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annotate kraken-report.xml @ 2:45ced9c12e18 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit cb6ebb843c71dcfc73aa05cc616f8e3229170108-dirty
author devteam
date Wed, 15 Jul 2015 15:22:27 -0400
parents bb3d55e8ef3d
children 9709eedcff4b
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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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1 <tool id="kraken-report" name="Kraken-report" version="1.1.0">
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2 <description>
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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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3 view a sample report of your classification
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <command>
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9 <![CDATA[
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bb3d55e8ef3d planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit cb1743eafd4ca98be0148d557770ef8635cc8d4c-dirty
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10 @SET_DATABASE_PATH@ &&
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11 kraken-report @INPUT_DATABASE@ "${kraken_output}" > "$output_report"
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12 ]]>
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13 </command>
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14 <inputs>
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15 <param format="tabular" label="Kraken output" name="kraken_output" type="data" help="Select taxonomy classification produced by kraken"/>
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16 <expand macro="input_database" />
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17 </inputs>
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18 <outputs>
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19 <data format="tabular" name="output_report" />
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20 </outputs>
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21 <help>
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22 <![CDATA[
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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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24 .. class:: warningmark
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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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26 **Note**: the database used must be the same as the one used in the original Kraken run
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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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28 -----
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30 **Output**
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31
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32 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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34 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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35 2. Number 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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36 3. Number of reads assigned directly to 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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37 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.
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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38 5. NCBI taxonomy ID
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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39 6. Indented scientific name
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41 The scientific names are indented using spaces, according to the tree
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42 structure specified by the taxonomy.
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43 ]]>
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44 </help>
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45 <expand macro="version_command" />
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46 <expand macro="requirements" />
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47 <expand macro="stdio" />
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48 <expand macro="citations" />
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49 </tool>