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annotate kraken-report.xml @ 4:9709eedcff4b draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
author devteam
date Fri, 18 Dec 2015 19:41:35 -0500
parents 45ced9c12e18
children e9e42bf5c6a8
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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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3 view a sample report of your classification
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4 </description>
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5
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements" />
9709eedcff4b planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
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10 <expand macro="stdio" />
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11 <expand macro="version_command" />
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12 <command>
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13 <![CDATA[
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14 @SET_DATABASE_PATH@ &&
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15 kraken-report @INPUT_DATABASE@ "${kraken_output}" > "$output_report"
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16 ]]>
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17 </command>
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18 <inputs>
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19 <param format="tabular" label="Kraken output" name="kraken_output" type="data" help="Select taxonomy classification produced by kraken"/>
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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>
9709eedcff4b planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
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26 <test>
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27 <param name="kraken_output" value="kraken_report_test1.tab" ftype="tabular"/>
9709eedcff4b planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
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28 <param name="kraken_database" value="test_db"/>
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29 <output name="output_report" file="kraken_report_test1_output.tab" ftype="tabular"/>
9709eedcff4b planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
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30 </test>
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31 </tests>
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32
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33 <help>
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34 <![CDATA[
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36 .. class:: warningmark
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38 **Note**: the database used must be the same as the one used in the original Kraken run
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40 -----
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42 **Output**
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43
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44 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
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46 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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47 2. Number of reads covered by the clade rooted at this taxon
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48 3. Number of reads assigned directly to this taxon
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49 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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50 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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51 6. Indented scientific name
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53 The scientific names are indented using spaces, according to the tree
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54 structure specified by the taxonomy.
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55 ]]>
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56 </help>
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57 <expand macro="citations" />
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58 </tool>