Mercurial > repos > iuc > mothur_unique_seqs

annotate unique.seqs.xml @ 6:84722a5b79af draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit debdcdbb89f9bf3e2c3eed05cb078eddb27d4684"
author iuc
date Mon, 02 Dec 2019 05:41:09 -0500
parents 837f454548b8
children a033f325ad8d
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1 <tool profile="16.07" id="mothur_unique_seqs" name="Unique.seqs" version="@WRAPPER_VERSION@.0">
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2 <description>Return unique sequences</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
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12 ## create symlinks to input datasets
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13 ln -s '$names' names.dat &&
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14 ln -s '$fasta' fasta.dat &&
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15
2
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16 echo 'unique.seqs(
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17 #if $names.is_of_type('mothur.names'):
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18 name=names.dat,
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19 #elif $names.is_of_type('mothur.count_table'):
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20 count=names.dat,
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21 #end if
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22 fasta=fasta.dat,
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23 format=$format
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24 )'
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25 | sed 's/ //g' ## mothur trips over whitespace
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26 | mothur
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27 | tee mothur.out.log
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28 ]]></command>
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29 <inputs>
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30 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
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31 <param name="names" type="data" format="mothur.names,mothur.count_table" optional="true" label="name file or count table - Sequences Names"/>
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32 <param name="format" type="select" label="output format">
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33 <option value="count" selected="true"> Count table </option>
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34 <option value="name"> Name file </option>
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35 </param>
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36 <expand macro="param-savelog"/>
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37 </inputs>
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38 <outputs>
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39 <expand macro="logfile-output"/>
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40 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.unique.*" label="${tool.name} on ${on_string}: fasta"/>
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41 <data name="out_names" format="mothur.names" from_work_dir="fasta*.names" label="${tool.name} on ${on_string}: names">
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42 <filter> format == "name" </filter>
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43 </data>
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44 <data name="out_count" format="mothur.count_table" from_work_dir="fasta*.count_table" label="${tool.name} on ${on_string}: count_table">
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45 <filter> format == "count" </filter>
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46 </data>
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47 </outputs>
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48 <tests>
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49 <test><!-- test with names file -->
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50 <param name="fasta" value="amazon.fasta"/>
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51 <param name="names" value="amazon1.names" ftype="mothur.names"/>
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52 <param name="format" value="name"/>
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53 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/>
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54 <output name="out_names" file="amazon.unique.names" ftype="mothur.names"/>
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55 <param name="savelog" value="true"/>
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56 <expand macro="logfile-test"/>
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57 </test>
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58 <test><!-- test with count file -->
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59 <param name="fasta" value="amazon.unique.fasta"/>
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60 <param name="names" value="amazon.count_table" ftype="mothur.count_table"/>
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61 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/>
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62 <output name="out_count" md5="2024cbb895f79346606ab196dd130639" ftype="mothur.count_table"/>
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63 <param name="savelog" value="true"/>
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64 <expand macro="logfile-test"/>
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65 </test>
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66 <test><!-- test wth fasta only -->
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67 <param name="fasta" value="amazon.fasta"/>
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68 <param name="format" value="name"/>
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69 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/>
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70 <output name="out_names" file="amazon.unique.names" ftype="mothur.names"/>
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71 <param name="savelog" value="true"/>
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72 <expand macro="logfile-test"/>
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73 </test>
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74 </tests>
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75 <help><![CDATA[
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76
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77 @MOTHUR_OVERVIEW@
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78
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79 **Command Documentation**
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80
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81 The unique.seqs_ command returns only the unique sequences found in a fasta-formatted sequence file and a name_ file that indicates those sequences that are identical to the reference sequence.
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82
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83 .. _name: https://www.mothur.org/wiki/Name_file
0468cb2dd83e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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84 .. _unique.seqs: https://www.mothur.org/wiki/Unique.seqs
0468cb2dd83e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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85
2
837f454548b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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86 ]]></help>
0
0468cb2dd83e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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87 <expand macro="citations"/>
0468cb2dd83e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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88 </tool>