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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 1590e274eaa41ea77a6017111f9122e0a58aa75d-dirty"
author iuc
date Tue, 03 Dec 2019 18:30:40 +0000
parents 1c163820e346
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1c163820e346 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken_report/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
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1 <tool id="kraken-report" name="Kraken-report" version="@WRAPPER_VERSION@">
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2 <description>view sample report of a classification</description>
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3
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="version_command" />
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9 <command detect_errors="exit_code"><![CDATA[
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10 @SET_DATABASE_PATH@ &&
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1c163820e346 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken_report/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
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12 kraken-report
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13 @INPUT_DATABASE@
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14 '${kraken_output}'
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15 > '$output_report'
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16 ]]></command>
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17 <inputs>
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18 <param name="kraken_output" type="data" format="tabular" label="Kraken output" help="Select taxonomy classification produced by kraken"/>
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19
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20 <expand macro="input_database" />
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21 </inputs>
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22 <outputs>
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23 <data format="tabular" name="output_report" />
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24 </outputs>
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25 <tests>
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26 <test>
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8ddbdc9cdc57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 1590e274eaa41ea77a6017111f9122e0a58aa75d-dirty"
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27 <param name="kraken_output" value="kraken-report/kraken_report_test1.tab" ftype="tabular"/>
8ddbdc9cdc57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 1590e274eaa41ea77a6017111f9122e0a58aa75d-dirty"
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28 <param name="kraken_database" value="new_style_test_entry"/>
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29 <output name="output_report" ftype="tabular" file="kraken-report/kraken_report_test1_output.tab"/>
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30 </test>
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31 </tests>
9709eedcff4b planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
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33 <help><![CDATA[
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35 .. class:: warningmark
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37 **Note**: the database used must be the same as the one used in the original Kraken run
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39 -----
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41 **Output**
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43 The output of kraken-report is tab-delimited, with one line per taxon. The fields of the output, from left-to-right, are as follows::
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45 1. Percentage of reads covered by the clade rooted at this taxon
45ced9c12e18 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit cb6ebb843c71dcfc73aa05cc616f8e3229170108-dirty
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46 2. Number of reads covered by the clade rooted at this taxon
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47 3. Number of reads assigned directly to this taxon
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48 4. A rank code, indicating (U)nclassified, (D)omain, (K)ingdom, (P)hylum, (C)lass, (O)rder, (F)amily, (G)enus, or (S)pecies. All other ranks are simply filled with a dash.
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49 5. NCBI taxonomy ID
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50 6. Indented scientific name
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52 The scientific names are indented using spaces, according to the tree
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53 structure specified by the taxonomy.
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54 ]]></help>
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55 <expand macro="citations" />
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56 </tool>