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1 <tool id="align_seqs" name="align_seqs" version="2.0.0">
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2 <description>Align sequences using a variety of alignment methods</description>
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3 <requirements>
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4 <requirement type="binary">align_seqs.py</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 qiime_wrapper.py
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8 --galaxy_outputdir='$log.extra_files_path'
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9 --galaxy_datasets='^\S+_aligned\.\S+$:'$aligned_fasta,'^\S+_log\.txt$:'$log,'^\S+_failures\.fasta$:'$failures
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10 align_seqs.py
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11 --input_fasta_fp=$input_fasta_fp
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12 --alignment_method=$alignment_method
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13 #if $alignment_method.__str__ == 'pynast':
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14 #if $alignment.template_fp != None and $alignment.template_fp.__str__ != 'None' and $alignment.template_fp.__str__ != '':
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15 --template_fp=$alignment.template_fp
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16 #end if
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17 --pairwise_alignment_method=$pairwise_alignment_method
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18 --min_length=$min_length
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19 --min_percent_id=$min_percent_id
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20 #if $blast_db != None and $blast_db.__str__ != 'None' and $blast_db.__str__ != '':
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21 --blast_db=$blast_db
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22 #end if
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23 #elif $alignment_method.__str__ == 'infernal':
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24 --template_fp=$alignment.template_fp
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25 #end if
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26
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27 --output_dir='$log.extra_files_path'
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28 </command>
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29 <inputs>
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30 <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp" help="path to the input fasta file (usually output from pick_rep_set) [REQUIRED]"/>
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31 <param name="alignment_method" type="select" label="alignment_method"
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32 help="Method for aligning sequences. [default: pynast]">
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33 <option value="pynast" selected="true">pynast</option>
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34 <option value="infernal">infernal</option>
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35 <option value="clustalw">clustalw</option>
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36 <option value="muscle">muscle</option>
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37 <option value="mafft">mafft</option>
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38 </param>
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39 <conditional name="alignment">
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40 <param name="source" type="select" label="Select Template from" help="">
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41 <option value="hist">History</option>
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42 <option value="ref">Cached Reference</option>
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43 </param>
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44 <when value="ref">
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45 <param name="template_fp" type="select" label="template - Select an alignment database " help="">
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46 <options>
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47 <column name="name" index="0" />
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48 <column name="value" index="1" />
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49 </options>
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50 </param>
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51 </when>
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52 <when value="hist">
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53 <param name="template_fp" type="data" format="txt" label="template_fp" optional="true"
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54 help="Filepath for template against [REQUIRED ONLY if for alignment_method pynast or infernal]"/>
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55 </when>
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56 </conditional> <!--alignment-->
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57 <param name="pairwise_alignment_method" type="select" label="pairwise_alignment_method"
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58 help="Method for performing pairwise alignment; only required for PyNAST. [default: uclust]">
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59 <option value="muscle">muscle</option>
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60 <option value="pair_hmm">pair_hmm</option>
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61 <option value="clustal">clustal</option>
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62 <option value="blast">blast</option>
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63 <option value="uclust" selected="true">uclust</option>
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64 <option value="mafft">mafft</option>
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65 </param>
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66 <param name="min_length" type="integer" optional="true" value="150" label="min_length"
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67 help="Minimum sequence length to include in alignment [default: 150]"/>
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68 <param name="min_percent_id" type="float" value="0.75" optional="true" label="min_percent_id"
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69 help="Minimum percent sequence identity to closest blast hit to include sequence in alignment [default: 0.75]"/>
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70 <param name="blast_db" type="data" format="txt" label="blast_db" optional="true"
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71 help="Database to blast against when -m pynast [default: created on-the-fly from template_alignment]"/>
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72 <!-- Template alignment must be in Stockholm format with corresponding secondary structure annotation when using InfernalAligner. -->
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73
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74 </inputs>
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75 <outputs>
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76 <data format="txt" name="log" label="${tool.name} on ${on_string}: log" />
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77 <data format="fasta" name="aligned_fasta" label="${tool.name} on ${on_string}: aligned fasta" />
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78 <data format="fasta" name="failures" label="${tool.name} on ${on_string}: failures" />
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79 </outputs>
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80 <tests>
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81 </tests>
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82 <help> .. class:: warningmark
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83 Note: MUSCLE alignment is still not verified. Use at your own risk.
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84
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85 For more information, see align_seqs_ in the Qiime documentation.
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86
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87 Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA
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88
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89 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
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90
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91 .. _align_seqs: http://qiime.org/scripts/align_seqs.html</help>
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92 </tool>
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93
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