Mercurial > repos > jjohnson > qiime
comparison alpha_rarefaction.xml @ 0:e5c3175506b7 default tip
Initial tool configs for qiime, most need work.
| author | Jim Johnson <jj@umn.edu> |
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| date | Sun, 17 Jul 2011 10:30:11 -0500 |
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| -1:000000000000 | 0:e5c3175506b7 |
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| 1 <tool id="alpha_rarefaction" name="alpha_rarefaction" version="1.2.0"> | |
| 2 <description>A workflow script for performing alpha rarefaction</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">alpha_rarefaction.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 --galaxy_summary_html='$output_html' | |
| 9 --galaxy_outputdir='$output_html.extra_files_path' | |
| 10 --galaxy_summary_template='$output_template' | |
| 11 ## --galaxy_datasets='^rarefaction_plots.html$:'$output_html | |
| 12 alpha_rarefaction.py | |
| 13 --otu_table_fp=$otu_table_fp | |
| 14 --mapping_fp=$mapping_fp | |
| 15 --output_dir=$output_html.extra_files_path | |
| 16 #if $parameter.source == 'hist': | |
| 17 --parameter_fp=$parameter_fp | |
| 18 #else: | |
| 19 --parameter_fp=$parameter_generated | |
| 20 #end if | |
| 21 --num_steps=$num_steps | |
| 22 $force | |
| 23 $print_only | |
| 24 $parallel | |
| 25 #if $tree_fp != None and $tree_fp.__str__ != 'None': | |
| 26 --tree_fp=$tree_fp | |
| 27 #end if | |
| 28 </command> | |
| 29 <inputs> | |
| 30 <param name="otu_table_fp" type="data" format="qiimeotutable" label="otu_table_fp" | |
| 31 help="the input otu table [REQUIRED]"/> | |
| 32 <param name="mapping_fp" type="data" format="qiimemapping" label="mapping_fp" | |
| 33 help="path to the mapping file [REQUIRED]"/> | |
| 34 <conditional name="parameter"> | |
| 35 <param name="source" type="select" label="Parameters from" help=""> | |
| 36 <option value="hist">Your History</option> | |
| 37 <option value="build">Build a Parameter file</option> | |
| 38 </param> | |
| 39 <when value="hist"> | |
| 40 <param name="parameter_fp" type="data" format="qiimeparams" label="parameter_fp" | |
| 41 help="path to the parameter file [REQUIRED]"/> | |
| 42 </when> <!-- hist --> | |
| 43 <when value="build"> | |
| 44 <!-- | |
| 45 params['alpha_diversity']['metrics'].split(',') | |
| 46 params['multiple_rarefactions'] | |
| 47 params['parallel']) | |
| 48 params['alpha_diversity']) | |
| 49 params['collate_alpha'] | |
| 50 params['make_rarefaction_plots'] | |
| 51 multiple_rarefactions.py | |
| 52 min seqs/sample | |
| 53 max seqs/sample | |
| 54 step | |
| 55 depth sequences per sample to subsample | |
| 56 num-reps | |
| 57 lineages_included | |
| 58 keep_empty_otus | |
| 59 alpha_diversity.py | |
| 60 collate_alpha.py | |
| 61 make_rarefaction_plots.py | |
| 62 --> | |
| 63 </when> <!-- build --> | |
| 64 </conditional> <!-- parameter --> | |
| 65 <param name="num_steps" type="integer" value="10" label="num_steps" | |
| 66 help="number of steps (or rarefied OTU table sizes) to make between min and max counts [default: 10]"/> | |
| 67 <param name="force" type="boolean" truevalue="--force" falsevalue="" checked="false" label="force" | |
| 68 help="Force overwrite of existing output directory (note: existing files in output_dir will not be removed) [default: ('NO', 'DEFAULT')]"/> | |
| 69 <param name="print_only" type="boolean" truevalue="--print_only" falsevalue="" checked="false" label="print_only" | |
| 70 help="Print the commands but don't call them -- useful for debugging [default: False]"/> | |
| 71 <param name="parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="false" label="parallel" | |
| 72 help="Run in parallel where available [default: False]"/> | |
| 73 <param name="tree_fp" type="data" format="txt" optional="true" label="tree_fp" | |
| 74 help="path to the tree file [default: REQUIRED for phylogenetic measures]"/> | |
| 75 </inputs> | |
| 76 <configfiles> | |
| 77 <configfile name="parameter_generated"> | |
| 78 alpha_diversity:metrics chao1,observed_species,PD_whole_tree | |
| 79 multiple_rarefactions_even_depth:num-reps 20 | |
| 80 parallel:jobs_to_start 2 | |
| 81 parallel:retain_temp_files False | |
| 82 parallel:seconds_to_sleep 60 | |
| 83 collate_alpha:example_path | |
| 84 make_rarefaction_plots:imagetype png | |
| 85 make_rarefaction_plots:resolution 75 | |
| 86 make_rarefaction_plots:background_color white | |
| 87 make_rarefaction_plots:prefs_path | |
| 88 </configfile> | |
| 89 <configfile name="output_template"> | |
| 90 <![CDATA[ | |
| 91 <html> | |
| 92 <body> | |
| 93 <a href="rarefaction_plots.html">rarefaction_plots.html</a> | |
| 94 </body> | |
| 95 </html> | |
| 96 ]]> | |
| 97 </configfile> | |
| 98 </configfiles> | |
| 99 <outputs> | |
| 100 <data format="html" name="output_html" label="alpha_rarefaction_plots"/> | |
| 101 </outputs> | |
| 102 <tests> | |
| 103 </tests> | |
| 104 <help> | |
| 105 | |
| 106 </help> | |
| 107 </tool> | |
| 108 |