Mercurial > repos > earlhaminst > t_coffee

annotate t_coffee.xml @ 2:df6527887a18 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 2773f69afb943d6f6a64c2060180af8bd8941e16
author earlhaminst
date Mon, 09 Jan 2017 14:26:41 -0500
parents b3833e5b50d4
children 78dd29aa7fc1
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794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
earlhaminst
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1 <tool id="t_coffee" name="T-Coffee" version="11.0.8">
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2 <description>multiple sequence alignment</description>
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earlhaminst
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3 <requirements>
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earlhaminst
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4 <requirement type="package" version="11.0.8">t_coffee</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" />
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8 </stdio>
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9 <version_command>
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10 t_coffee -version | grep Version
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earlhaminst
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11 </version_command>
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earlhaminst
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12 <command>
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13 <![CDATA[
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14 #if str($input_type.filter_fasta) == 'yes'
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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15 #set $input = '-infile=stdin'
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16 python '$__tool_directory__/filter_by_fasta_ids.py' '$input_type.identifiers' '$input_type.fasta_input' |
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17 #end if
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18
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19 #set $method_opt = ''
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20 #if $method01
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21 #set $method_opt += str($method01) + ','
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22 #end if
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23 #if $method02
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earlhaminst
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24 #set $method_opt += str($method02) + ','
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25 #end if
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26 #if $method03
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27 #set $method_opt += str($method03) + ','
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28 #end if
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29 #if $method_opt
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30 #set $method_opt = '-method ' + $method_opt[:-1]
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31 #end if
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32
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33 #set $output_opt = ''
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34 #if $outputs
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35 #set $outputs_arr = str($outputs).split(',')
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36 #for $o in $outputs_arr
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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37 #if $o not in ['cigar', 'dnd']
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
earlhaminst
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38 #set $output_opt += $o + ','
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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39 #end if
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40 #end for
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41 #if 'cigar' in $outputs_arr and 'fasta_aln' not in $outputs_arr
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42 #set $output_opt += 'fasta_aln,'
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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43 #end if
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44 #else
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45 #set $outputs_arr = []
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46 #end if
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47 #if $output_opt
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48 #set $output_opt = '-output ' + $output_opt[:-1]
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49 #end if
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50
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51 t_coffee '$input' $method_opt $output_opt -n_core \${GALAXY_SLOTS:-1} -run_name t_coffee_out -quiet
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52
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53 #if 'cigar' in $outputs_arr
1
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54 && python '$__tool_directory__/t_coffee_to_cigar.py' t_coffee_out.fasta_aln > '$cigar'
0
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55 #end if
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56 ]]>
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57 </command>
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58 <inputs>
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59 <conditional name="input_type">
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60 <param name="filter_fasta" type="select" label="Filter FASTA input?">
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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 <when value="yes">
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65 <param name="fasta_input" type="data" format="fasta" label="FASTA sequences" />
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66 <param name="identifiers" type="data" format="txt" label="List of FASTA sequence IDs" />
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67 </when>
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68 <when value="no">
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69 <param name="input" type="data" format="fasta" label="FASTA sequences" />
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70 </when>
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71 </conditional>
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72 <param name="method01" type="select" display="checkboxes" multiple="true" label="Pairwise Structual Method">
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73 <option value="sap_pair">sap_pair</option>
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74 <option value="TMalign_pair">TMalign_pair</option>
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75 <option value="mustang_pair">mustang_pair</option>
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76 </param>
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77 <param name="method02" type="select" display="checkboxes" multiple="true" label="Multiple Sequence Alignment Methods">
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78 <option value="pcma_msa">pcma_msa</option>
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79 <option value="clustalw_msa">clustalw_msa</option>
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80 <option value="dialigntx_msa">dialigntx_msa</option>
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81 <option value="poa_msa">poa_msa</option>
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82 <option value="muscle_msa">muscle_msa</option>
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83 <option value="probcons_msa">probcons_msa</option>
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84 <option value="t_coffee_msa">t_coffee_msa</option>
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85 <option value="amap_msa">amap_msa</option>
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86 <option value="kalign_msa">kalign_msa</option>
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87 </param>
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88 <param name="method03" type="select" display="checkboxes" multiple="true" label="Pairwise Sequence Alignment Methods">
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89 <option value="fast_pair">fast_pair</option>
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90 <option value="clustalw_pair">clustalw_pair</option>
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91 <option value="lalign_id_pair">lalign_id_pair</option>
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92 <option value="slow_pair">slow_pair</option>
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93 <option value="proba_pair">proba_pair</option>
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94 </param>
2
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95 <param name="outputs" type="select" multiple="true" optional="false" display="checkboxes" label="Output formats">
0
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96 <option value="cigar">CIGAR</option>
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97 <option value="clustalw_aln">clustalw_aln</option>
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98 <option value="dnd" selected="true">dnd</option>
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99 <option value="fasta_aln">fasta_aln</option>
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100 <option value="fasta_seq">fasta_seq</option>
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101 <option value="msf_aln">msf_aln</option>
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102 <option value="phylip">phylip</option>
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103 <option value="pir_aln">pir_aln</option>
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104 <option value="pir_seq">pir_seq</option>
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105 <option value="score_ascii">score_ascii</option>
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106 <option value="score_html">score_html</option>
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107 </param>
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108 </inputs>
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109 <outputs>
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110 <data name="cigar" format="tabular" label="${tool.name} on ${on_string}: cigar" >
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111 <filter>'cigar' in outputs</filter>
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112 </data>
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113 <data name="clustalw_aln" format="clustalw" label="${tool.name} on ${on_string}: clustalw_aln" from_work_dir="t_coffee_out.clustalw_aln">
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114 <filter>'clustalw_aln' in outputs</filter>
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115 </data>
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116 <data name="dnd" format="nhx" label="${tool.name} on ${on_string}: newick.dnd" from_work_dir="t_coffee_out.dnd">
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117 <filter>'dnd' in outputs</filter>
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118 </data>
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119 <data name="fasta_aln" format="fasta" label="${tool.name} on ${on_string}: fasta_aln" from_work_dir="t_coffee_out.fasta_aln">
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120 <filter>'fasta_aln' in outputs</filter>
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121 </data>
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122 <data name="fasta_seq" format="fasta" label="${tool.name} on ${on_string}: fasta_seq" from_work_dir="t_coffee_out.fasta_seq">
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123 <filter>'fasta_seq' in outputs</filter>
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124 </data>
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125 <data name="msf_aln" format="msf" label="${tool.name} on ${on_string}: msf_aln" from_work_dir="t_coffee_out.msf_aln">
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126 <filter>'msf_aln' in outputs</filter>
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127 </data>
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128 <data name="phylip" format="phyloxml" label="${tool.name} on ${on_string}: phylip" from_work_dir="t_coffee_out.phylip">
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129 <filter>'phylip' in outputs</filter>
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130 </data>
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131 <data name="pir_aln" format="pir" label="${tool.name} on ${on_string}: pir_aln" from_work_dir="t_coffee_out.pir_aln">
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132 <filter>'pir_aln' in outputs</filter>
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133 </data>
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134 <data name="pir_seq" format="pir" label="${tool.name} on ${on_string}: pir_seq" from_work_dir="t_coffee_out.pir_seq">
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135 <filter>'pir_seq' in outputs</filter>
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136 </data>
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137 <data name="score_ascii" format="ascii" label="${tool.name} on ${on_string}: score_ascii" from_work_dir="t_coffee_out.score_ascii">
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138 <filter>'score_ascii' in outputs</filter>
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139 </data>
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140 <data name="score_html" format="html" label="${tool.name} on ${on_string}: score_html" from_work_dir="t_coffee_out.score_html">
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141 <filter>'score_html' in outputs</filter>
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142 </data>
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143 </outputs>
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144 <tests>
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145 <test>
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146 <param name="filter_fasta" value="no" />
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147 <param name="input" value="input.fasta" ftype="fasta" />
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148 <param name="method02" value="clustalw_msa" />
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149 <param name="outputs" value="fasta_aln" />
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150 <output name="fasta_aln" file="output1.fasta" />
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151 </test>
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152 <test>
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153 <param name="filter_fasta" value="yes" />
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154 <param name="fasta_input" value="input.fasta" ftype="fasta" />
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155 <param name="identifiers" value="ids.txt" ftype="txt" />
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156 <param name="method02" value="clustalw_msa" />
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157 <param name="outputs" value="cigar" />
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158 <output name="cigar" file="cigar.tabular" />
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159 </test>
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160 </tests>
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161 <help>
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162 **What it does**
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163
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164 This tool is a wrapper for the T-Coffee multiple sequence alignment suite. The input is a set of sequences in FASTA format. Apart from running on the complete FASTA input, it can also run on a subset of sequences by providing a list of the FASTA IDs.
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165
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166 This wrapper offers selected advanced T-Coffee options like the selection of the alignment methods to use: ''Pairwise Structual Method'', ''Multiple Sequence Alignment Methods'' or ''Pairwise Sequence Alignment Methods''.
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167
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168 The T-Coffee documentation can be found at http://www.tcoffee.org/Projects/tcoffee/ .
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169
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170 **Example**
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171
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172 Suppose you have 5 sequences in FASTA format::
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173
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174 >1aboA
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175 NLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPS
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176 NYITPVN
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177 >1ycsB
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178 KGVIYALWDYEPQNDDELPMKEGDCMTIIHREDEDEIEWWWARLNDKEGY
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179 VPRNLLGLYP
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180 >1pht
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181 GYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPEEIG
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182 WLNGYNETTGERGDFPGTYVEYIGRKKISP
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183 >1vie
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184 DRVRKKSGAAWQGQIVGWYCTNLTPEGYAVESEAHPGSVQIYPVAALERI
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185 N
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186 >1ihvA
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187 NFRVYYRDSRDPVWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRD
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188
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189 By selecting "Yes" in output fasta_aln in the wrapper, the user will obtain the multiple alignment in FASTA format::
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190
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191 >1aboA
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192 NL-FVA---LYDFVASGDNTLSITKGEKLR-------VLGYN-------H
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193 NGEWCEA--QTKN-GQGWVPSNYIT------PVN
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194 >1ycsB
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195 KGVIYA---LWDYEPQNDDELPMKEGDCMT-------IIHREDE-----D
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196 EIEWWWA--RLND-KEGYVPRNLLG------LYP
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197 >1pht
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198 GYQYRA---LYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPE
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199 EIGWLNGYNETTG-ERGDFPGTYVEYIGRKKISP
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200 >1vie
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201 DR-----------VRK--KSGAAWQGQIVGWYCTNLTPEGYAVE------
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202 ------S--EAHPGSVQIYPVAALE------RIN
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203 >1ihvA
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204 NF-RVYYRDSRDPVWKGPA-KLLWKGEGAV-------VIQDN-------S
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205 DI--------------KVVPRRKAK-----IIRD
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206 </help>
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207 <citations>
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208 <citation type="doi">10.1006/jmbi.2000.4042</citation>
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209 </citations>
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210 </tool>