Mercurial > repos > iuc > mothur_primer_design

annotate primer.design.xml @ 2:fb7c0871d8af draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:03:11 -0400
parents 79490c77c27f
children 6e8cdd7e6825
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79490c77c27f 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_primer_design" name="Primer.design" version="@WRAPPER_VERSION@.0">
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2 <description>identify sequence fragments that are specific to particular OTUs</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
2
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10 @SHELL_OPTIONS@
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11
2
fb7c0871d8af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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12 ## create symlinks to input datasets
fb7c0871d8af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 ln -s '$fasta' fasta.dat &&
fb7c0871d8af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$otu' otu.dat &&
fb7c0871d8af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 ln -s '$name' name.dat &&
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16 ln -s '$count' count.dat &&
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17
2
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18 echo 'primer.design(
fb7c0871d8af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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19 fasta=fasta.dat,
fb7c0871d8af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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20 list=otu.dat,
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21 #if $label:
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22 label=$label,
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23 #end if
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24 otulabel=$otulabel,
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25 #if $name:
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26 name=name.dat,
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27 #end if
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28 #if $count:
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29 count=count.dat,
fb7c0871d8af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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30 #end if
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31 #if $cutoff:
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32 cutoff=$cutoff,
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33 #end if
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34 #if $mintm:
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35 mintm=$mintm,
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36 #end if
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37 #if $maxtm:
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38 maxtm=$maxtm,
fb7c0871d8af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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39 #end if
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40 pdiffs=$pdiffs,
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41 length=$length,
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42 processors='\${GALAXY_SLOTS:-8}'
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43 )'
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44 | sed 's/ //g' ## mothur trips over whitespace
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45 | mothur
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46 | tee mothur.out.log
0
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47 ]]></command>
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48 <inputs>
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49 <param name="fasta" type="data" format="mothur.align" label="fasta - provide aligned fasta file"/>
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50 <param name="otu" type="data" format="mothur.list" label="list - OTU list file"/>
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51 <param name="label" type="select" optional="true" multiple="false" label="label - OTU Labels" help="If none selected, the first label in your file will be used">
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52 <expand macro="labeloptions"/>
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53 </param>
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54 <param name="otulabel" type="select" optional="false" multiple="false" label="otulabel - choose an OTU name">
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55 <options>
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56 <filter type="data_meta" ref="otu" key="otulabels"/>
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57 </options>
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58 </param>
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59 <param name="name" type="data" format="mothur.names" optional="true" label="name - names file associated with your fasta file"/>
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60 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count table associated with your fasta file"/>
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61 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - specify the number of differences allowed in the primer" help=""/>
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62 <param name="length" type="integer" value="18" min="0" label="length - indicate the length of the primer" help=""/>
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63 <param name="mintm" type="integer" value="" optional="true" label="mintm - indicate minimum melting temperature" help=""/>
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64 <param name="maxtm" type="integer" value="" optional="true" label="maxtm - indicate maximum melting temperature" help=""/>
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65 <param name="cutoff" type="integer" value="" optional="true" min="0" max="100" label="cutoff - set a percentage of sequences that support the base" help="For example: cutoff=97 would only return a sequence that only showed ambiguities for bases that were not supported by at least 97% of sequences."/>
2
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66 <expand macro="param-savelog"/>
0
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67 </inputs>
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68 <outputs>
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69 <expand macro="logfile-output"/>
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70 <data name="fasta_out" format="mothur.align" from_work_dir="otu*.cons.fasta" label="${tool.name} on ${on_string}: cons.fasta"/>
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71 <data name="summary_out" format="tabular" from_work_dir="otu*.primer.summary" label="${tool.name} on ${on_string}: primer.summary"/>
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72 <data name="list_out" format="mothur.list" from_work_dir="otu*.pick.*" label="${tool.name} on ${on_string}: pick.list"/>
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73 </outputs>
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74 <tests>
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75 <test>
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76 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
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77 <param name="otu" value="amazon.align_head.list" ftype="mothur.list"/>
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78 <param name="otulabel" value="Otu1"/>
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79 <param name="label" value="0.30"/>
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80 <output name="fasta_out" md5="a5c8c17814f02124194dba2e37f566c7" ftype="mothur.align"/>
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81 <output name="summary_out" md5="8dd341c49c26c6d0f8026b34cb7bc925" ftype="tabular"/>
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82 <output name="list_out" md5="0a73804f3d48c668b4dab85c76d2c767" ftype="mothur.list"/>
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83 <param name="savelog" value="true"/>
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84 <expand macro="logfile-test"/>
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85 </test>
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86 </tests>
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87 <help><![CDATA[
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88
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89 @MOTHUR_OVERVIEW@
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90
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91 **Command Documentation**
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92
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93 The primer.design_ allows you to identify sequence fragments that are specific to particular OTUs.
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94
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95 .. _primer.design: https://www.mothur.org/wiki/Primer.design
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96
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97 ]]></help>
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98 <citations>
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99 <citation type="doi">10.1128/AEM.01541-09</citation>
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100 </citations>
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101 </tool>