Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/chimera.check.xml @ 36:040410b8167e default tip
Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.
author | galaxyuser <galaxy_user@agr.g.ca> |
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date | Mon, 10 Nov 2014 15:40:02 -0500 |
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1 <tool id="mothur_chimera_check" name="Chimera.check" version="1.21.0" force_history_refresh="True"> |
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2 <description>Find putative chimeras using chimeraCheck</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='chimera.check' |
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.chimeracheck\.chimeras?$:'$out_file |
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7 --outputdir='$logfile.extra_files_path' |
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8 --fasta=$fasta |
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9 --reference=$alignment.template |
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10 #if int($ksize.__str__) > 0: |
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11 --ksize=$ksize |
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12 #end if |
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13 #if int($increment.__str__) > 0: |
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14 --increment=$increment |
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15 #end if |
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16 #if $svg.gen == 'yes': |
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17 --svg=true |
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18 #if $svg.name.__str__ != "None" and len($svg.name.__str__) > 0: |
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19 --name='$svg.name' |
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20 #end if |
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21 #if $svg.as_datasets.__str__ == "yes": |
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22 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' |
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23 --new_datasets='^(\S+)\.chimeracheck\.svg$:svg' |
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24 #end if |
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25 #end if |
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26 --processors=8 |
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27 </command> |
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28 <inputs> |
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29 <param name="fasta" type="data" format="align" label="fasta - Candiate Aligned Sequences"/> |
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30 <conditional name="alignment"> |
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31 <param name="source" type="select" label="Select Reference Template from" help=""> |
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32 <option value="hist">History</option> |
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33 <option value="ref">Cached Reference</option> |
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34 </param> |
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35 <when value="ref"> |
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36 <param name="template" type="select" label="reference - Select an alignment database " help=""> |
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37 <options from_data_table="mothur_aligndb"> |
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38 </options> |
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39 </param> |
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40 </when> |
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41 <when value="hist"> |
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42 <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/> |
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43 </when> |
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44 </conditional> |
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45 <param name="ksize" type="integer" value="7" label="ksize - kmer length to determine differences between sequence fragments (uses default if < 1)"/> |
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46 <param name="increment" type="integer" value="10" label="increment - Increment for window slide on each iteration (uses default if < 1)" |
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47 help="Default is 10, but you may set it up to sequence length minus twice the window."/> |
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48 <conditional name="svg"> |
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49 <param name="gen" type="select" label="svg - Generate a SVG plot for each query sequence" help=""> |
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50 <option value="no" selected="true">No</option> |
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51 <option value="yes">Yes</option> |
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52 </param> |
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53 <when value="no"/> |
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54 <when value="yes"> |
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55 <param name="name" type="data" format="names" optional="true" label="name - Names of queries for which to generate SVG plot"/> |
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56 <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each image"/> |
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57 </when> |
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58 </conditional> |
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59 </inputs> |
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60 <outputs> |
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61 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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62 <data format="txt" name="out_file" label="${tool.name} on ${on_string}: chimeracheck.chimeras" /> |
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63 </outputs> |
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64 <requirements> |
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65 <requirement type="package" version="1.33">mothur</requirement> |
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66 </requirements> |
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67 <tests> |
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68 </tests> |
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69 <help> |
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70 **Mothur Overview** |
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71 |
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72 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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73 in the Department of Microbiology and Immunology at The University of Michigan, |
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74 provides bioinformatics for the microbial ecology community. |
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75 |
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76 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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77 |
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78 **Command Documenation** |
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79 |
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80 The chimera.check_ command identifies putative chimeras using the chimeraCheck approach. It looks at distance of left side of query to it's closest match + distance of right side of query to it's closest match - distance of whole query and its closest match over several windows. |
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81 |
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82 Note: following the RDP model this method does not determine whether or not a sequence is chimeric, but allows you to determine that based on the IS values produced. |
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83 |
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84 .. _chimera.check: http://www.mothur.org/wiki/Chimera.check |
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85 |
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86 |
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87 </help> |
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88 </tool> |