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