Mercurial > repos > bebatut > qiime
annotate 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 |
---|---|
date | Tue, 02 Feb 2016 05:50:37 -0500 |
parents | |
children |
rev | line source |
---|---|
0
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
1 <tool id="qiime_pick_rep_set" name="pick rep set" version="1.9.1galaxy1"> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
2 <description>Pick representative set of sequences</description> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
3 |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
4 <macros> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
5 <import>macros.xml</import> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
6 </macros> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
7 |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
8 <expand macro="requirements" /> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
9 |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
10 <command> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
11 <![CDATA[ |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
12 pick_rep_set.py |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
13 -i $input_file |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
14 -m $rep_set_picking_method |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
15 -s $sort_by |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
16 #if str($fasta_file) != 'None': |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
17 -f $fasta_file |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
18 #end if |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
19 -o $result_fp -l rep_set.log |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
20 |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
21 #if str($reference_seqs_fp) != 'None': |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
22 -r $reference_seqs_fp |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
23 #end if |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
24 ]]> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
25 </command> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
26 |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
27 <inputs> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
28 <param label="-i/--input_file: Path to input otu mapping file [REQUIRED]" name="input_file" optional="False" type="data"/> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
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"/> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
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"> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
31 <option value="random">random</option> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
32 <option value="longest">longest</option> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
33 <option value="most_abundant">most_abundant</option> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
34 <option value="first">first</option> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
35 </param> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
36 <param label="-s/--sort_by: sort by otu or seq_id [default: otu]" name="sort_by" optional="True" type="select"> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
37 <option value="otu">otu</option> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
38 <option value="seq_id">seq_id</option> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
39 </param> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
40 <param label="-r/--reference_seqs_fp: collection of preferred representative sequences [default: None]" name="reference_seqs_fp" optional="True" type="data"/> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
41 </inputs> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
42 |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
43 <outputs> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
44 <data format="fasta" name="result_fp" label="rep_set_seqs.fasta"/> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
45 </outputs> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
46 |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
47 <tests> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
48 <test> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
49 </test> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
50 </tests> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
51 |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
52 <help><![CDATA[ |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
53 **How it does?** |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
54 |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
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. |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
56 |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
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. |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
58 ]]> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
59 </help> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
60 |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
61 <citations> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
62 <expand macro="citations" /> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
63 </citations> |
c1bd0c560018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
bebatut
parents:
diff
changeset
|
64 </tool> |