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

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author devteam
date Wed, 15 Jul 2015 15:22:27 -0400
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children a539aeea69fc
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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-mpa-report" name="Kraken-mpa-report" version="1.1.0">
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2 <expand macro="version_command" />
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3 <expand macro="requirements" />
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4 <expand macro="stdio" />
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5 <description>
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6 view report of classification for multiple samples
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7 </description>
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8 <macros>
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9 <import>macros.xml</import>
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10 </macros>
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11 <command>
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12 <![CDATA[
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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14 #for $input_count, $input_classification in enumerate( $classification ):
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15 ln -s "${input_classification}" "sample_${input_count}" &&
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16 #end for
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18 kraken-mpa-report @INPUT_DATABASE@
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20 #for $input_count, $input_classification in enumerate( $classification ):
45ced9c12e18 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit cb6ebb843c71dcfc73aa05cc616f8e3229170108-dirty
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21 "sample_${input_count}"
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22 #end for
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24 ${show_zeros}
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25 ${header_line}
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27 > "$output_report"
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30 ]]>
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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31 </command>
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32 <inputs>
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33 <param multiple="True" name="classification" type="data" format="tabular" label="Kraken output"/>
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34 <param name="show_zeros" type="boolean" truevalue="--show-zeros" falsevalue="" checked="False" label="Display taxa even if they lack a read in any sample" help="--show-zeros"/>
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 <param name="header_line" type="boolean" truevalue="--header-line" falsevalue="" checked="False" label="Display a header line indicating sample IDs" help="--header-line"/>
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36 <expand macro="input_database" />
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37 </inputs>
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38 <outputs>
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39 <data format="tabular" name="output_report" />
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40 </outputs>
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41 <help>
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42 <![CDATA[
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44 .. class:: warningmark
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46 **Note**: the database used must be the same as the one used in the original Kraken run
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48 -----
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50 **What is Does**
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52 Kraken-mpa-report summarizes read counts across taxonomic ranks for multiple samples. This is convenient for comparing results across multiple expreriments, conditions, locations, etc. It support sthe following parameters::
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54 --show-zeros Display taxa even if they lack a read in any sample
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55 --header-line Display a header line indicating sample IDs
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56 (sample IDs are the filenames)
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58 -----
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60 **Output**
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62 The output of kraken-mpa-report is tab-delimited, with one line per taxon.
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68 ]]>
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69 </help>
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70 <expand macro="citations" />
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71 </tool>