="ofile1" format="fasta" />
    <data name="ofile2" format="vectorstrip" />
  </outputs>
  <!--  <tests>
    <test>
      <param name="input1" value="1.fasta"/>
      <param name="input2" value="2.fasta"/>

      <param name="linkerb" value=""/>
      <param name="out_format1" value="fasta"/>
      <output name="ofile1" file="emboss_vectorstrip_out.fasta"/>
    </test>
  </tests> -->
  <help>
    You can view the original documentation here_.

    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/vectorstrip.html
  </help>
  <expand macro="citations" />
</tool>