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Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
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1 <tool id="align_seqs" name="align_seqs" version="1.2.0">
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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=$align.alignment_method
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13 #if $align.alignment_method == 'pynast':
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14 --template_fp=$align.alignment.template_fp
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15 --pairwise_alignment_method=$align.pairwise_alignment_method
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16 --min_length=$align.min_length
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17 --min_percent_id=$align.min_percent_id
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18 --blast_db=$align.blast_db
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19 #elif $align.alignment_method == 'infernal':
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20 --template_fp=$align.alignment.template_fp
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21 #elif $align.alignment_method == 'clustalw':
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22 #echo ''
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23 #elif $align.alignment_method == 'muscle':
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24 #echo ''
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25 #elif $align.alignment_method == 'mafft':
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26 #echo ''
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27 #end if
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28
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29 --output_dir='$log.extra_files_path'
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30 </command>
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31 <inputs>
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32 <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
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33 help="path to the input fasta file [REQUIRED]"/>
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34
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35 <conditional name="align">
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36 <param name="alignment_method" type="select" label="alignment_method"
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37 help="Method for aligning sequences. Valid choices are: pynast, infernal, clustalw, muscle, infernal, mafft [default: pynast]">
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38 <option value="pynast" selected="true">pynast</option>
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39 <option value="infernal">infernal</option>
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40 <option value="clustalw">clustalw</option>
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41 <option value="muscle">muscle</option>
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42 <option value="mafft">mafft</option>
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43 </param>
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44
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45 <when value="pynast">
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46 <conditional name="alignment">
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47 <param name="source" type="select" label="Select Template from" help="">
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48 <option value="hist">History</option>
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49 <option value="ref">Cached Reference</option>
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50 </param>
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51 <when value="ref">
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52 <param name="template_fp" type="select" label="template - Select an alignment database " help="">
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53 <options from_file="mothur_aligndb.loc">
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54 <column name="name" index="0" />
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55 <column name="value" index="1" />
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56 </options>
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57 </param>
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58 </when>
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59 <when value="hist">
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60 <param name="template_fp" type="data" format="txt" label="template_fp"
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61 help="Filepath for template against [REQUIRED if for alignment_method pynast or infernal]"/>
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62 </when>
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63 </conditional>
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64 <param name="pairwise_alignment_method" type="select" label="pairwise_alignment_method"
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65 help="method for performing pairwise alignment in PyNAST. Valid choices are muscle, pair_hmm, clustal, blast, uclust, mafft [default: uclust]">
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66 <option value="muscle">muscle</option>
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67 <option value="pair_hmm">pair_hmm</option>
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68 <option value="clustal">clustal</option>
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69 <option value="blast">blast</option>
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70 <option value="uclust" selected="true">uclust</option>
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71 <option value="mafft">mafft</option>
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72 </param>
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73 <param name="min_length" type="integer" value="150" label="min_length"
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74 help="Minimum sequence length to include in alignment [default: 150]"/>
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75 <param name="min_percent_id" type="float" value="0.75" label="min_percent_id"
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76 help="Minimum percent sequence identity to closest blast hit to include sequence in alignment [default: 0.75]"/>
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77 <param name="blast_db" type="text" label="blast_db" optional="true"
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78 help="Database to blast against when -m pynast [default: created on-the-fly from template_alignment]"/>
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79 </when> <!-- pynast -->
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80
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81 <when value="infernal">
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82 <!-- Template alignment must be in Stockholm format with corresponding secondary structure annotation when using InfernalAligner. -->
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83 <conditional name="alignment">
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84 <param name="source" type="select" label="Select Template from" help="">
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85 <option value="hist">History</option>
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86 <option value="ref">Cached Reference</option>
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87 </param>
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88 <when value="ref">
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89 <param name="template_fp" type="select" label="template - Select an alignment database " help="">
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90 <options from_file="mothur_aligndb.loc">
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91 <column name="name" index="0" />
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92 <column name="value" index="1" />
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93 </options>
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94 </param>
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95 </when>
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96 <when value="hist">
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97 <param name="template_fp" type="data" format="txt" label="template_fp"
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98 help="Filepath for template against [REQUIRED if for alignment_method pynast or infernal]"/>
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99 </when>
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100 </conditional>
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101 </when> <!-- infernal -->
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102
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103 <when value="clustalw">
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104 </when> <!-- clustalw -->
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105 <when value="muscle">
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106 </when> <!-- muscle -->
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107 <when value="mafft">
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108 </when> <!-- mafft -->
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109
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110 </conditional> <!-- align -->
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111
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112
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113 </inputs>
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114 <outputs>
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115 <data format="txt" name="log" label="${tool.name} on ${on_string}: log" />
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116 <data format="fasta" name="aligned_fasta" label="${tool.name} on ${on_string}: aligned fasta" />
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117 <data format="fasta" name="failures" label="${tool.name} on ${on_string}: failures" >
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118 <filter>align['alignment_method'] == 'pynast'</filter>
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119 </data>
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120 </outputs>
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121 <tests>
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122 </tests>
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123 <help>
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124
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125 </help>
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126 </tool>
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127