Mercurial > repos > bebatut > qiime
comparison pick_rep_set.xml @ 0:c1bd0c560018 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
| author | bebatut |
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| date | Tue, 02 Feb 2016 05:50:37 -0500 |
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| -1:000000000000 | 0:c1bd0c560018 |
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| 1 <tool id="qiime_pick_rep_set" name="pick rep set" version="1.9.1galaxy1"> | |
| 2 <description>Pick representative set of sequences</description> | |
| 3 | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 | |
| 8 <expand macro="requirements" /> | |
| 9 | |
| 10 <command> | |
| 11 <![CDATA[ | |
| 12 pick_rep_set.py | |
| 13 -i $input_file | |
| 14 -m $rep_set_picking_method | |
| 15 -s $sort_by | |
| 16 #if str($fasta_file) != 'None': | |
| 17 -f $fasta_file | |
| 18 #end if | |
| 19 -o $result_fp -l rep_set.log | |
| 20 | |
| 21 #if str($reference_seqs_fp) != 'None': | |
| 22 -r $reference_seqs_fp | |
| 23 #end if | |
| 24 ]]> | |
| 25 </command> | |
| 26 | |
| 27 <inputs> | |
| 28 <param label="-i/--input_file: Path to input otu mapping file [REQUIRED]" name="input_file" optional="False" type="data"/> | |
| 29 <param label="-f/--fasta_file: Path to input fasta file [REQUIRED if not picking against a reference set; default: None]" name="fasta_file" optional="True" type="data"/> | |
| 30 <param label="-m/--rep_set_picking_method: Method for picking representative sets. Valid choices are random, longest, most_abundant, first [default: first (first chooses cluster seed when picking otus with uclust)]" name="rep_set_picking_method" optional="True" type="select"> | |
| 31 <option value="random">random</option> | |
| 32 <option value="longest">longest</option> | |
| 33 <option value="most_abundant">most_abundant</option> | |
| 34 <option value="first">first</option> | |
| 35 </param> | |
| 36 <param label="-s/--sort_by: sort by otu or seq_id [default: otu]" name="sort_by" optional="True" type="select"> | |
| 37 <option value="otu">otu</option> | |
| 38 <option value="seq_id">seq_id</option> | |
| 39 </param> | |
| 40 <param label="-r/--reference_seqs_fp: collection of preferred representative sequences [default: None]" name="reference_seqs_fp" optional="True" type="data"/> | |
| 41 </inputs> | |
| 42 | |
| 43 <outputs> | |
| 44 <data format="fasta" name="result_fp" label="rep_set_seqs.fasta"/> | |
| 45 </outputs> | |
| 46 | |
| 47 <tests> | |
| 48 <test> | |
| 49 </test> | |
| 50 </tests> | |
| 51 | |
| 52 <help><![CDATA[ | |
| 53 **How it does?** | |
| 54 | |
| 55 After picking OTUs, you can then pick a representative set of sequences. For each OTU, you will end up with one sequence that can be used in subsequent analyses. | |
| 56 | |
| 57 The output from pick_rep_set.py is a single FASTA file containing one sequence per OTU. The FASTA header lines will be the OTU identifier (from here on used as the unique sequence identifier) followed by a space, followed by the sequence identifier originally associated with the representative sequence. The name of the output FASTA file will be <input_sequences_filepath>_rep_set.fasta by default, or can be specified via the "-o" parameter. | |
| 58 ]]> | |
| 59 </help> | |
| 60 | |
| 61 <citations> | |
| 62 <expand macro="citations" /> | |
| 63 </citations> | |
| 64 </tool> |