Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/chimera.check.xml @ 1:fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:35:35 -0400 |
parents | 3202a38e44d9 |
children | e990ac8a0f58 |
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Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
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1 <tool id="mothur_chimera_check" name="Chimera.check" version="1.16.0" 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 --template=$alignment.template |
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10 #if int($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 $svg.gen == 'yes': |
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17 --svg=true |
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18 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' |
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19 --new_datasets='^(\S+)\.chimeracheck\.svg$:svg' |
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20 #if $name.__str__ != "None" and len($name.__str__) > 0: |
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21 --name='$name' |
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22 #end if |
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23 #end if |
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24 --processors=2 |
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25 </command> |
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26 <inputs> |
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27 <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/> |
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28 <conditional name="alignment"> |
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29 <param name="source" type="select" label="Select Template from" help=""> |
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30 <option value="hist">History</option> |
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31 <option value="ref">Cached Reference</option> |
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32 </param> |
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33 <when value="ref"> |
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34 <param name="template" type="select" label="template - Select an alignment database " help=""> |
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35 <options from_file="mothur_aligndb.loc"> |
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36 <column name="name" index="0" /> |
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37 <column name="value" index="1" /> |
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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="template - Template 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 </when> |
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57 </conditional> |
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58 </inputs> |
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59 <outputs> |
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60 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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61 <data format="txt" name="out_file" label="${tool.name} on ${on_string}: chimeracheck.chimeras" /> |
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62 </outputs> |
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63 <requirements> |
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64 <requirement type="binary">mothur</requirement> |
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65 </requirements> |
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66 <tests> |
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67 </tests> |
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68 <help> |
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69 **Mothur Overview** |
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70 |
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71 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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72 in the Department of Microbiology and Immunology at The University of Michigan, |
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73 provides bioinformatics for the microbial ecology community. |
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74 |
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75 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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76 |
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77 **Command Documenation** |
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78 |
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79 The chimera.check_ command identifies putative chimeras using the chimeraCheck approach. 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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80 |
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81 .. _chimera.check: http://www.mothur.org/wiki/Chimera.check |
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82 |
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83 |
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84 </help> |
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85 </tool> |