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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="alpha_rarefaction" name="alpha_rarefaction" version="1.2.0">
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2 <description>A workflow script for performing alpha rarefaction</description>
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3 <requirements>
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4 <requirement type="binary">alpha_rarefaction.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_summary_html='$output_html'
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9 --galaxy_outputdir='$output_html.extra_files_path'
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10 --galaxy_summary_template='$output_template'
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11 ## --galaxy_datasets='^rarefaction_plots.html$:'$output_html
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12 alpha_rarefaction.py
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13 --otu_table_fp=$otu_table_fp
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14 --mapping_fp=$mapping_fp
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15 --output_dir=$output_html.extra_files_path
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16 #if $parameter.source == 'hist':
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17 --parameter_fp=$parameter_fp
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18 #else:
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19 --parameter_fp=$parameter_generated
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20 #end if
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21 --num_steps=$num_steps
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22 $force
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23 $print_only
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24 $parallel
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25 #if $tree_fp != None and $tree_fp.__str__ != 'None':
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26 --tree_fp=$tree_fp
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27 #end if
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28 </command>
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29 <inputs>
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30 <param name="otu_table_fp" type="data" format="qiimeotutable" label="otu_table_fp"
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31 help="the input otu table [REQUIRED]"/>
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32 <param name="mapping_fp" type="data" format="qiimemapping" label="mapping_fp"
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33 help="path to the mapping file [REQUIRED]"/>
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34 <conditional name="parameter">
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35 <param name="source" type="select" label="Parameters from" help="">
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36 <option value="hist">Your History</option>
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37 <option value="build">Build a Parameter file</option>
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38 </param>
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39 <when value="hist">
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40 <param name="parameter_fp" type="data" format="qiimeparams" label="parameter_fp"
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41 help="path to the parameter file [REQUIRED]"/>
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42 </when> <!-- hist -->
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43 <when value="build">
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44 <!--
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45 params['alpha_diversity']['metrics'].split(',')
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46 params['multiple_rarefactions']
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47 params['parallel'])
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48 params['alpha_diversity'])
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49 params['collate_alpha']
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50 params['make_rarefaction_plots']
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51 multiple_rarefactions.py
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52 min seqs/sample
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53 max seqs/sample
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54 step
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55 depth sequences per sample to subsample
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56 num-reps
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57 lineages_included
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58 keep_empty_otus
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59 alpha_diversity.py
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60 collate_alpha.py
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61 make_rarefaction_plots.py
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62 -->
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63 </when> <!-- build -->
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64 </conditional> <!-- parameter -->
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65 <param name="num_steps" type="integer" value="10" label="num_steps"
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66 help="number of steps (or rarefied OTU table sizes) to make between min and max counts [default: 10]"/>
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67 <param name="force" type="boolean" truevalue="--force" falsevalue="" checked="false" label="force"
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68 help="Force overwrite of existing output directory (note: existing files in output_dir will not be removed) [default: ('NO', 'DEFAULT')]"/>
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69 <param name="print_only" type="boolean" truevalue="--print_only" falsevalue="" checked="false" label="print_only"
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70 help="Print the commands but don't call them -- useful for debugging [default: False]"/>
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71 <param name="parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="false" label="parallel"
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72 help="Run in parallel where available [default: False]"/>
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73 <param name="tree_fp" type="data" format="txt" optional="true" label="tree_fp"
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74 help="path to the tree file [default: REQUIRED for phylogenetic measures]"/>
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75 </inputs>
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76 <configfiles>
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77 <configfile name="parameter_generated">
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78 alpha_diversity:metrics chao1,observed_species,PD_whole_tree
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79 multiple_rarefactions_even_depth:num-reps 20
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80 parallel:jobs_to_start 2
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81 parallel:retain_temp_files False
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82 parallel:seconds_to_sleep 60
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83 collate_alpha:example_path
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84 make_rarefaction_plots:imagetype png
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85 make_rarefaction_plots:resolution 75
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86 make_rarefaction_plots:background_color white
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87 make_rarefaction_plots:prefs_path
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88 </configfile>
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89 <configfile name="output_template">
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90 <![CDATA[
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91 <html>
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92 <body>
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93 <a href="rarefaction_plots.html">rarefaction_plots.html</a>
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94 </body>
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95 </html>
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96 ]]>
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97 </configfile>
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98 </configfiles>
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99 <outputs>
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100 <data format="html" name="output_html" label="alpha_rarefaction_plots"/>
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101 </outputs>
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102 <tests>
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103 </tests>
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104 <help>
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105
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106 </help>
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107 </tool>
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108