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1 <tool id="kraken-report" name="Kraken-report" version="1.0.0">
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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 <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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10 kraken-report @INPUT_DATABASE@ "${kraken_output}" > "$output_report"
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11 ]]>
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12 </command>
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13 <inputs>
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14 <param format="tabular" label="Input the Sequenced Kraken Output from your Current History" name="kraken_output" type="data" />
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15 <expand macro="input_database" />
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16 </inputs>
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17 <outputs>
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18 <data format="tabular" name="output_report" />
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19 </outputs>
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20 <help>
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21 <![CDATA[
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22
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23 ***Note that the database used must be the same as the one used to generate
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24 the output file, or the report script may encounter problems.***
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25
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26
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27
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28 **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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29
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30 1)Percentage of reads covered by the clade rooted at this taxon
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31
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32 2)Number of reads covered by the clade rooted at this taxon
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33
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34 3)Number of reads assigned directly to this taxon
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35
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36 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 -.
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37
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38 5)NCBI taxonomy ID
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39
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40 6)Indented scientific name
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41
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42 The scientific names are indented using spaces, according to the tree
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43 structure specified by the taxonomy.
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44 ]]>
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45 </help>
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46 <expand macro="version_command" />
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47 <expand macro="requirements" />
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48 <expand macro="stdio" />
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49 <expand macro="citations" />
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50 </tool>
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