Mercurial > repos > jjohnson > qiime
comparison jackknifed_beta_diversity.xml @ 0:e5c3175506b7 default tip
Initial tool configs for qiime, most need work.
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Sun, 17 Jul 2011 10:30:11 -0500 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:e5c3175506b7 |
|---|---|
| 1 <tool id="jackknifed_beta_diversity" name="jackknifed_beta_diversity" version="1.2.1"> | |
| 2 <description>A workflow script for performing jackknifed UPGMA clustering and build jackknifed 2d and 3D PCoA plots.</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">jackknifed_beta_diversity.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 --galaxy_tmpdir='$__new_file_path__' | |
| 9 jackknifed_beta_diversity.py | |
| 10 --otu_table_fp=$otu_table_fp | |
| 11 --output_dir=$__new_file_path__ | |
| 12 $force | |
| 13 #if $parameter.source == 'hist': | |
| 14 --parameter_fp=$parameter_fp | |
| 15 #else: | |
| 16 --parameter_fp=$parameter_generated | |
| 17 #end if | |
| 18 --seqs_per_sample=$seqs_per_sample | |
| 19 --mapping_fp=$mapping_fp | |
| 20 --tree_fp=$tree_fp | |
| 21 --master_tree=$master_tree | |
| 22 $print_only | |
| 23 $parallel | |
| 24 </command> | |
| 25 <inputs> | |
| 26 <param name="otu_table_fp" type="data" format="fasta" label="otu_table_fp" | |
| 27 help="the input fasta file [REQUIRED]"/> | |
| 28 | |
| 29 <param name="seqs_per_sample" type="integer" value="-1" label="seqs_per_sample" | |
| 30 help="number of sequences to include in each jackknifed subset [REQUIRED]"/> | |
| 31 <param name="mapping_fp" type="data" format="tabular" label="mapping_fp" | |
| 32 help="path to the mapping file [REQUIRED]"/> | |
| 33 | |
| 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 | |
| 66 <param name="tree_fp" type="data" format="txt" label="tree_fp" | |
| 67 help="path to the tree file [default: ('NO', 'DEFAULT'); REQUIRED for phylogenetic measures]"/> | |
| 68 <param name="master_tree" type="text" value="consensus" label="master_tree" | |
| 69 help="method for computing master trees in jackknife analysis. 'consensus': consensus of trees from jackknifed otu tables. 'full': tree generated from input (unsubsambled) otu table. [default: consensus]"/> | |
| 70 <param name="force" type="boolean" truevalue="--force" falsevalue="" checked="false" label="force" | |
| 71 help="Force overwrite of existing output directory (note: existing files in output_dir will not be removed) [default: ('NO', 'DEFAULT')]"/> | |
| 72 <param name="print_only" type="boolean" truevalue="--print_only" falsevalue="" checked="false" label="print_only" | |
| 73 help="Print the commands but don't call them -- useful for debugging [default: False]"/> | |
| 74 <param name="parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="false" label="parallel" | |
| 75 help="Run in parallel where available [default: False]"/> | |
| 76 </inputs> | |
| 77 <configfiles> | |
| 78 <configfile name="parameter_generated"> | |
| 79 alpha_diversity:metrics chao1,observed_species,PD_whole_tree | |
| 80 multiple_rarefactions_even_depth:num-reps 20 | |
| 81 parallel:jobs_to_start 2 | |
| 82 parallel:retain_temp_files False | |
| 83 parallel:seconds_to_sleep 60 | |
| 84 collate_alpha:example_path | |
| 85 make_rarefaction_plots:imagetype png | |
| 86 make_rarefaction_plots:resolution 75 | |
| 87 make_rarefaction_plots:background_color white | |
| 88 make_rarefaction_plots:prefs_path | |
| 89 </configfile> | |
| 90 </configfiles> | |
| 91 | |
| 92 <outputs> | |
| 93 | |
| 94 </outputs> | |
| 95 <tests> | |
| 96 </tests> | |
| 97 <help> | |
| 98 | |
| 99 </help> | |
| 100 </tool> | |
| 101 |