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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 3a94fbf6a188ea81441ef2f654ba5a74bff56f22
author iuc
date Tue, 12 Mar 2024 16:10:45 +0000
parents 1902d3de4a4f
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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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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="xrefs"/>
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8 <expand macro="requirements" />
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9 <expand macro="version_command" />
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10 <command detect_errors="exit_code"><![CDATA[
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11 @SET_DATABASE_PATH@ &&
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13 kraken-report
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14 @INPUT_DATABASE@
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15 '${kraken_output}'
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16 > '$output_report'
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17 ]]></command>
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18 <inputs>
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19 <param name="kraken_output" type="data" format="tabular" label="Kraken output" help="Select taxonomy classification produced by kraken"/>
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21 <expand macro="input_database" />
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22 </inputs>
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23 <outputs>
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24 <data format="tabular" name="output_report" />
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="kraken_output" value="kraken-report/kraken_report_test1.tab" ftype="tabular"/>
1902d3de4a4f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
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29 <param name="kraken_database" value="new_style_test_entry"/>
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30 <output name="output_report" ftype="tabular" file="kraken-report/kraken_report_test1_output.tab"/>
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31 </test>
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32 </tests>
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34 <help><![CDATA[
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36 .. class:: warningmark
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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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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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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46 1. Percentage of reads covered by the clade rooted at this taxon
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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.
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50 5. NCBI taxonomy ID
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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 ]]></help>
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56 <expand macro="citations" />
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57 </tool>