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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="pick_otus_through_otu_table" name="pick_otus_through_otu_table" version="1.2.0">
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2 <description>A workflow script for picking OTUs through building OTU tables</description>
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3 <requirements>
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4 <requirement type="binary">pick_otus_through_otu_table.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='$log.extra_files_path'
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9 --galaxy_datasets='^log_\S+\.txt$:'$log,'^\S+_otus.txt$:'$seqs_otus,'^\S+_rep_set.fasta$:'$seqs_rep_set,'^\S+_rep_set_tax_assignments.txt$:'$seqs_rep_set_tax_assignments,'^\S+_otu_table.txt$:'$seqs_otu_table,'^\S+_rep_set_aligned.fasta$:'$seqs_rep_set_aligned,'^\S+_rep_set_aligned_pfiltered.fasta$:'$seqs_rep_set_aligned_pfiltered,'^\S+_rep_set.tre$:'$seqs_rep_set_tre
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10 pick_otus_through_otu_table.py
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11 --input_fp=$input_fp
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12 #if $parameter.source == 'hist':
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13 --parameter_fp=$parameter.parameter_fp
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14 #else:
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15 --parameter_fp=$parameter_generated
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16 #end if
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17 #if $denoise.choice == 'yes':
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18 --sff_fp=$denoise.sff_fp
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19 --mapping_fp=$denoise.mapping_fp
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20 #end if
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21 --output_dir='$log.extra_files_path'
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22 --force
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23 $parallel
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24 </command>
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25 <inputs>
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26 <param name="input_fp" type="data" format="fasta" label="input_fp"
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27 help="the input fasta file [REQUIRED]"/>
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28 <conditional name="parameter">
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29 <param name="source" type="select" label="Grouping Design from" help="">
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30 <option value="hist">Your History</option>
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31 <option value="build">Build a grouping design</option>
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32 </param>
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33 <when value="hist">
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34 <param name="parameter_fp" type="data" format="qiimeparams" label="parameter_fp"
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35 help="path to the parameter file [REQUIRED]"/>
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36 </when> <!-- hist -->
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37 <when value="build">
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38 </when> <!-- build -->
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39 </conditional> <!-- parameter -->
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40 <conditional name="denoise">
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41 <param name="choice" type="select" label="Denoise (requires sff flowgram and a mapping faile)" help="">
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42 <option value="no">No</option>
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43 <option value="yes">Yes</option>
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44 </param>
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45 <when value="yes">
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46 <param name="sff_fp" type="data" format="ssf" label="sff_fp"
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47 help="the sff flowgram file [REQUIRED for denoising]"/>
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48 <param name="mapping_fp" type="data" format="qiimemapping" label="mapping_fp"
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49 help="the mapping filepath [REQUIRED for denoising]"/>
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50 </when> <!-- hist -->
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51 <when value="no"/>
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52 </conditional> <!-- denoise -->
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53 <param name="parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="false" label="parallel"
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54 help="Run in parallel where available [default: False]"/>
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55 </inputs>
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56 <!-- Construct a parameter file
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57 -->
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58 <configfiles>
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59 <configfile name="parameter_generated">
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60 ##OTU picker parameters
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61 pick_otus:otu_picking_method uclust
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62 pick_otus:clustering_algorithm furthest
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63 pick_otus:max_cdhit_memory 400
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64 pick_otus:refseqs_fp
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65 pick_otus:blast_db
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66 pick_otus:similarity 0.97
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67 pick_otus:max_e_value 1e-10
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68 pick_otus:prefix_prefilter_length
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69 pick_otus:trie_prefilter
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70 pick_otus:prefix_length
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71 pick_otus:suffix_length
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72 pick_otus:optimal_uclust
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73 pick_otus:exact_uclust
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74 pick_otus:user_sort
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75 pick_otus:suppress_presort_by_abundance_uclust
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76 pick_otus:suppress_new_clusters
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77 pick_otus:suppress_uclust_stable_sort
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78 pick_otus:max_accepts
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79 pick_otus:max_rejects
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80 pick_otus:word_length
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81 pick_otus:stepwords
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82 ##Representative set picker parameters
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83 pick_rep_set:rep_set_picking_method first
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84 pick_rep_set:sort_by otu
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85 ##Multiple sequence alignment parameters
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86 align_seqs:template_fp
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87 align_seqs:alignment_method pynast
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88 align_seqs:pairwise_alignment_method uclust
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89 align_seqs:blast_db
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90 align_seqs:min_length 150
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91 align_seqs:min_percent_id 75.0
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92 ##Alignment filtering (prior to tree-building) parameters
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93 filter_alignment:lane_mask_fp
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94 filter_alignment:allowed_gap_frac 0.999999
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95 filter_alignment:remove_outliers False
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96 filter_alignment:threshold 3.0
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97 ##Taxonomy assignment parameters
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98 assign_taxonomy:id_to_taxonomy_fp
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99 assign_taxonomy:reference_seqs_fp
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100 assign_taxonomy:assignment_method rdp
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101 assign_taxonomy:blast_db
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102 assign_taxonomy:confidence 0.8
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103 #assign_taxonomy:e_value 0.001
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104 ##Phylogenetic tree building parameters
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105 make_phylogeny:tree_method fasttree
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106 make_phylogeny:root_method tree_method_default
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107 ##align_seqs:template_fp
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108 ##filter_alignment:lane_mask_fp
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109 </configfile>
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110 </configfiles>
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111 <outputs>
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112 <!--
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113 This script will produce a set of cluster centroids (as a FASTA file)
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114 and a cluster mapping file (from denoise.py if sff.txt and mapping file were provided),
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115 an OTU mapping file (pick_otus.py),
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116 a representative set of sequences (FASTA file from pick_rep_set.py),
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117 a sequence alignment file (FASTA file from align_seqs.py),
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118 taxonomy assignment file (from assign_taxonomy.py),
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119 a filtered sequence alignment (from filter_alignment.py),
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120 a phylogenetic tree (Newick file from make_phylogeny.py) and an OTU table (from make_otu_table.py).
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121
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122 wf_da2/log_20110305084135.txt
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123 wf_da2/uclust_picked_otus/seqs_otus.txt
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124 wf_da/uclust_picked_otus/rep_set/seqs_rep_set.fasta
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125 wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/seqs_rep_set_tax_assignments.txt
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126 wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table//seqs_otu_table.txt
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127 wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/seqs_rep_set_aligned.fasta
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128 wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/seqs_rep_set_aligned_pfiltered.fasta
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129 wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set.tre
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130
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131
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132 wf_da2/log_20110305084135.txt
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133 wf_da2/uclust_picked_otus/rep_set/pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set.tre
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134 wf_da2/uclust_picked_otus/rep_set/pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set_phylogeny.log
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135 wf_da2/uclust_picked_otus/rep_set/pynast_aligned_seqs/seqs_rep_set_aligned.fasta
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136 wf_da2/uclust_picked_otus/rep_set/pynast_aligned_seqs/seqs_rep_set_aligned_pfiltered.fasta
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137 wf_da2/uclust_picked_otus/rep_set/pynast_aligned_seqs/seqs_rep_set_failures.fasta
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138 wf_da2/uclust_picked_otus/rep_set/pynast_aligned_seqs/seqs_rep_set_log.txt
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139 wf_da2/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table/seqs_otu_table.txt
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140 wf_da2/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/seqs_rep_set_tax_assignments.log
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141 wf_da2/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/seqs_rep_set_tax_assignments.txt
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142 wf_da2/uclust_picked_otus/rep_set/seqs_rep_set.fasta
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143 wf_da2/uclust_picked_otus/rep_set/seqs_rep_set.log
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144 wf_da2/uclust_picked_otus/seqs_clusters.uc
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145 wf_da2/uclust_picked_otus/seqs_otus.log
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146 wf_da2/uclust_picked_otus/seqs_otus.txt
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147
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148 wf_da2/log_20110305084135.txt
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149 wf_da2/uclust_picked_otus/seqs_otus.txt
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150 wf_da/uclust_picked_otus/rep_set/seqs_rep_set.fasta
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151 wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/seqs_rep_set_tax_assignments.txt
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152 wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table/seqs_otu_table.txt
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153 wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/seqs_rep_set_aligned.fasta
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154 wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/seqs_rep_set_aligned_pfiltered.fasta
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155 wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set.tre
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156 -->
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157 <data format="txt" name="log" label="${tool.name} on ${on_string}: log" />
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158 <data format="qiimeotu" name="seqs_otus" label="${tool.name} on ${on_string}: seqs_otus" />
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159 <data format="fasta" name="seqs_rep_set" label="${tool.name} on ${on_string}: seqs_rep_set.fasta" />
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160 <data format="seq.taxonomy" name="seqs_rep_set_tax_assignments" label="${tool.name} on ${on_string}: seqs_rep_set_tax_assignments" />
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161 <data format="qiimeotutable" name="seqs_otu_table" label="${tool.name} on ${on_string}: seqs_otu_table" />
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162 <data format="align" name="seqs_rep_set_aligned" label="${tool.name} on ${on_string}: seqs_rep_set_aligned.fasta" />
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163 <data format="align" name="seqs_rep_set_aligned_pfiltered" label="${tool.name} on ${on_string}: seqs_rep_set_aligned_pfiltered.fasta" />
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164 <data format="tre" name="seqs_rep_set_tre" label="${tool.name} on ${on_string}: seqs_rep_set.tre" />
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165
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166
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167 </outputs>
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168 <tests>
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169 </tests>
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170 <help>
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171
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172 The steps performed by this function are:
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173 0) Optionally denoise the sequences (if sff_input_fp=True);
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174 1) Pick OTUs;
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175 2) Pick a representative set;
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176 3) Align the representative set;
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177 4) Assign taxonomy;
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178 5) Filter the alignment prior to tree building - remove positions
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179 which are all gaps, and specified as 0 in the lanemask
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180 6) Build a phylogenetic tree;
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181 7) Build an OTU table.
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182
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183
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184 pick_otus_through_otu_table.py -i split_library_output/seqs.fna -p custom_parameters.txt -o wf_da --print_only
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185
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186 python /usr/local/bin/pick_otus.py -i split_library_output/seqs.fna -o wf_da/uclust_picked_otus --max_e_value 1e-10 --clustering_algorithm furthest --similarity 0.97 --otu_picking_method uclust --max_cdhit_memory 400
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187
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188 python /usr/local/bin/pick_rep_set.py -i wf_da/uclust_picked_otus/seqs_otus.txt -f split_library_output/seqs.fna -l wf_da/uclust_picked_otus/rep_set//seqs_rep_set.log -o wf_da/uclust_picked_otus/rep_set//seqs_rep_set.fasta --rep_set_picking_method first --sort_by otu
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189
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190 python /usr/local/bin/assign_taxonomy.py -o wf_da/uclust_picked_otus/rep_set//rdp_assigned_taxonomy -i wf_da/uclust_picked_otus/rep_set//seqs_rep_set.fasta --confidence 0.8 --assignment_method rdp
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191
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192 python /usr/local/bin/make_otu_table.py -i wf_da/uclust_picked_otus/seqs_otus.txt -t wf_da/uclust_picked_otus/rep_set//rdp_assigned_taxonomy/seqs_rep_set_tax_assignments.txt -o wf_da/uclust_picked_otus/rep_set//rdp_assigned_taxonomy/otu_table//seqs_otu_table.txt
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193
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194 python /usr/local/bin/align_seqs.py -i wf_da/uclust_picked_otus/rep_set//seqs_rep_set.fasta -o wf_da/uclust_picked_otus/rep_set//pynast_aligned_seqs --alignment_method pynast --pairwise_alignment_method uclust --min_percent_id 75.0 --min_length 150
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195
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196 python /usr/local/bin/filter_alignment.py -o wf_da/uclust_picked_otus/rep_set//pynast_aligned_seqs -i wf_da/uclust_picked_otus/rep_set//pynast_aligned_seqs/seqs_rep_set_aligned.fasta --allowed_gap_frac 0.999999 --threshold 3.0
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197
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198 python /usr/local/bin/make_phylogeny.py -i wf_da/uclust_picked_otus/rep_set//pynast_aligned_seqs/seqs_rep_set_aligned_pfiltered.fasta -o wf_da/uclust_picked_otus/rep_set//pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set.tre -l wf_da/uclust_picked_otus/rep_set//pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set_phylogeny.log --root_method tree_method_default --tree_method fasttree
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199
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200
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201 </help>
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202 </tool>
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203