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1 <tool id="clustalw" name="ClustalW" version="0.1">
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2 <requirements>
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3 <requirement type="package" version="2.1">clustalw2</requirement>
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4 </requirements>
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5 <description>multiple sequence alignment program for DNA or proteins</description>
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6 <command interpreter="python">
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7 rgClustalw.py -i "$input" -o "$output" -s "$out_order" -l "$outlog" -t "$outname" -d "$dnarna"
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8 #if ($range.mode=="part")
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9 -b "$range.seq_range_start" -e "$range.seq_range_end"
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10 #end if
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11 #if ($outcontrol.outform=="clustal")
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12 -f "CLUSTAL"
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13 #if ($outcontrol.out_seqnos=="ON")
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14 -q "ON"
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15 #end if
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16 #end if
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17 #if ($outcontrol.outform=="phylip")
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18 -f "PHYLIP"
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19 #end if
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20 #if ($outcontrol.outform=="fasta")
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21 -f "FASTA"
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22 #end if
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23 </command>
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24 <inputs>
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25 <page>
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26 <param format="fasta" name="input" type="data" label="Fasta File" />
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27 <param name="outname" label="Name for output files to make it easy to remember what you did" type="text" size="50" value="Clustal_run" />
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28 <param name="dnarna" type="select" label="Data Type">
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29 <option value="DNA" selected="True">DNA nucleotide sequences</option>
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30 <option value="PROTEIN">Protein sequences</option>
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31 </param>
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32 <conditional name="outcontrol">
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33 <param name="outform" type="select" label="Output alignment format">
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34 <option value="clustal" selected="True">Native Clustal output format</option>
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35 <option value="phylip">Phylip format</option>
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36 <option value="fasta">Fasta format</option>
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37 </param>
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38 <when value="fasta" />
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39 <when value="phylip" />
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40 <when value="clustal">
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41 <param name="out_seqnos" type="select" label="Show residue numbers in clustal format output">
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42 <option value="ON">yes</option>
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43 <option value="OFF" selected="true">no</option>
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44 </param>
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45 </when>
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46 </conditional>
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47 <param name="out_order" type="select" label="Output Order">
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48 <option value="ALIGNED">aligned</option>
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49 <option value="INPUT">same order as input file</option>
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50 </param>
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51
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52 <conditional name="range">
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53 <param name="mode" type="select" label="Output complete alignment (or specify part to output)">
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54 <option value="complete">complete alignment</option>
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55 <option value="part">only part of the alignment</option>
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56 </param>
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57 <when value="complete">
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58 </when>
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59 <when value="part">
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60 <param name="seq_range_start" size="5" type="integer" value="1" label="start point" help="sequence range to write">
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61 </param>
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62 <param name="seq_range_end" size="5" type="integer" value="99999" label="end point" >
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63 </param>
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64 </when>
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65 </conditional>
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66 </page>
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67 </inputs>
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68 <outputs>
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69 <data format="clustal" name="output" label="${outname}_output.${outcontrol.outform}">
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70 <change_format>
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71 <when input="outcontrol.outform" value="phylip" format="phylip" />
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72 <when input="outcontrol.outform" value="fasta" format="fasta" />
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73 </change_format>
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74 </data>
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75 <data format="txt" name="outlog" label="${outname}_clustal_log.txt"/>
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76 </outputs>
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77 <tests>
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78 <test>
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79 <param name="input" value="rgClustal_testin.fasta" />
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80 <param name="outname" value="" />
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81 <param name="outform" value="fasta" />
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82 <param name="dnarna" value="DNA" />
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83 <param name="mode" value="complete" />
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84 <param name="out_order" value="ALIGNED" />
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85 <output name="output" file="rgClustal_testout.fasta" ftype="fasta" />
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86 <output name="outlog" file="rgClustal_testout.log" ftype="txt" lines_diff="5" />
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87 </test>
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88 </tests>
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89 <help>
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90
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91 **Note**
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92
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93 This tool allows you to run a multiple sequence alignment with ClustalW2 (see Clustsrc_) using the default options.
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94
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95 For a tutorial introduction, see ClustalW2_
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96
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97 You can align DNA or protein sequences in the input file which should be multiple sequences to be aligned in a fasta file
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98
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99 A log will be output to your history showing the output Clustal would normally write to standard output.
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100
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101 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
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102 the output format, you can create a 'Logo' image using the Sequence Logo tool.
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103
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104 If Clustal format is chosen, you have the option of adding basepair counts to the output
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105
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106 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
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107
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108 ----
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109
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110 **Attribution**
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111
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112 Clustal attribution and associated documentation are available at Clustsrc_
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113
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114 The first iteration of this Galaxy wrapper was written by Hans-Rudolf Hotz - see Clustfirst_
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115
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116 It was modified by Ross Lazarus for the rgenetics project - tests and some additional parameters were added
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117
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118 This wrapper is released licensed under the LGPL_
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119
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120 .. _ClustalW2: http://www.ebi.ac.uk/2can/tutorials/protein/clustalw.html
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121
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122 .. _Clustsrc: http://www.clustal.org
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123
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124 .. _Clustfirst: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html
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125
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126 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
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127
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128 </help>
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129
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130 </tool>
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131
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