Mercurial > repos > iuc > krakentools_beta_diversity
annotate beta_diversity.xml @ 4:c254d75b8b67 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit f37828f1d6b9c53cc2e7ea334ee9a2fb8dbd8711
author | iuc |
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date | Tue, 20 Jun 2023 20:03:30 +0000 |
parents | fc2077c654fb |
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fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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1 <tool id="krakentools_beta_diversity" name="Krakentools: calculates beta diversity (Bray-Curtis dissimilarity)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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2 <description>from Kraken, Krona and Bracken files</description> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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3 <macros> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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4 <import>macros.xml</import> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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5 </macros> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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6 <expand macro="biotools"/> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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7 <expand macro="requirements"/> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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8 <expand macro="version"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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9 <command detect_errors="exit_code"><![CDATA[ |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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10 beta_diversity.py |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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11 --inputs |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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12 #for $input in $inputs |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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13 '$input' |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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14 #end for |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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15 --type '$sample.type' |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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16 #if $sample.type == 'kreport' |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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17 --level '$sample.level' |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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18 #else if $sample.type == 'krona' |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
parents:
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19 --level '$sample.level' |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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20 #end if |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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21 > '$output' |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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22 ]]></command> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
parents:
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23 <inputs> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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24 <param argument="--inputs" type="data" multiple="true" format="tabular" label="Taxonomy file(s)" help="The files can be generated by Kraken, Bracken or Krona"/> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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25 <conditional name="sample"> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
parents:
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26 <param argument="--type" type="select" label="Specify type of input file(s)"> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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27 <option value="single" selected="true">Single tabular data file</option> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
parents:
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28 <option value="simple">Tabular data files</option> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
parents:
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29 <option value="bracken">Braken species abundance file</option> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
parents:
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30 <option value="kreport">Kraken report file</option> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
parents:
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31 <option value="krona">Krona file</option> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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32 </param> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
parents:
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33 <when value="single"/> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
parents:
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34 <when value="simple"/> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
parents:
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35 <when value="bracken"/> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
parents:
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36 <when value="kreport"> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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37 <expand macro="param_level"/> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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38 </when> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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39 <when value="krona"> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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40 <expand macro="param_level"/> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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41 </when> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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42 </conditional> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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43 |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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44 </inputs> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
parents:
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45 <outputs> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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46 <data name="output" format="txt" /> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
parents:
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47 </outputs> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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48 <tests> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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49 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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50 <param name="inputs" value="beta_bracken_1.tabular,beta_bracken_2.tabular,beta_bracken_3.tabular"/> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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51 <param name="type" value="bracken"/> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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52 <output name="output" ftype="txt"> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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53 <assert_contents> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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54 <has_text text="0.629"/> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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55 <has_text text="0.993"/> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
parents:
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56 <has_text text="0.995"/> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
parents:
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57 </assert_contents> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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58 </output> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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59 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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60 <test> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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61 <param name="inputs" value="beta_kreport_1.tabular,beta_kreport_2.tabular,beta_kreport_3.tabular"/> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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62 <param name="type" value="kreport"/> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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63 <output name="output" ftype="txt"> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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64 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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65 <has_text text="0.584"/> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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66 <has_text text="0.996"/> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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67 <has_text text="0.995"/> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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68 </assert_contents> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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69 </output> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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70 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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71 <test> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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72 <param name="inputs" value="beta_krona_1.tabular,beta_krona_2.tabular"/> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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73 <param name="type" value="krona"/> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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74 <param name="level" value="G"/> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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75 <output name="output" ftype="txt"> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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76 <assert_contents> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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77 <has_text text="0.993"/> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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78 </assert_contents> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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79 </output> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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80 </test> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
iuc
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81 </tests> |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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82 <help><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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83 KrakenTools is a suite of scripts to be used alongside the Kraken, KrakenUniq, Kraken 2, or Bracken programs. These scripts are designed to help Kraken users with downstream analysis of Kraken results. This program calculates the beta diversity (Bray-Curtis dissimilarity) from kraken, krona and bracken files. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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84 |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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85 Input |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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86 ------ |
fc2077c654fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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87 Bracken files, Kraken and Kracken2 report files and Krona files. Additionally, you can pass any tab-separated file and specify the columns with the taxonomical information and read counts (--cols). |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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88 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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89 Output |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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91 Beta diversity of the input files |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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92 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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93 ]]></help> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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94 <expand macro="citations"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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95 </tool> |