Mercurial > repos > azuzolo > qiime1_3_0
comparison qiime/pick_rep_set.xml @ 0:003162f90751 draft
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| author | azuzolo |
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| date | Wed, 06 Jun 2012 16:40:30 -0400 |
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| -1:000000000000 | 0:003162f90751 |
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| 1 <tool id="pick_rep_set" name="pick_rep_set" version="2.0.0"> | |
| 2 <description>Pick representative set of sequences</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">pick_rep_set.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 pick_rep_set.py | |
| 9 --input_file=$input_file | |
| 10 #if $reference_seqs_fp.__str__ != 'None' or $reference_seqs_fp != None and $reference_seqs_fp.__str__ == '': | |
| 11 --reference_seqs_fp=$reference_seqs_fp | |
| 12 #else: | |
| 13 --fasta_file=$fasta_file | |
| 14 #end if | |
| 15 --rep_set_picking_method=$rep_set_picking_method | |
| 16 --sort_by=$sort_by | |
| 17 --log_fp=$log_fp | |
| 18 --result_fp=$result_fp | |
| 19 </command> | |
| 20 <inputs> | |
| 21 <param name="input_file" type="data" format="qiimeotu" label="input_file" | |
| 22 help="Path to input otu mapping file (usually output from pick_otus) [REQUIRED]"/> | |
| 23 <param name="fasta_file" type="data" format="fasta" optional="true" label="fasta_file" | |
| 24 help="Path to input fasta file [REQUIRED if not picking against a reference set; default: None]"/> | |
| 25 <param name="rep_set_picking_method" type="select" label="rep_set_picking_method" | |
| 26 help="Method for picking representative sets. [default: first]"> | |
| 27 <option value="random">random</option> | |
| 28 <option value="longest">longest</option> | |
| 29 <option value="most_abundant">most_abundant</option> | |
| 30 <option value="first" selected="true">first</option> | |
| 31 </param> | |
| 32 <param name="sort_by" type="select" value="otu" label="sort_by" > | |
| 33 <option value="otu" selected="true">otu</option> | |
| 34 <option value="seq_id">seq_id</option> | |
| 35 </param> | |
| 36 <param name="reference_seqs_fp" type="data" format="fasta" optional="true" label="reference_seqs_fp" | |
| 37 help="collection of preferred representative sequences"/> | |
| 38 </inputs> | |
| 39 <outputs> | |
| 40 <data format="txt" name="log_fp" label="${tool.name} on ${on_string}: log" /> | |
| 41 <data format="fasta" name="result_fp" label="${tool.name} on ${on_string}: rep_set.fasta" /> | |
| 42 </outputs> | |
| 43 <tests> | |
| 44 </tests> | |
| 45 <help>For more information, see pick_rep_set_ in the Qiime documentation. | |
| 46 | |
| 47 Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA | |
| 48 | |
| 49 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN | |
| 50 | |
| 51 .. _pick_rep_set: http://qiime.org/scripts/pick_rep_set.html</help> | |
| 52 </tool> | |
| 53 |