comparison rgClustalw.xml @ 3:d6694932c5e0 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit 31dd2ec1d105282421df5d6801c65cdcfd589f59

2:f8aad74cc8c1

<tool id="clustalw" name="ClustalW" version="0.1">
   <requirements>
      <requirement type="package" version="2.1">clustalw2</requirement>
   </requirements>
   <description>multiple sequence alignment program for DNA or proteins</description>
   <command interpreter="python"> 
    rgClustalw.py -i "$input" -o "$output" -s "$out_order" -l "$outlog" -t "$outname" -d "$dnarna"
    #if   ($range.mode=="part")
-b "$range.seq_range_start" -e "$range.seq_range_end"
    #end if
    #if ($outcontrol.outform=="clustal")
-f "CLUSTAL"
    #if ($outcontrol.out_seqnos=="ON")
-q "ON"
    #end if
    #end if
    #if ($outcontrol.outform=="phylip")
-f "PHYLIP"
    #end if
    #if ($outcontrol.outform=="fasta")
-f "FASTA"
    #end if
   </command>
  <inputs>
   <page>
    <param format="fasta" name="input" type="data" label="Fasta File" />
    <param name="outname" label="Name for output files to make it easy to remember what you did" type="text" value="Clustal_run" />
    <param name="dnarna" type="select" label="Data Type">
      <option value="DNA" selected="True">DNA nucleotide sequences</option>
      <option value="PROTEIN">Protein sequences</option>
    </param>
    <conditional name="outcontrol">
      <param name="outform" type="select" label="Output alignment format">
        <option value="clustal" selected="True">Native Clustal output format</option>
        <option value="phylip">Phylip format</option>
        <option value="fasta">Fasta format</option>
      </param>
      <when value="fasta" />
      <when value="phylip" />
      <when value="clustal">
       <param name="out_seqnos" type="select" label="Show residue numbers in clustal format output">
         <option value="ON">yes</option>
         <option value="OFF" selected="true">no</option>
       </param>
      </when>
    </conditional>
    <param name="out_order" type="select" label="Output Order">
      <option value="ALIGNED">aligned</option>
      <option value="INPUT">same order as input file</option>
    </param>

    <conditional name="range">
        <param name="mode" type="select" label="Output complete alignment (or specify part to output)">
          <option value="complete">complete alignment</option>
          <option value="part">only part of the alignment</option>
        </param>
        <when value="complete">
        </when>
        <when value="part">    
           <param name="seq_range_start" type="integer" value="1" label="start point" help="sequence range to write">
           </param>
           <param name="seq_range_end" type="integer" value="99999" label="end point" >
           </param> 
        </when>
    </conditional>
   </page>
  </inputs>
  <outputs>
    <data format="clustal" name="output"  label="${outname}_output.${outcontrol.outform}">
       <change_format>
           <when input="outcontrol.outform" value="phylip" format="phylip" />
           <when input="outcontrol.outform" value="fasta" format="fasta" />
       </change_format>
    </data>
    <data format="txt" name="outlog"  label="${outname}_clustal_log.txt"/>
  </outputs>
  <tests>
     <test>
      <param name="input" value="rgClustal_testin.fasta" />
      <param name="outname" value="" />
      <param name="outform" value="fasta" />
      <param name="dnarna" value="DNA" />
      <param name="mode" value="complete" />
      <param name="out_order" value="ALIGNED" />
      <output name="output" file="rgClustal_testout.fasta" ftype="fasta" />
      <output name="outlog" file="rgClustal_testout.log" ftype="txt" lines_diff="5" />
     </test>
  </tests>
  <help>

**Note**

This tool allows you to run a multiple sequence alignment with ClustalW2 (see Clustsrc_) using the default options.
 
For a tutorial introduction, see ClustalW2_

You can align DNA or protein sequences in the input file which should be multiple sequences to be aligned in a fasta file

A log will be output to your history showing the output Clustal would normally write to standard output.

The alignments will appear as a clustal format file or optionally, as phylip or fasta format files in your history. If you choose fasta as 
the output format, you can create a 'Logo' image using the Sequence Logo tool.

If Clustal format is chosen, you have the option of adding basepair counts to the output

A subsequence of the alignment can be output by setting the Output complete parameter to "Partial" and defining the offset and end of the subsequence to be output 

----

**Attribution**

Clustal attribution and associated documentation are available at Clustsrc_

The first iteration of this Galaxy wrapper was written by Hans-Rudolf Hotz - see Clustfirst_

It was modified by Ross Lazarus for the rgenetics project - tests and some additional parameters were added

This wrapper is released licensed under the LGPL_

.. _ClustalW2: http://www.ebi.ac.uk/2can/tutorials/protein/clustalw.html  

.. _Clustsrc: http://www.clustal.org

.. _Clustfirst: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html

.. _LGPL: http://www.gnu.org/copyleft/lesser.html

    </help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btm404</citation>
    </citations>
</tool>

3:d6694932c5e0

<tool id="clustalw" name="ClustalW" version="2.1">
    <description>multiple sequence alignment program for DNA or proteins</description>
    <requirements>
        <requirement type="package" version="2.1">clustalw</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
ln -s '$input' input.fasta &&
clustalw2 -INFILE=input.fasta -OUTFILE='$output' -OUTORDER=$out_order -TYPE=$dnarna
#if $outcontrol.outform == "clustal"
    -OUTPUT=CLUSTAL
    #if $outcontrol.out_seqnos == "ON"
        -SEQNOS=ON
    #end if
#end if
#if $outcontrol.outform == "phylip"
    -OUTPUT=PHYLIP
#end if
#if $outcontrol.outform == "fasta"
    -OUTPUT=FASTA
#end if
#if $range.mode == "part"
    -RANGE=${range.seq_range_start},${range.seq_range_end}
#end if
    ]]></command>
    <inputs>
        <param name="input" type="data" format="fasta" label="FASTA file" />
        <param name="dnarna" type="select" label="Data type">
            <option value="DNA" selected="True">DNA nucleotide sequences</option>
            <option value="PROTEIN">Protein sequences</option>
        </param>
        <conditional name="outcontrol">
            <param name="outform" type="select" label="Output alignment format">
                <option value="clustal" selected="True">Native Clustal output format</option>
                <option value="phylip">PHYLIP format</option>
                <option value="fasta">FASTA format</option>
            </param>
            <when value="fasta" />
            <when value="phylip" />
            <when value="clustal">
                <param name="out_seqnos" type="boolean" truevalue="ON" falsevalue="OFF" label="Show residue numbers in clustal format output" />
            </when>
        </conditional>
        <param name="out_order" type="select" label="Output order">
            <option value="ALIGNED">Aligned</option>
            <option value="INPUT">Same order as input file</option>
        </param>
        <conditional name="range">
            <param name="mode" type="select" label="Output complete alignment (or specify part to output)">
                <option value="complete">Complete alignment</option>
                <option value="part">Only part of the alignment</option>
            </param>
            <when value="complete" />
            <when value="part">
                <param name="seq_range_start" type="integer" value="1" label="Start point" help="Sequence range to write" />
                <param name="seq_range_end" type="integer" value="99999" label="End point" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format="clustal" label="${tool.name} on ${on_string}: ${outcontrol.outform}">
            <change_format>
                <when input="outcontrol.outform" value="phylip" format="phylip" />
                <when input="outcontrol.outform" value="fasta" format="fasta" />
            </change_format>
        </data>
        <data name="dnd" format="nhx" label="${tool.name} on ${on_string}: dnd" from_work_dir="input.dnd" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="rgClustal_testin.fasta" />
            <param name="outform" value="fasta" />
            <param name="dnarna" value="DNA" />
            <param name="mode" value="complete" />
            <param name="out_order" value="ALIGNED" />
            <output name="output" file="rgClustal_testout.fasta" ftype="fasta" />
            <output name="dnd" file="rgClustal_testin.dnd" ftype="nhx" />
        </test>
    </tests>
    <help><![CDATA[
**Note**

This tool allows you to run a multiple sequence alignment with ClustalW_ using the default options.

You can align DNA or protein sequences in the input file which should be multiple sequences to be aligned in a FASTA file.

The alignments will appear as a clustal format file or optionally, as PHYLIP or FASTA format files in your history. If you choose FASTA as
the output format, you can create a 'Logo' image using the Sequence Logo tool.

If Clustal format is chosen, you have the option of adding basepair counts to the output.

A subsequence of the alignment can be output by setting the Output complete parameter to "Partial" and defining the offset and end of the subsequence to be output.

----

**Attribution**

The first iteration of this Galaxy wrapper was written by Hans-Rudolf Hotz.

It was modified by Ross Lazarus for the rgenetics project - tests and some additional parameters were added.

This wrapper is released licensed under the LGPL_.

.. _ClustalW: http://www.clustal.org/clustal2/

.. _LGPL: https://www.gnu.org/copyleft/lesser.html
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btm404</citation>
    </citations>
</tool>