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