Mercurial > repos > iuc > krakentools_combine_kreports

comparison 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
children
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3:073c867c5244 4:4960abe31b4d
1 <tool id="krakentools_combine_kreports" name="Krakentools: Combine multiple Kraken reports" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="krakentools_combine_kreports" name="Krakentools: Combine multiple Kraken reports" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
2 <description>into a combined report file</description> 2 <description>into a combined report file</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="biotools"/> 6 <expand macro="biotools"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="version"/> 8 <expand macro="version"/>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 combine_kreports.py 10 #if $display_headers:
11 #for $report in $reports
12 ln -s '$report' '${report.element_identifier}' &&
13 #end for
14 #end if
15
16 combine_kreports.py
11 --reports 17 --reports
12 #for $report in $reports 18 #if $display_headers:
13 '$report' 19 #for $report in $reports
14 #end for 20 '${report.element_identifier}'
15 --output '$output' 21 #end for
22 #else:
23 #for $report in $reports
24 '${report}'
25 #end for
26 #end if
27 --output '$output'
16 $display_headers 28 $display_headers
17 $only_combined 29 $only_combined
18 ]]></command> 30 ]]></command>
19 <inputs> 31 <inputs>
20 <param argument="--reports" type="data" multiple="true" format="tabular" label="Kraken report file(s)" /> 32 <param argument="--reports" type="data" multiple="true" format="tabular" label="Kraken report file(s)" />
33 <test> 45 <test>
34 <param name="reports" value="beta_kreport_1.tabular,beta_kreport_3.tabular"/> 46 <param name="reports" value="beta_kreport_1.tabular,beta_kreport_3.tabular"/>
35 <param name="display_headers" value="--no-headers"/> 47 <param name="display_headers" value="--no-headers"/>
36 <param name="only_combined" value="--only-combined"/> 48 <param name="only_combined" value="--only-combined"/>
37 <output name="output" file="only_combined_count.tabular"/> 49 <output name="output" file="only_combined_count.tabular"/>
50 </test>
51 <test>
52 <param name="reports" value="beta_kreport_1.tabular,beta_kreport_3.tabular"/>
53 <param name="display_headers" value="--display-headers"/>
54 <param name="only_combined" value="--only-combined"/>
55 <output name="output">
56 <assert_contents>
57 <has_text text="#Number of Samples:"/>
58 <has_text text="#S1"/>
59 <has_text text="#S2"/>
60 <has_text text="#perc"/>
61 </assert_contents>
62 </output>
38 </test> 63 </test>
39 </tests> 64 </tests>
40 <help><![CDATA[ 65 <help><![CDATA[
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. 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.
42 67