Mercurial > repos > earlhaminst > t_coffee

annotate t_coffee.xml @ 9:e3507be607eb draft default tip

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/t_coffee commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
author earlhaminst
date Mon, 24 Feb 2025 11:00:35 +0000
parents ae69d14b6fbf
children
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ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
earlhaminst
parents: 7
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1 <tool id="t_coffee" name="T-Coffee" version="@TOOL_VERSION@">
0
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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2 <description>multiple sequence alignment</description>
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ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
earlhaminst
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3 <macros>
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
earlhaminst
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4 <token name="@TOOL_VERSION@">13.45.0.4846264</token>
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
earlhaminst
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5 </macros>
0
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6 <requirements>
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ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
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7 <requirement type="package" version="@TOOL_VERSION@">t-coffee</requirement>
0
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8 </requirements>
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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9 <stdio>
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10 <exit_code range="1:" level="fatal" />
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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11 </stdio>
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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12 <version_command>
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13 t_coffee -version | grep Version
0
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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14 </version_command>
7
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15 <command use_shared_home="false"><![CDATA[
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
earlhaminst
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16 #if str($input_type.filter_fasta) == 'yes'
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
earlhaminst
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17 #set $input = 'temp.fasta'
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
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18 python '$__tool_directory__/filter_by_fasta_ids.py' '$input_type.identifiers' '$input_type.fasta_input' > temp.fasta &&
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
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19 #end if
0
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20
7
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21 #set $method_opt = ''
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
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22 #if $method01
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
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23 #set $method_opt += str($method01) + ','
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
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24 #end if
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
earlhaminst
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25 #if $method02
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
earlhaminst
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26 #set $method_opt += str($method02) + ','
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
earlhaminst
parents: 6
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27 #end if
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
earlhaminst
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28 #if $method03
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
earlhaminst
parents: 6
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29 #set $method_opt += str($method03) + ','
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
earlhaminst
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30 #end if
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
earlhaminst
parents: 6
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31 #if $method_opt
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
earlhaminst
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32 #set $method_opt = '-method ' + $method_opt[:-1]
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
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33 #end if
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
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34
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35 #set $output_opt = ''
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
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36 #if $outputs
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
earlhaminst
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37 #set $outputs_arr = str($outputs).split(',')
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
earlhaminst
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38 #for $o in $outputs_arr
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
earlhaminst
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39 #if $o != 'dnd'
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
earlhaminst
parents: 6
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40 #set $output_opt += $o + ','
0
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41 #end if
7
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42 #end for
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43 #else
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
earlhaminst
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44 #set $outputs_arr = []
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45 #end if
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
earlhaminst
parents: 6
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46 #if $output_opt
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
earlhaminst
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47 #set $output_opt = '-output ' + $output_opt[:-1]
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48 #end if
0
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49
7
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50 t_coffee '$input' $method_opt $output_opt -n_core \${GALAXY_SLOTS:-1} -run_name t_coffee_out -quiet
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
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51 ]]></command>
0
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52 <inputs>
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53 <conditional name="input_type">
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54 <param name="filter_fasta" type="select" label="Filter FASTA input?">
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55 <option value="no">No</option>
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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56 <option value="yes">Yes</option>
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57 </param>
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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58 <when value="yes">
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59 <param name="fasta_input" type="data" format="fasta" label="FASTA sequences" />
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60 <param name="identifiers" type="data" format="txt" label="List of FASTA sequence IDs" />
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61 </when>
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62 <when value="no">
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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63 <param name="input" type="data" format="fasta" label="FASTA sequences" />
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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64 </when>
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
earlhaminst
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65 </conditional>
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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66 <param name="method03" type="select" display="checkboxes" multiple="true" label="Pairwise Sequence Alignment Methods">
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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67 <option value="fast_pair">fast_pair</option>
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68 <option value="clustalw_pair">clustalw_pair</option>
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69 <option value="lalign_id_pair">lalign_id_pair</option>
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70 <option value="slow_pair">slow_pair</option>
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71 <option value="proba_pair">proba_pair</option>
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ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
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72 <option value="t_coffee_pair">t_coffee_pair</option>
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
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73 </param>
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
earlhaminst
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74 <param name="method01" type="select" display="checkboxes" multiple="true" label="Pairwise Structual Alignment Methods">
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
earlhaminst
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75 <option value="sap_pair">sap_pair</option>
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
earlhaminst
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76 <option value="mustang_pair">mustang_pair</option>
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
earlhaminst
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77 <option value="TMalign_pair">TMalign_pair</option>
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
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78 </param>
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
earlhaminst
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79 <param name="method02" type="select" display="checkboxes" multiple="true" label="Multiple Sequence Alignment Methods">
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
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80 <option value="3dcoffee_msa">3dcoffee_msa</option>
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
earlhaminst
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81 <option value="mafft_msa">mafft_msa</option>
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
earlhaminst
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82 <option value="clustalw_msa">clustalw_msa</option>
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
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83 <option value="dialigntx_msa">dialigntx_msa</option>
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
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84 <option value="poa_msa">poa_msa</option>
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85 <option value="probcons_msa">probcons_msa</option>
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86 <option value="muscle_msa">muscle_msa</option>
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87 <option value="t_coffee_msa">t_coffee_msa</option>
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88 <option value="kalign_msa">kalign_msa</option>
0
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89 </param>
9
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90 <param name="outputs" type="select" multiple="true" optional="false" label="Output formats">
0
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91 <option value="clustalw_aln">clustalw_aln</option>
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92 <option value="dnd" selected="true">dnd</option>
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93 <option value="fasta_aln">fasta_aln</option>
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94 <option value="fasta_seq">fasta_seq</option>
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95 <option value="msf_aln">msf_aln</option>
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96 <option value="phylip">phylip</option>
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97 <option value="pir_aln">pir_aln</option>
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98 <option value="pir_seq">pir_seq</option>
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99 <option value="score_ascii">score_ascii</option>
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100 <option value="score_html">score_html</option>
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101 </param>
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102 </inputs>
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103 <outputs>
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104 <data name="clustalw_aln" format="clustal" label="${tool.name} on ${on_string}: clustalw_aln" from_work_dir="t_coffee_out.clustalw_aln">
0
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105 <filter>'clustalw_aln' in outputs</filter>
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106 </data>
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107 <data name="dnd" format="nhx" label="${tool.name} on ${on_string}: newick.dnd" from_work_dir="t_coffee_out.dnd">
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108 <filter>'dnd' in outputs</filter>
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109 </data>
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110 <data name="fasta_aln" format="fasta" label="${tool.name} on ${on_string}: fasta_aln" from_work_dir="t_coffee_out.fasta_aln">
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111 <filter>'fasta_aln' in outputs</filter>
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112 </data>
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113 <data name="fasta_seq" format="fasta" label="${tool.name} on ${on_string}: fasta_seq" from_work_dir="t_coffee_out.fasta_seq">
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114 <filter>'fasta_seq' in outputs</filter>
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115 </data>
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116 <data name="msf_aln" format="msf" label="${tool.name} on ${on_string}: msf_aln" from_work_dir="t_coffee_out.msf_aln">
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117 <filter>'msf_aln' in outputs</filter>
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118 </data>
8
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119 <data name="phylip" format="phylip" label="${tool.name} on ${on_string}: phylip" from_work_dir="t_coffee_out.phylip">
0
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120 <filter>'phylip' in outputs</filter>
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121 </data>
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122 <data name="pir_aln" format="pir" label="${tool.name} on ${on_string}: pir_aln" from_work_dir="t_coffee_out.pir_aln">
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123 <filter>'pir_aln' in outputs</filter>
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124 </data>
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125 <data name="pir_seq" format="pir" label="${tool.name} on ${on_string}: pir_seq" from_work_dir="t_coffee_out.pir_seq">
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126 <filter>'pir_seq' in outputs</filter>
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127 </data>
8
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128 <data name="score_ascii" format="txt" label="${tool.name} on ${on_string}: score_ascii" from_work_dir="t_coffee_out.score_ascii">
0
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129 <filter>'score_ascii' in outputs</filter>
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130 </data>
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131 <data name="score_html" format="html" label="${tool.name} on ${on_string}: score_html" from_work_dir="t_coffee_out.score_html">
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132 <filter>'score_html' in outputs</filter>
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133 </data>
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134 </outputs>
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135 <tests>
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136 <test expect_num_outputs="1">
0
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137 <param name="filter_fasta" value="no" />
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138 <param name="input" value="input.fasta" ftype="fasta" />
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139 <param name="method02" value="clustalw_msa" />
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140 <param name="outputs" value="fasta_aln" />
8
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141 <output name="fasta_aln" file="output1.fasta" />
0
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142 </test>
8
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143 <test expect_num_outputs="1">
0
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144 <param name="filter_fasta" value="yes" />
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145 <param name="fasta_input" value="input.fasta" ftype="fasta" />
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146 <param name="identifiers" value="ids.txt" ftype="txt" />
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147 <param name="method02" value="clustalw_msa" />
3
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148 <param name="outputs" value="fasta_aln" />
8
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149 <output name="fasta_aln" file="output2.fasta" />
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150 </test>
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151 <!-- Test all non-builtin methods and all outputs -->
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152 <test expect_num_outputs="10">
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153 <param name="filter_fasta" value="no" />
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154 <param name="input" value="input.fasta" ftype="fasta" />
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155 <param name="method03" value="clustalw_pair,t_coffee_pair" />
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156 <param name="method01" value="sap_pair,mustang_pair,TMalign_pair" />
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157 <param name="method02" value="mafft_msa,clustalw_msa,dialigntx_msa,poa_msa,probcons_msa,muscle_msa,t_coffee_msa,kalign_msa" />
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
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158 <param name="outputs" value="clustalw_aln,dnd,fasta_aln,fasta_seq,msf_aln,phylip,pir_aln,pir_seq,score_ascii,score_html" />
9
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159 <output name="clustalw_aln">
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160 <assert_contents>
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161 <has_size size="44953" delta="1000" />
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162 </assert_contents>
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163 </output>
8
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
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164 <output name="dnd" file="output3.nhx" />
9
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165 <output name="fasta_aln">
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166 <assert_contents>
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167 <has_size size="21797" delta="500" />
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168 </assert_contents>
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169 </output>
8
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170 <output name="fasta_seq" file="output3.fasta_seq" />
9
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171 <output name="msf_aln">
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172 <assert_contents>
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173 <has_size size="41823" delta="1000" />
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174 </assert_contents>
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175 </output>
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176 <output name="phylip">
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177 <assert_contents>
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178 <has_size size="27310" delta="600" />
e3507be607eb planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/t_coffee commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
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179 </assert_contents>
e3507be607eb planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/t_coffee commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
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180 </output>
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181 <output name="pir_aln">
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182 <assert_contents>
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183 <has_size size="21827" delta="500" />
e3507be607eb planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/t_coffee commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
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184 </assert_contents>
e3507be607eb planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/t_coffee commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
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185 </output>
8
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
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186 <output name="pir_seq" file="output3.pir_seq" />
9
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187 <output name="score_ascii">
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188 <assert_contents>
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189 <has_size size="42613" delta="1000" />
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190 </assert_contents>
e3507be607eb planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/t_coffee commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
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191 </output>
8
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
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192 <output name="score_html">
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
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193 <assert_contents>
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
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194 <has_text text="ENSMUST00000091" />
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
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195 <has_text text="ENSCAFT00000026" />
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
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196 <has_text text="ENSMUST00000005" />
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
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197 <has_text text="ENSRNOT00000019" />
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
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198 <has_text text="ENSPTRT00000013" />
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
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199 </assert_contents>
ae69d14b6fbf "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
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200 </output>
0
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201 </test>
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202 </tests>
7
0a189243186d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
earlhaminst
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203 <help><![CDATA[
0
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earlhaminst
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204 **What it does**
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205
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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206 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.
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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207
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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208 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''.
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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209
9
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210 The T-Coffee documentation can be found at https://tcoffee.org/Projects/tcoffee/index.html .
0
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211
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212 **Example**
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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213
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214 Suppose you have 5 sequences in FASTA format::
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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215
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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216 >1aboA
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
earlhaminst
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217 NLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPS
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
earlhaminst
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218 NYITPVN
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219 >1ycsB
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
earlhaminst
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220 KGVIYALWDYEPQNDDELPMKEGDCMTIIHREDEDEIEWWWARLNDKEGY
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
earlhaminst
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221 VPRNLLGLYP
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
earlhaminst
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222 >1pht
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
earlhaminst
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223 GYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPEEIG
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
earlhaminst
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224 WLNGYNETTGERGDFPGTYVEYIGRKKISP
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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225 >1vie
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
earlhaminst
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226 DRVRKKSGAAWQGQIVGWYCTNLTPEGYAVESEAHPGSVQIYPVAALERI
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
earlhaminst
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227 N
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228 >1ihvA
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
earlhaminst
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229 NFRVYYRDSRDPVWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRD
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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230
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231 By selecting "Yes" in output fasta_aln in the wrapper, the user will obtain the multiple alignment in FASTA format::
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232
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233 >1aboA
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234 NL-FVA---LYDFVASGDNTLSITKGEKLR-------VLGYN-------H
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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235 NGEWCEA--QTKN-GQGWVPSNYIT------PVN
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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236 >1ycsB
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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237 KGVIYA---LWDYEPQNDDELPMKEGDCMT-------IIHREDE-----D
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
earlhaminst
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238 EIEWWWA--RLND-KEGYVPRNLLG------LYP
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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239 >1pht
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
earlhaminst
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240 GYQYRA---LYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPE
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
earlhaminst
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241 EIGWLNGYNETTG-ERGDFPGTYVEYIGRKKISP
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
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242 >1vie
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
earlhaminst
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243 DR-----------VRK--KSGAAWQGQIVGWYCTNLTPEGYAVE------
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
earlhaminst
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244 ------S--EAHPGSVQIYPVAALE------RIN
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245 >1ihvA
794a6e864a96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
earlhaminst
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246 NF-RVYYRDSRDPVWKGPA-KLLWKGEGAV-------VIQDN-------S
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247 DI--------------KVVPRRKAK-----IIRD
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248 ]]></help>
0
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249 <citations>
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250 <citation type="doi">10.1006/jmbi.2000.4042</citation>
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251 </citations>
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252 </tool>