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Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
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1 <tool id="identify_chimeric_seqs" name="identify_chimeric_seqs" version="1.2.0">
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2 <description>Identify chimeric sequences in input FASTA file</description>
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3 <requirements>
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4 <requirement type="binary">identify_chimeric_seqs.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 identify_chimeric_seqs.py
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9 --input_fasta_fp=$input_fasta_fp
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10 #if $pick.chimera_detection_method == 'ChimeraSlayer':
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11 --chimera_detection_method=$pick.chimera_detection_method
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12 --aligned_reference_seqs_fp=$pick.aligned_reference_seqs_fp
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13 --min_div_ratio=$pick.min_div_ratio
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14 $pick.keep_intermediates
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15 #elif $pick.chimera_detection_method == 'blast_fragments':
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16 --chimera_detection_method=$pick.chimera_detection_method
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17 --id_to_taxonomy_fp=$pick.id_to_taxonomy_fp
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18 --reference_seqs_fp=$pick.reference_seqs_fp
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19 --blast_db=$pick.blast_db
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20 --num_fragments=$pick.num_fragments
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21 --taxonomy_depth=$pick.taxonomy_depth
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22 --max_e_value=$pick.max_e_value
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23 #end if
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24 --output_fp=$output_fp
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25 </command>
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26 <inputs>
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27 <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
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28 help="path to the input fasta file [REQUIRED]"/>
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29 <conditional name="pick">
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30 <param name="chimera_detection_method" type="select" label="chimera_detection_method"
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31 help="Chimera detection method. Choices: blast_fragments or ChimeraSlayer. [default:ChimeraSlayer]">
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32 <option value="blast_fragments">blast_fragments</option>
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33 <option value="ChimeraSlayer" selected="true">ChimeraSlayer</option>
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34 </param>
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35 <when value="ChimeraSlayer">
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36 <param name="aligned_reference_seqs_fp" type="data" format="txt" label="aligned_reference_seqs_fp"
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37 help="Path to (Py)Nast aligned reference sequences. REQUIRED when method ChimeraSlayer [default: ('NO', 'DEFAULT')]"/>
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38 <param name="min_div_ratio" type="float" value="0.0" label="min_div_ratio"
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39 help="min divergence ratio (passed to ChimeraSlayer). If set to None uses ChimeraSlayer default value. [default: %default]"/>
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40 <param name="keep_intermediates" type="boolean" truevalue="--keep_intermediates" falsevalue="" checked="false" label="keep_intermediates"
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41 help="Keep intermediate files, useful for debugging [default: False]"/>
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42 </when>
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43 <when value="blast_fragments">
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44 <param name="blast_db" type="text" label="blast_db"
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45 help="Database to blast against. Must provide either --blast_db or --reference_seqs_fp when method is blast_fragments [default: ('NO', 'DEFAULT')]"/>
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46 <param name="reference_seqs_fp" type="data" format="txt" label="reference_seqs_fp"
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47 help="Path to reference sequences (used to build a blast db when method blast_fragments). [default: ('NO', 'DEFAULT'); REQUIRED when method blast_fragments if no blast_db is provided;]"/>
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48 <param name="id_to_taxonomy_fp" type="data" format="tabular" label="id_to_taxonomy_fp"
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49 help="Path to tab-delimited file mapping sequences to assigned taxonomy. Each assigned taxonomy is provided as a comma-separated list. [default: ('NO', 'DEFAULT'); REQUIRED when method is blast_fragments]"/>
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50 <param name="taxonomy_depth" type="integer" value="4" label="taxonomy_depth"
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51 help="Number of taxonomic divisions to consider when comparing taxonomy assignments [default: 4]"/>
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52 <param name="num_fragments" type="integer" value="3" label="num_fragments"
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53 help="Number of fragments to split sequences into (i.e., number of expected breakpoints + 1) [default: 3]"/>
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54 <param name="max_e_value" type="float" value="1e-30" label="max_e_value"
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55 help="Max e-value to assign taxonomy [default: 1e-30]"/>
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56 </when>
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57 </conditional> <!-- pick -->
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58 </inputs>
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59 <outputs>
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60 <data format="txt" name="output_fp" label="${tool.name} on ${on_string}: chimeras"/>
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61 </outputs>
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62 <tests>
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63 </tests>
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64 <help>
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65
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66 </help>
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67 </tool>
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