Mercurial > repos > iuc > mothur_remove_lineage

annotate remove.lineage.xml @ 0:152eaafb14ba 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 16:47:08 -0400
parents
children b4939bc52ca7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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1 <tool profile="16.07" id="mothur_remove_lineage" name="Remove.lineage" version="@WRAPPER_VERSION@.0">
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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2 <description>Picks by taxon</description>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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3 <macros>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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4 <import>macros.xml</import>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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5 </macros>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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6 <expand macro="requirements"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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7 <expand macro="version_command"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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8 <command detect_errors="aggressive"><![CDATA[
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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9 #import re
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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10 ## create symlinks to input datasets
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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11 ln -s "$file.taxonomy" file.taxonomy.dat &&
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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12 #if $file.filetype == "useconstaxonomy":
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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13 ln -s "$file.shared" file.shared.dat &&
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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14 ln -s "$file.list" file.list.dat &&
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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15 #end if
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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16 ln -s "$fasta_in" fasta_in.dat &&
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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17 ln -s "$group_in" group_in.dat &&
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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18 ln -s "$alignreport_in" alignreport_in.dat &&
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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19 ln -s "$list_in" list_in.dat &&
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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20 ln -s "$name_in" name_in.dat &&
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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21 ln -s "$count" count.dat &&
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 echo 'remove.lineage(
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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24 #if $file.filetype == "usetaxonomy":
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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25 taxonomy=file.taxonomy.dat
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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26 #else
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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27 constaxonomy=file.taxonomy.dat
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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28 #if $file.shared:
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 ,shared=file.shared.dat
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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30 #end if
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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31 #if $file.list:
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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32 ,list=file.list.dat
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 #end if
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 #end if
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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35 #if $file.taxons:
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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36 #set taxonstring=str($file.taxons).replace(",","-")
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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37 ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxonstring ))'"'
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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38 #elif $taxon:
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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39 ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxon.value )).replace(",","-")'"'
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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40 #end if
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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41 #if $fasta_in:
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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42 ,fasta=fasta_in.dat
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 #end if
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 #if $group_in:
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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45 ,group=group_in.dat
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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46 #end if
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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47 #if $alignreport_in:
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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48 ,alignreport=alignreport_in.dat
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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49 #end if
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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50 #if $list_in:
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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51 ,list=list_in.dat
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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52 #end if
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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53 #if $name_in:
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54 ,name=name_in.dat
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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55 ,dups=$dups
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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56 #end if
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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57 #if $count:
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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58 ,count=count.dat
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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59 #end if
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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60 )'
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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61 | sed 's/ //g' ## mothur trips over whitespace
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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62 | mothur
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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63 ]]></command>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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64 <inputs>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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65 <conditional name="file">
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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66 <param name="filetype" type="select" label="choose which file is used">
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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67 <option value="usetaxonomy" selected="true">taxonomy</option>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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68 <option value="useconstaxonomy">constaxonomy</option>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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69 </param>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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70 <when value="usetaxonomy">
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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71 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy" help="please make sure your file has no quotation marks in it"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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72 <param name="taxons" type="select" size="120" optional="true" multiple="true" label="Browse Taxons from Taxonomy">
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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73 <options from_dataset="taxonomy">
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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74 <column name="name" index="1"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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75 <column name="value" index="1"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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76 <filter type="unique_value" name="unique_taxon" column="1"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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77 <filter type="sort_by" name="sorted_taxon" column="1"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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78 </options>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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79 <sanitizer>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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80 <valid initial="default">
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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81 <add preset="string.printable"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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82 <add value=";"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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83 <remove value="&quot;"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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84 <remove value="&apos;"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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85 </valid>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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86 </sanitizer>
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87 </param>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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88 </when>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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89 <when value="useconstaxonomy">
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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90 <param name="taxonomy" type="data" format="mothur.cons.taxonomy" label="constaxonomy - Constaxonomy file. Provide either a constaxonomy file or a taxonomy file" help="please make sure your file has no quotation marks in it"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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91 <param name="taxons" type="select" size="120" optional="true" multiple="true" label="Browse Taxons from Taxonomy">
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92 <options from_dataset="taxonomy">
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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93 <column name="name" index="2"/>
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94 <column name="value" index="2"/>
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95 <filter type="unique_value" name="unique_taxon" column="2"/>
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96 <filter type="sort_by" name="sorted_taxon" column="2"/>
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97 </options>
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98 <sanitizer>
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99 <valid initial="default">
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100 <add preset="string.printable"/>
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101 <add value=";"/>
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102 <remove value="&quot;"/>
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103 <remove value="&apos;"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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104 </valid>
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105 </sanitizer>
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106 </param>
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107 <param name="shared" type="data" format="mothur.shared" label="shared - shared file" optional="true"/>
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108 <param name="list" type="data" format="mothur.list" label="list - list file" optional="true"/>
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109 </when>
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110 </conditional>
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111 <param name="taxon" type="text" area="True" size="5x120" label="taxon - Manually select Taxons for filtering" help="If no taxons selected from file, Enter 1 or more taxons separated by dashes here, e.g. Bacteria;Firmicutes;-Bacteria;Actinobacteria; "/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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112 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
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113 <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Groups"/>
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114 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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115 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
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116 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
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117 <param name="dups" type="boolean" truevalue="true" falsevalue="false" checked="true" label="dups - Apply to duplicate names"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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118 <param name="count" type="data" format="mothur.count_table" optional="true" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. It can also contain group information"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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119 </inputs>
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120 <outputs>
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121 <expand macro="logfile-output"/>
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122 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="file.taxonomy*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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123 <data format_source="fasta_in" name="fasta_out" from_work_dir="fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta">
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124 <filter>fasta_in</filter>
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125 </data>
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126 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.group">
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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127 <filter>group_in</filter>
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128 </data>
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129 <data name="count_out" format="mothur.count_table" from_work_dir="count*.pick.*" label="${tool.name} on ${on_string}: pick.count_table">
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130 <filter>count</filter>
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131 </data>
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132 <collection name="list_out" type="list" label="${tool.name} on ${on_string}: pick.list">
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133 <filter>list_in</filter>
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134 <discover_datasets pattern="list_in.*?\.(?P&lt;designation&gt;.*)\.pick.*" format="mothur.list"/>
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135 </collection>
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136 <data name="name_out" format="mothur.names" from_work_dir="name_in*.pick.*" label="${tool.name} on ${on_string}: pick.name">
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137 <filter>name_in</filter>
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138 </data>
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139 <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport_in*.pick.*" label="${tool.name} on ${on_string}: pick.align.report">
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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140 <filter>alignreport_in</filter>
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141 </data>
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142 </outputs>
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143 <tests>
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144 <test><!-- test with defaults and single taxon -->
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145 <param name="filetype" value="usetaxonomy"/>
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146 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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147 <param name="taxon" value="Bacteria;Firmicutes;"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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148 <param name="count" value="amazon.count_table"/>
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149 <output name="taxonomy_out" md5="a2a72b7f53ef6c907b8c4db906fcf03e"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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150 <output name="count_out" md5="6f89b3b99f337414d98f70fcda4b248e"/>
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151 </test>
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152 <test><!-- test with multiple taxons and all additional files -->
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153 <param name="filetype" value="usetaxonomy"/>
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154 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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155 <param name="taxon" value="Bacteria;Firmicutes;,Bacteria;Actinobacteria;"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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156 <param name="group_in" value="abrecovery.groups" ftype="mothur.groups"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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157 <param name="fasta_in" value="abrecovery.fasta" ftype="fasta"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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158 <param name="name_in" value="abrecovery.names" ftype="mothur.names"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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159 <param name="alignreport_in" value="Mock_S280_L001_R1_001_small.contigs.report" ftype="mothur.align.report"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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160 <param name="list_in" value="amazon.an.list" ftype="mothur.list"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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161 <output name="taxonomy_out" md5="449200280fa6c332854204fe78a9bd12"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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162 <output name="group_out" md5="119a2642bd730aad03f7d6c1f8b57a0b" ftype="mothur.groups"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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163 <output name="fasta_out" md5="2c8415a797011e15f19ad85a9c994551" ftype="fasta"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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164 <output name="name_out" md5="712b28c3a84d3c16ef202340717e3a91" ftype="mothur.names"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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165 <output name="alignreport_out" md5="d94be921c3ad1786db3e60dc23c3bc04" ftype="mothur.align.report"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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166 <output_collection name="list_out" count="36">
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167 <element name="0.05" md5="5d4195793e2fc50979b377df468c436a" ftype="mothur.list"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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168 </output_collection>
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169 </test>
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170 <test><!-- test with taxons from file -->
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171 <param name="filetype" value="usetaxonomy"/>
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172 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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173 <param name="taxons" value="Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Dorea(99);,Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Roseburia(47);"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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174 <output name="taxonomy_out" md5="57b4ab4e5b68f8c7d88a0f591c4fe4a1"/>
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175 </test>
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176 <test><!-- test with constaxonomy file -->
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177 <param name="filetype" value="useconstaxonomy"/>
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178 <param name="taxonomy" value="example.constaxonomy" ftype="mothur.cons.taxonomy"/>
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179 <param name="taxon" value="Bacteria;Bacteroidetes;"/>
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180 <output name="taxonomy_out" md5="751fd9b99828998dd909115634027e5e"/>
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181 </test>
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182 <test><!-- test with constaxonomy file and taxons from file -->
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183 <param name="filetype" value="useconstaxonomy"/>
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184 <param name="taxonomy" value="example.constaxonomy" ftype="mothur.cons.taxonomy"/>
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185 <param name="taxons" value="Bacteria(100);Firmicutes(100);Clostridia(70);Clostridiales(70);Lachnospiraceae(51);unclassified;,Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);unclassified;unclassified;unclassified;"/>
152eaafb14ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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186 <output name="taxonomy_out" md5="017f53dd82f3e1afcf48778034b51685"/>
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187 </test>
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188 </tests>
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189 <help>
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190 <![CDATA[
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191
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192 @MOTHUR_OVERVIEW@
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193
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194 **Command Documenation**
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195
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196 The remove.lineage_ command reads a taxonomy_ file and a taxon and generates a new file that contains only the sequences in the that are not from that taxon. You may also include either a fasta, name_, group_, list_, or align.report_ file to this command and mothur will generate new files for each of those containing only the selected sequences.
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197
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198 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline
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199 .. _name: http://www.mothur.org/wiki/Name_file
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200 .. _group: http://www.mothur.org/wiki/Group_file
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201 .. _list: http://www.mothur.org/wiki/List_file
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202 .. _align.report: http://www.mothur.org/wiki/Align.seqs
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203 .. _remove.lineage: http://www.mothur.org/wiki/Remove.lineage
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204
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205 ]]>
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206 </help>
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207 <expand macro="citations"/>
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208 </tool>