Mercurial > repos > iuc > krakentools_combine_kreports

annotate combine_kreports.xml @ 2:e0d3f5969458 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 92c58a65005708fbd56b27b86969c01a1258ddb9
author iuc
date Wed, 15 Mar 2023 18:18:07 +0000
parents d65105d99074
children 4960abe31b4d
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d65105d99074 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
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1 <tool id="krakentools_combine_kreports" name="Krakentools: Combine multiple Kraken reports" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
d65105d99074 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
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2 <description>into a combined report file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="biotools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="version"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 combine_kreports.py
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11 --reports
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12 #for $report in $reports
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13 '$report'
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14 #end for
d65105d99074 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
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15 --output '$output'
d65105d99074 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
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16 $display_headers
d65105d99074 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
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17 $only_combined
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18 ]]></command>
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19 <inputs>
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20 <param argument="--reports" type="data" multiple="true" format="tabular" label="Kraken report file(s)" />
d65105d99074 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
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21 <param name="display_headers" type="boolean" checked="true" truevalue="--display-headers" falsevalue="--no-headers" label="display headers in output"/>
d65105d99074 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
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22 <param name="only_combined" type="boolean" checked="false" truevalue="--only-combined" falsevalue="" label="display only combined read counts and percentages"/>
d65105d99074 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
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23 </inputs>
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24 <outputs>
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25 <data name="output" format="tabular" />
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="reports" value="beta_kreport_1.tabular,beta_kreport_3.tabular"/>
d65105d99074 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
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30 <param name="display_headers" value="--no-headers"/>
d65105d99074 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
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31 <output name="output" file="combined_kreport.tabular"/>
d65105d99074 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
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32 </test>
d65105d99074 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
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33 <test>
d65105d99074 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
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34 <param name="reports" value="beta_kreport_1.tabular,beta_kreport_3.tabular"/>
d65105d99074 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
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35 <param name="display_headers" value="--no-headers"/>
d65105d99074 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
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36 <param name="only_combined" value="--only-combined"/>
d65105d99074 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
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37 <output name="output" file="only_combined_count.tabular"/>
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38 </test>
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39 </tests>
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40 <help><![CDATA[
d65105d99074 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
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41 KrakenTools is a suite of scripts to be used alongside the Kraken, KrakenUniq, Kraken 2, or Bracken programs. These scripts are designed to help Kraken users with downstream analysis of Kraken results. This script combines multiple Kraken reports into a combined report file.
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42
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43 Input
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44 ------
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45 Kraken-style reports to combine
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46
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47 Output
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48 ------
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49 Combine Kraken reports
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50
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51 Input file format (tab-delimited)
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52 - percentage of total reads
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53 - number of reads (including reads within subtree)
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54 - number of reads (only at this level)
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55 - taxonomic classification level (U, D, P, C, O, F, G, S,...etc)
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56 - NCBI taxonomic ID
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57 - name of level
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58
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59 Output file format (tab-delimited)
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60 - percentage of total reads (for summed reads)
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61 - combined number of reads (including reads within subtree)
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62 - combined number of reads (only at this level)
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63 - S1_all_reads, S1_lvl_reads, S2_all_reads, S2_lvl_reads, ...etc.
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64 - taxonomic classification level (U, D, P, C, O, F, G, S,...etc)
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65 - NCBI taxonomic ID
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66 - name of level
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67
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68 ]]></help>
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69 <expand macro="citations"/>
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70 </tool>