Mercurial > repos > iuc > krakentools_combine_kreports

annotate combine_kreports.xml @ 4:4960abe31b4d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit b57c22bb6ff8bbc2730c909713689311be4c3eaa
author iuc
date Thu, 01 Aug 2024 15:46:48 +0000
parents d65105d99074
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1 <tool id="krakentools_combine_kreports" name="Krakentools: Combine multiple Kraken reports" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
0
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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[
4
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10 #if $display_headers:
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11 #for $report in $reports
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12 ln -s '$report' '${report.element_identifier}' &&
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13 #end for
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14 #end if
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16 combine_kreports.py
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17 --reports
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18 #if $display_headers:
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19 #for $report in $reports
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20 '${report.element_identifier}'
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21 #end for
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22 #else:
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23 #for $report in $reports
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24 '${report}'
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25 #end for
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26 #end if
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27 --output '$output'
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28 $display_headers
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29 $only_combined
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30 ]]></command>
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31 <inputs>
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32 <param argument="--reports" type="data" multiple="true" format="tabular" label="Kraken report file(s)" />
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33 <param name="display_headers" type="boolean" checked="true" truevalue="--display-headers" falsevalue="--no-headers" label="display headers in output"/>
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34 <param name="only_combined" type="boolean" checked="false" truevalue="--only-combined" falsevalue="" label="display only combined read counts and percentages"/>
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35 </inputs>
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36 <outputs>
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37 <data name="output" format="tabular" />
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="reports" value="beta_kreport_1.tabular,beta_kreport_3.tabular"/>
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42 <param name="display_headers" value="--no-headers"/>
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43 <output name="output" file="combined_kreport.tabular"/>
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44 </test>
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45 <test>
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46 <param name="reports" value="beta_kreport_1.tabular,beta_kreport_3.tabular"/>
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47 <param name="display_headers" value="--no-headers"/>
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48 <param name="only_combined" value="--only-combined"/>
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49 <output name="output" file="only_combined_count.tabular"/>
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50 </test>
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51 <test>
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52 <param name="reports" value="beta_kreport_1.tabular,beta_kreport_3.tabular"/>
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53 <param name="display_headers" value="--display-headers"/>
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54 <param name="only_combined" value="--only-combined"/>
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55 <output name="output">
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56 <assert_contents>
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57 <has_text text="#Number of Samples:"/>
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58 <has_text text="#S1"/>
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59 <has_text text="#S2"/>
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60 <has_text text="#perc"/>
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61 </assert_contents>
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62 </output>
0
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63 </test>
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64 </tests>
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65 <help><![CDATA[
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66 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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67
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68 Input
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69 ------
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70 Kraken-style reports to combine
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71
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72 Output
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73 ------
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74 Combine Kraken reports
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75
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76 Input file format (tab-delimited)
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77 - percentage of total reads
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78 - number of reads (including reads within subtree)
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79 - number of reads (only at this level)
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80 - taxonomic classification level (U, D, P, C, O, F, G, S,...etc)
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81 - NCBI taxonomic ID
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82 - name of level
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83
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84 Output file format (tab-delimited)
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85 - percentage of total reads (for summed reads)
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86 - combined number of reads (including reads within subtree)
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87 - combined number of reads (only at this level)
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88 - S1_all_reads, S1_lvl_reads, S2_all_reads, S2_lvl_reads, ...etc.
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89 - taxonomic classification level (U, D, P, C, O, F, G, S,...etc)
d65105d99074 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
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90 - NCBI taxonomic ID
d65105d99074 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
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91 - name of level
d65105d99074 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
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92
d65105d99074 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
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93 ]]></help>
d65105d99074 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
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94 <expand macro="citations"/>
d65105d99074 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
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95 </tool>