Mercurial > repos > iuc > mothur_primer_design

annotate primer.design.xml @ 0:41cc6c979aa2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:45:41 -0400
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children 525400c8be71
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41cc6c979aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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1 <tool profile="16.07" id="mothur_primer_design" name="Primer.design" version="@WRAPPER_VERSION@.0">
41cc6c979aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>identify sequence fragments that are specific to particular OTUs</description>
41cc6c979aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
41cc6c979aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
41cc6c979aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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9 ## create symlinks to input datasets
41cc6c979aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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10 ln -s "$fasta" fasta.dat &&
41cc6c979aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 ln -s "$otu" otu.dat &&
41cc6c979aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 ln -s "$name" name.dat &&
41cc6c979aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 ln -s "$count" count.dat &&
41cc6c979aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14
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15 echo 'primer.design(
41cc6c979aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 fasta=fasta.dat,
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17 list=otu.dat,
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18 #if $label:
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19 label=$label,
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20 #end if
41cc6c979aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 otulabel=$otulabel,
41cc6c979aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 #if $name:
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23 name=name.dat,
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24 #end if
41cc6c979aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 #if $count:
41cc6c979aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 count=count.dat,
41cc6c979aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 #end if
41cc6c979aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 #if $cutoff:
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29 cutoff=$cutoff,
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30 #end if
41cc6c979aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 #if $mintm:
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32 mintm=$mintm,
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33 #end if
41cc6c979aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 #if $maxtm:
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35 maxtm=$maxtm,
41cc6c979aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 #end if
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37 pdiffs=$pdiffs,
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38 length=$length,
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39 processors='\${GALAXY_SLOTS:-8}'
41cc6c979aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 )'
41cc6c979aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 | sed 's/ //g' ## mothur trips over whitespace
41cc6c979aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 | mothur
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43 ]]></command>
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44 <inputs>
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45 <param name="fasta" type="data" format="mothur.align" label="fasta - provide aligned fasta file"/>
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46 <param name="otu" type="data" format="mothur.list" label="list - OTU list file"/>
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47 <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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48 <expand macro="labeloptions"/>
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49 </param>
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50 <param name="otulabel" type="select" optional="false" multiple="false" label="otulabel - choose an OTU name">
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51 <options>
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52 <filter type="data_meta" ref="otu" key="otulabels"/>
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53 </options>
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54 </param>
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55 <param name="name" type="data" format="mothur.names" optional="true" label="name - names file associated with your fasta file"/>
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56 <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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57 <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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58 <param name="length" type="integer" value="18" min="0" label="length - indicate the length of the primer" help=""/>
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59 <param name="mintm" type="integer" value="" optional="true" label="mintm - indicate minimum melting temperature" help=""/>
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60 <param name="maxtm" type="integer" value="" optional="true" label="maxtm - indicate maximum melting temperature" help=""/>
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61 <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."/>
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62 </inputs>
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63 <outputs>
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64 <expand macro="logfile-output"/>
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65 <data name="fasta_out" format="mothur.align" from_work_dir="otu*.cons.fasta" label="${tool.name} on ${on_string}: cons.fasta"/>
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66 <data name="summary_out" format="tabular" from_work_dir="otu*.primer.summary" label="${tool.name} on ${on_string}: primer.summary"/>
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67 <data name="list_out" format="mothur.list" from_work_dir="otu*.pick.*" label="${tool.name} on ${on_string}: pick.list"/>
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68 </outputs>
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69 <tests>
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70 <test>
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71 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
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72 <param name="otu" value="amazon.align_head.list" ftype="mothur.list"/>
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73 <param name="otulabel" value="Otu1"/>
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74 <param name="label" value="0.30"/>
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75 <output name="fasta_out" md5="a5c8c17814f02124194dba2e37f566c7" ftype="mothur.align"/>
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76 <output name="summary_out" md5="8dd341c49c26c6d0f8026b34cb7bc925" ftype="tabular"/>
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77 <output name="list_out" md5="0a73804f3d48c668b4dab85c76d2c767" ftype="mothur.list"/>
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78 <expand macro="logfile-test"/>
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79 </test>
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80 </tests>
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81 <help>
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82 <![CDATA[
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83
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84 @MOTHUR_OVERVIEW@
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85
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86 **Command Documenation**
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87
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88 The primer.design_ allows you to identify sequence fragments that are specific to particular OTUs.
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89
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90 .. _primer.design: http://www.mothur.org/wiki/Primer.design
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91
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92 ]]>
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93 </help>
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94 <citations>
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95 <citation type="doi">10.1128/AEM.01541-09</citation>
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96 </citations>
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97 </tool>