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annotate kraken-mpa-report.xml @ 3:9ae975c30dde draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit c5dd035dbee6021f3555755cf4c814e760cecd09
author devteam
date Wed, 23 Mar 2016 11:01:19 -0400
parents c4fb5dc47fce
children a3a7440fc618
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1 <?xml version="1.0"?>
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2 <tool id="kraken-mpa-report" name="Kraken-mpa-report" version="1.2.1">
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3 <description>view report of classification for multiple samples</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="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command>
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11 <![CDATA[
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13 #for $input_count, $input_classification in enumerate( $classification ):
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14 ln -s "${input_classification}" "sample_${input_count}" &&
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15 #end for
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17 @SET_DATABASE_PATH@ && kraken-mpa-report @INPUT_DATABASE@
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19 #for $input_count, $input_classification in enumerate( $classification ):
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20 "sample_${input_count}"
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21 #end for
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23 ${show_zeros}
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24 ${header_line}
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26 > "$output_report"
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27 ]]>
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28 </command>
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29 <inputs>
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30 <param format="tabular" label="Kraken output" multiple="True" name="classification" type="data" />
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31 <param checked="False" falsevalue="" help="--show-zeros" label="Display taxa even if they lack a read in any sample" name="show_zeros" truevalue="--show-zeros" type="boolean" />
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32 <param checked="False" falsevalue="" help="--header-line" label="Display a header line indicating sample IDs" name="header_line" truevalue="--header-line" type="boolean" />
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33 <expand macro="input_database" />
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34 </inputs>
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35 <outputs>
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36 <data format="tabular" name="output_report" />
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="classification" value="kraken_mpa_report_input1.tab,kraken_mpa_report_input2.tab" ftype="tabular"/>
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41 <param name="show_zeros" value="--show-zeros"/>
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42 <param name="header_line" value="--header-line"/>
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43 <param name="kraken_database" value="test_db"/>
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44 <output name="output_report" file="kraken_mpa_report_test1_output.tab" ftype="tabular"/>
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45 </test>
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46 </tests>
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47 <help>
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48 <![CDATA[
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50 .. class:: warningmark
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52 **Note**: the database used must be the same as the one used in the original Kraken run
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54 -----
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56 **What is Does**
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58 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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59
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60 --show-zeros Display taxa even if they lack a read in any sample
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61 --header-line Display a header line indicating sample IDs
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62 (sample IDs are the filenames)
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64 -----
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66 **Output**
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68 The output of kraken-mpa-report is tab-delimited, with one line per taxon.
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69
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70 ]]>
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71 </help>
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72 <expand macro="citations" />
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73 </tool>