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1 <tool id="T_coffee" name="T-COFFEE" version="10.00.r1613">
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2 <description>multiple aligment</description>
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3 <command interpreter="perl">
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4 tcoffee.pl $input $method01 $method02 $method03 $dnd $msf_aln $clustalw_aln $pir_aln $fasta_aln $phylip $pir_seq $fasta_seq $score_ascii $score_html
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5 </command>
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6
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7 <inputs>
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8 <param format="fasta" name="input" type="data" label="Source file"/>
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9 <param name="method01" type="select" display="checkboxes" multiple="true" label="Pairwise Structual Method">
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10 <option value="sap_pair">sap_pair</option>
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11 <option value="TMalign_pair">TMalign_pair</option>
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12 <option value="mustang_pair">mustang_pair</option>
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13 </param>
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14 <param name="method02" type="select" display="checkboxes" multiple="true" label="Multiple Sequence Alignment Methods">
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15 <option value="pcma_msa">pcma_msa</option>
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16 <option value="clustalw_msa">clustalw_msa</option>
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17 <option value="dialigntx_msa">dialigntx_msa</option>
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18 <option value="poa_msa">poa_msa</option>
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19 <option value="muscle_msa">muscle_msa</option>
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20 <option value="probcons_msa">probcons_msa</option>
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21 <option value="t_coffee_msa">t_coffee_msa</option>
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22 <option value="amap_msa">amap_msa</option>
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23 <option value="kalign_msa">kalign_msa</option>
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24 </param>
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25 <param name="method03" type="select" display="checkboxes" multiple="true" label="Pairwise Sequence Alignment Methods">
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26 <option value="fast_pair">fast_pair</option>
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27 <option value="clustalw_pair">clustalw_pair</option>
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28 <option value="lalign_id_pair">lalign_id_pair</option>
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29 <option value="slow_pair">slow_pair</option>
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30 <option value="proba_pair">proba_pair</option>
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31 </param>
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32 <param name="format_output_dnd" type="select" display="radio" label="Output newick">
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33 <option value="no">No</option>
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34 <option value="yes">Yes</option>
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35 </param>
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36 <param name="format_output_msf_aln" type="select" display="radio" label="Output msf_aln">
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37 <option value="no">No</option>
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38 <option value="yes">Yes</option>
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39 </param>
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40 <param name="format_output_clustalw_aln" type="select" display="radio" label="Output clustalw_aln">
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41 <option value="no">No</option>
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42 <option value="yes">Yes</option>
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43 </param>
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44 <param name="format_output_pir_aln" type="select" display="radio" label="Output pir_aln">
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45 <option value="no">No</option>
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46 <option value="yes">Yes</option>
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47 </param>
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48 <param name="format_output_fasta_aln" type="select" display="radio" label="Output fasta_aln">
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49 <option value="no">No</option>
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50 <option value="yes">Yes</option>
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51 </param>
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52 <param name="format_output_phylip" type="select" display="radio" label="Output phylip">
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53 <option value="no">No</option>
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54 <option value="yes">Yes</option>
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55 </param>
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56 <param name="format_output_pir_seq" type="select" display="radio" label="Output pir_seq">
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57 <option value="no">No</option>
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58 <option value="yes">Yes</option>
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59 </param>
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60 <param name="format_output_fasta_seq" type="select" display="radio" label="Output fasta_seq">
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61 <option value="no">No</option>
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62 <option value="yes">Yes</option>
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63 </param>
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64 <param name="format_output_score_ascii" type="select" display="radio" label="Output score_ascii">
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65 <option value="no">No</option>
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66 <option value="yes">Yes</option>
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67 </param>
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68 <param name="format_output_score_html" type="select" display="radio" label="Output score_html">
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69 <option value="no">No</option>
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70 <option value="yes">Yes</option>
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71 </param>
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72 </inputs>
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73
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74 <outputs>
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75 <data format="nhx" name="dnd" label="${tool.name} on ${on_string}: newick.dnd" >
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76 <filter>format_output_dnd == "yes"</filter>
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77 </data>
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78 <data format="msf" name="msf_aln" label="${tool.name} on ${on_string}: msf_aln" >
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79 <filter>format_output_msf_aln == "yes"</filter>
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80 </data>
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81 <data format="clustalw" name="clustalw_aln" label="${tool.name} on ${on_string}: clustalw_aln" >
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82 <filter>format_output_clustalw_aln == "yes"</filter>
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83 </data>
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84 <data format="pir" name="pir_aln" label="${tool.name} on ${on_string}: pir_aln" >
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85 <filter>format_output_pir_aln == "yes"</filter>
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86 </data>
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87 <data format="fasta" name="fasta_aln" label="${tool.name} on ${on_string}: fasta_aln" >
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88 <filter>format_output_fasta_aln == "yes"</filter>
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89 </data>
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90 <data format="phyloxml" name="phylip" label="${tool.name} on ${on_string}: phylip" >
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91 <filter>format_output_phylip == "yes"</filter>
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92 </data>
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93 <data format="pir" name="pir_seq" label="${tool.name} on ${on_string}: pir_seq" >
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94 <filter>format_output_pir_seq == "yes"</filter>
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95 </data>
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96 <data format="fasta" name="fasta_seq" label="${tool.name} on ${on_string}: fasta_seq" >
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97 <filter>format_output_fasta_seq == "yes"</filter>
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98 </data>
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99 <data format="ascii" name="score_ascii" label="${tool.name} on ${on_string}: score_ascii" >
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100 <filter>format_output_score_ascii == "yes"</filter>
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101 </data>
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102 <data format="html" name="score_html" label="${tool.name} on ${on_string}: score_html" >
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103 <filter>format_output_score_html == "yes"</filter>
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104 </data>
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105 </outputs>
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106
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107 <stdio>
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108 <exit_code range="1:" level="fatal" description="Error" />
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109 </stdio>
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110
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111 </tool>
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