Mercurial > repos > iuc > mothur_unique_seqs

annotate unique.seqs.xml @ 3:84e71b1537f3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 10:07:44 -0500
parents a8d6c0935377
children a05a8d7ce8dd
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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[
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10 @SHELL_OPTIONS@
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11
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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
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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 </inputs>
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37 <outputs>
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38 <expand macro="logfile-output"/>
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39 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.unique.*" label="${tool.name} on ${on_string}: fasta"/>
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40 <data name="out_names" format="mothur.names" from_work_dir="fasta*.names" label="${tool.name} on ${on_string}: names">
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41 <filter> format == "name" </filter>
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42 </data>
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43 <data name="out_count" format="mothur.count_table" from_work_dir="fasta*.count_table" label="${tool.name} on ${on_string}: count_table">
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44 <filter> format == "count" </filter>
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45 </data>
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46 </outputs>
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47 <tests>
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48 <test><!-- test with names file -->
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49 <param name="fasta" value="amazon.fasta"/>
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50 <param name="names" value="amazon1.names" ftype="mothur.names"/>
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51 <param name="format" value="name"/>
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52 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/>
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53 <output name="out_names" file="amazon.unique.names" ftype="mothur.names"/>
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54 <expand macro="logfile-test"/>
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55 </test>
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56 <test><!-- test with count file -->
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57 <param name="fasta" value="amazon.unique.fasta"/>
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58 <param name="names" value="amazon.count_table" ftype="mothur.count_table"/>
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59 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/>
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60 <output name="out_count" md5="2024cbb895f79346606ab196dd130639" ftype="mothur.count_table"/>
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61 <expand macro="logfile-test"/>
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62 </test>
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63 <test><!-- test wth fasta only -->
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64 <param name="fasta" value="amazon.fasta"/>
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65 <param name="format" value="name"/>
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66 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/>
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67 <output name="out_names" file="amazon.unique.names" ftype="mothur.names"/>
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68 <expand macro="logfile-test"/>
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69 </test>
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70 </tests>
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71 <help><![CDATA[
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72
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73 @MOTHUR_OVERVIEW@
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74
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75 **Command Documentation**
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76
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77 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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78
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79 .. _name: https://www.mothur.org/wiki/Name_file
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80 .. _unique.seqs: https://www.mothur.org/wiki/Unique.seqs
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81
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82 ]]></help>
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83 <expand macro="citations"/>
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84 </tool>