Mercurial > repos > iuc > mothur_chimera_ccode

annotate chimera.ccode.xml @ 0:3eca08ae427b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:14:11 -0400
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children ad1b47de42a3
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0
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_chimera_ccode" name="Chimera.ccode" version="@WRAPPER_VERSION@.0">
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Find putative chimeras using ccode</description>
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
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4 <import>macros.xml</import>
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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8 <expand macro="version_command"/>
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 <command><![CDATA[
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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10 @SHELL_OPTIONS@
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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11
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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12 ## create symlinks to input datasets
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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13 ln -s "$fasta" fasta.dat &&
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14 ln -s "$alignment.template" alignment.template.dat &&
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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15 #if $mask.source2 == "history":
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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16 ln -s "$mask.input" mask.input.dat &&
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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17 #end if
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18
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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19 echo 'chimera.ccode(
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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20 fasta=fasta.dat,
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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21 reference=alignment.template.dat,
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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22 filter=$filter,
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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23 #if $mask.source2 == "default":
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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24 mask=default,
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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25 #elif $mask.source2 == "history":
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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26 mask=mask.input.dat,
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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27 #end if
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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28 #if int($window) > 0:
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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29 window=$window,
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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30 #end if
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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31 #if int($numwanted) > 0:
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 numwanted=$numwanted,
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 #end if
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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34 processors='\${GALAXY_SLOTS:-8}'
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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35 )'
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36 | sed 's/ //g' ## mothur trips over whitespace
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37 | mothur
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38 | tee mothur.out.log
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 ]]></command>
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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40 <inputs>
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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41 <param name="fasta" type="data" format="mothur.align" label="fasta - Candiate Aligned Sequences"/>
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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42 <conditional name="alignment">
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43 <param name="source" type="select" label="Select Reference Template from" help="">
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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44 <option value="hist">History</option>
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45 <option value="ref">Cached Reference</option>
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46 </param>
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47 <when value="ref">
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48 <param name="template" type="select" label="reference - Select an alignment database" help="">
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49 <options from_data_table="mothur_aligndb">
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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50 </options>
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51 </param>
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52 </when>
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53 <when value="hist">
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54 <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/>
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55 </when>
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56 </conditional>
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57 <param name="filter" type="boolean" falsevalue="False" truevalue="True" checked="false" label="filter - Apply a 50% soft vertical filter"/>
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58 <conditional name="mask">
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59 <param name="source2" type="select" label="Mask option">
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60 <option value="">None</option>
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61 <option value="default">default ecoli mask</option>
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62 <option value="history">From Your History</option>
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63 </param>
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64 <when value="history">
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65 <param name="input" type="data" format="mothur.filter" label="Mask for the reference file" help=""/>
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66 </when>
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67 <when value=""/>
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68 <when value="default"/>
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69 </conditional>
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70 <param name="window" type="integer" value="0" label="window - Length of sequence you want in each window analyzed (default if &lt; 1)" help="Recommended window size is between 5 and 20% of your trimmed sequence length. Default is 10% of the sequence length."/>
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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71 <param name="numwanted" type="integer" value="20" label="numwanted - Number of sequences compared with each query (uses default if set to 0)"/>
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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72 </inputs>
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73 <outputs>
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74 <expand macro="logfile-output"/>
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75 <data name="out_file" format="txt" from_work_dir="fasta.*ccode.chimeras" label="${tool.name} on ${on_string}: ccode.chimeras"/>
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76 <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*ccode.accnos" label="${tool.name} on ${on_string}: ccode.accnos"/>
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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77 <data name="mapinfo" format="tabular" from_work_dir="*.mapinfo" label="${tool.name} on ${on_string}: mapinfo"/>
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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78 </outputs>
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79 <tests>
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80 <test>
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81 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
3eca08ae427b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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82 <param name="source" value="hist"/>
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83 <param name="template" value="HMP_MOCK.v35.align"/>
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84 <output name="out_file" ftype="txt">
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85 <assert_contents>
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86 <has_line_matching expression="^Window\tAvgQ\t\(sdQ\)\tAvgR\t\(sdR\)\tRatio\tAnova$"/>
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87 </assert_contents>
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88 </output>
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89 <output name="out_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ccode.accnos" ftype="mothur.accnos"/>
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90 <output name="mapinfo" md5="ef3353b1467fe95a24153513917e6444" ftype="tabular"/>
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91 <expand macro="logfile-test"/>
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92 </test>
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93 <test> <!-- test with default ecoli mask -->
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94 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
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95 <param name="source" value="hist"/>
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96 <param name="template" value="HMP_MOCK.v35.align"/>
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97 <param name="source2" value="default"/>
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98 <param name="window" value="100"/>
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99 <output name="out_file" ftype="txt">
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100 <assert_contents>
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101 <has_line_matching expression="^Window\tAvgQ\t\(sdQ\)\tAvgR\t\(sdR\)\tRatio\tAnova$"/>
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102 </assert_contents>
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103 </output>
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104 <output name="out_accnos" md5="47ddf86ec36aafd495aa902b3e06ffca" ftype="mothur.accnos"/>
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105 <output name="mapinfo" md5="25221b1e109d9c0a939efb319e7a9896" ftype="tabular"/>
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106 <expand macro="logfile-test"/>
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107 </test>
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108 </tests>
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109 <help>
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110 <![CDATA[
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111
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112 @MOTHUR_OVERVIEW@
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113
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114 **Command Documentation**
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115
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116 The chimera.ccode_ command identifies putative chimeras using the ccode approach (Chimera and Cross-Over Detection and Evaluation). Ccode_ compares differences in distances, for each word, between query sequence and reference sequences, and reference sequences and themselves.
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117
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118 This method was written using the algorithms described in the paper_ "Evaluating putative chimeric sequences from PCR-amplified products" by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.
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119
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120 The program can analyze sequences for any required word length. Generally, values of 5-20% of sequence length appear to deliver accurate results, for example, working on 16S rDNA sequences with a full-length of #1500 nt. It should be noted that the use of fragments either too long or too short might result in a reduction of sensitivity.
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121
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122 .. _Ccode: http://www.microextreme.net/downloads.html
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123 .. _paper: http://bioinformatics.oxfordjournals.org/content/21/3/333.full.pdf
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124 .. _chimera.ccode: https://www.mothur.org/wiki/Chimera.ccode
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125
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126 ]]>
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127 </help>
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128 <expand macro="citations"/>
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129 </tool>