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annotate est-abundance.xml @ 2:a5145865e467 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2a7a1f987c8fd07ae19140dd0ae86ff2a710de52"
author iuc
date Thu, 17 Oct 2019 15:50:37 -0400
parents b7b1c8bf7ae0
children e1d4cab2daea
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2
a5145865e467 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2a7a1f987c8fd07ae19140dd0ae86ff2a710de52"
iuc
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1 <tool id="est_abundance" name="Estimate Abundance at Taxonomic Level" version="@TOOL_VERSION@+galaxy0">
0
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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2 <description>Bayesian Reestimation of Abundance with KrakEN</description>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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3 <macros>
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4 <import>macros.xml</import>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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5 </macros>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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6 <edam_topics>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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7 <edam_topic>topic_3174</edam_topic>
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8 <edam_topic>topic_3697</edam_topic>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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9 </edam_topics>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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10 <edam_operations>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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11 <edam_operation>operation_2238</edam_operation>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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12 </edam_operations>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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13 <expand macro="requirements" />
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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14 <command detect_errors="exit_code"><![CDATA[
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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15 est_abundance.py
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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16 -i '$input'
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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17 -k '$kmer_distr.fields.path'
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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18 -l $level
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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19 -t $threshold
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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20 -o '$report'
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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21 ]]>
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22 </command>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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23 <inputs>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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24 <param name="input" type="data" format="tabular" label="Kraken report file" />
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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25 <param label="Select a Kmer distribution" name="kmer_distr" type="select">
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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26 <options from_data_table="bracken_databases">
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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27 <validator message="No database is available" type="no_options" />
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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28 </options>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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29 </param>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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30 <param name="level" type="select" label="Level" help="Level to push all reads to" >
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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31 <option value="S" selected="true">Species</option>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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32 <option value="G">Genus</option>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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33 <option value="F">Family</option>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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34 <option value="O">Order</option>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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35 <option value="C">Class</option>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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36 <option value="P">Phylum</option>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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37 <option value="D">Domain</option>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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38 </param>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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39 <param name="threshold" type="integer" value="10" label="Number of mismatches allowed when matching tag"
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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40 help="Threshold for the minimum number of reads kraken must assign to a classification for that
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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41 classification to be considered in the final abundance estimation." />
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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42 </inputs>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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43 <outputs>
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44 <data name="report" format="tabular" label="${tool.name} on ${on_string}: Report" />
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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45 </outputs>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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46 <tests>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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47 <test>
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48 <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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49 <param name="level" value="S" />
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50 <param name="bracken_database" value="test_entry"/>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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51 <output name="report" file="NC_003198.1_simulated_bracken_report.txt" ftype="tabular"/>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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52 </test>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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53 <test>
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54 <param name="input" value="NC_011750.1_simulated_kraken_report.txt" ftype="tabular"/>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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55 <param name="level" value="S" />
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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56 <param name="bracken_database" value="test_entry"/>
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57 <output name="report" file="NC_011750.1_simulated_bracken_report.txt" ftype="tabular"/>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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58 </test>
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59 </tests>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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60 <help>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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61 <![CDATA[
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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62 Documentation can be found at `site <http://ccb.jhu.edu/software/bracken/index.shtml?t=manual>`_.
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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63 ]]></help>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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64 <expand macro="citations" />
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65 </tool>