Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/chimera.slayer.xml @ 0:3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:32:23 -0400 |
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children | fcc0778f6987 |
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1 <tool id="mothur_chimera_slayer" name="Chimera.slayer" version="1.15.0"> |
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2 <description>Find putative chimeras using slayer</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='chimera.slayer' |
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.slayer\.chimeras$:'$out_file,'^\S+\.slayer\.accnos$:'$out_accnos |
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7 --outputdir='$logfile.extra_files_path' |
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8 --tmpdir='${logfile.extra_files_path}/input' |
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9 --fasta=$fasta |
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10 --template=$alignment.template |
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11 #if $options.setby == 'user': |
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12 --search=$options.search |
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13 --window=$options.window |
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14 --increment=$options.increment |
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15 --match=$options.match |
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16 --mismatch=$options.mismatch |
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17 --numwanted=$options.numwanted |
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18 --parents=$options.parents |
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19 --minsim=$options.minsim |
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20 --mincov=$options.mincov |
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21 --iters=$options.iters |
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22 --minbs=$options.minbs |
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23 --minsnp=$options.minsnp |
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24 --divergence=$options.divergence |
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25 #end if |
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26 </command> |
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27 <inputs> |
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28 <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/> |
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29 <conditional name="alignment"> |
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30 <param name="source" type="select" label="Select Template from" help=""> |
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31 <option value="hist">History</option> |
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32 <option value="ref">Cached Reference</option> |
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33 </param> |
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34 <when value="ref"> |
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35 <param name="template" type="select" label="template - Select an alignment database " help=""> |
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36 <options from_file="mothur_aligndb.loc"> |
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37 <column name="name" index="0" /> |
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38 <column name="value" index="1" /> |
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39 </options> |
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40 </param> |
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41 </when> |
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42 <when value="hist"> |
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43 <param name="template" type="data" format="fasta" label="template - Template to align with" help=""/> |
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44 </when> |
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45 </conditional> |
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46 <conditional name="options"> |
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47 <param name="setby" type="select" label="Slayer Options" help=""> |
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48 <option value="default">Use default settings</option> |
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49 <option value="user">Manually set options</option> |
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50 </param> |
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51 <when value="default"/> |
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52 <when value="user"> |
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53 <param name="search" type="select" label="search - Search method for finding the closest parent" help=""> |
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54 <option value="distance" selected="true">distance</option> |
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55 <option value="kmer">kmer</option> |
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56 <option value="blast">blast</option> |
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57 </param> |
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58 <param name="window" type="integer" value="50" label="window - Window size for searching for chimeras (default 50)" /> |
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59 <param name="increment" type="integer" value="5" label="increment - Increment for window slide on each iteration (default 5)" /> |
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60 <param name="match" type="integer" value="5" label="match - Reward matched bases (default 5)"/> |
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61 <param name="mismatch" type="integer" value="-4" label="mismatch - Penalty for mismatched bases (default -4)"/> |
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62 <param name="numwanted" type="integer" value="15" label="numwanted - Number of potential parents to to compare with query sequence (default 15)"/> |
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63 <param name="parents" type="integer" value="3" label="parents - Number of potential parents to investigate from the numwanted best matches"/> |
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64 <param name="minsim" type="integer" value="90" label="minsim - Minimum similarity % between the query and parent (default 90)"/> |
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65 <param name="mincov" type="integer" value="70" label="mincov - Minimum coverage % of closest matches in template and the query (default 70)"/> |
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66 <param name="iters" type="integer" value="100" label="iters - Number of bootstrap iterations to try (default 100)"/> |
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67 <param name="minbs" type="integer" value="90" label="minbs - Minimum bootstrap support % for calling a sequence chimeric (default 90)"/> |
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68 <param name="minsnp" type="integer" value="100" label="minsnp - Percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default 100)"/> |
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69 <param name="divergence" type="float" value="1.007" label="divergence - Divergence cutoff for chimera determination (default 1.007)"/> |
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70 </when> |
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71 </conditional> |
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72 </inputs> |
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73 <outputs> |
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74 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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75 <data format="txt" name="out_file" label="${tool.name} on ${on_string}: slayer.chimeras" /> |
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76 <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: slayer.accnos" /> |
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77 </outputs> |
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78 <requirements> |
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79 <requirement type="binary">mothur</requirement> |
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80 </requirements> |
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81 <tests> |
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82 </tests> |
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83 <help> |
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84 **Mothur Overview** |
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85 |
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86 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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87 in the Department of Microbiology and Immunology at The University of Michigan, |
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88 provides bioinformatics for the microbial ecology community. |
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89 |
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90 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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91 |
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92 **Command Documenation** |
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93 |
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94 The chimera.slayer_ command identifies putative chimeras using the slayer approach. |
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95 |
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96 .. _chimera.slayer: http://www.mothur.org/wiki/Chimera.slayer |
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97 |
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98 |
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99 </help> |
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100 </tool> |