Mercurial > repos > iuc > krakentools_combine_kreports

comparison combine_kreports.xml @ 0:d65105d99074 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
author iuc
date Mon, 13 Feb 2023 10:23:11 +0000
parents
children 4960abe31b4d
comparison
equal deleted inserted replaced
-1:000000000000 0:d65105d99074
1 <tool id="krakentools_combine_kreports" name="Krakentools: Combine multiple Kraken reports" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>into a combined report file</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="biotools"/>
7 <expand macro="requirements"/>
8 <expand macro="version"/>
9 <command detect_errors="exit_code"><![CDATA[
10 combine_kreports.py
11 --reports
12 #for $report in $reports
13 '$report'
14 #end for
15 --output '$output'
16 $display_headers
17 $only_combined
18 ]]></command>
19 <inputs>
20 <param argument="--reports" type="data" multiple="true" format="tabular" label="Kraken report file(s)" />
21 <param name="display_headers" type="boolean" checked="true" truevalue="--display-headers" falsevalue="--no-headers" label="display headers in output"/>
22 <param name="only_combined" type="boolean" checked="false" truevalue="--only-combined" falsevalue="" label="display only combined read counts and percentages"/>
23 </inputs>
24 <outputs>
25 <data name="output" format="tabular" />
26 </outputs>
27 <tests>
28 <test>
29 <param name="reports" value="beta_kreport_1.tabular,beta_kreport_3.tabular"/>
30 <param name="display_headers" value="--no-headers"/>
31 <output name="output" file="combined_kreport.tabular"/>
32 </test>
33 <test>
34 <param name="reports" value="beta_kreport_1.tabular,beta_kreport_3.tabular"/>
35 <param name="display_headers" value="--no-headers"/>
36 <param name="only_combined" value="--only-combined"/>
37 <output name="output" file="only_combined_count.tabular"/>
38 </test>
39 </tests>
40 <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.
42
43 Input
44 ------
45 Kraken-style reports to combine
46
47 Output
48 ------
49 Combine Kraken reports
50
51 Input file format (tab-delimited)
52 - percentage of total reads
53 - number of reads (including reads within subtree)
54 - number of reads (only at this level)
55 - taxonomic classification level (U, D, P, C, O, F, G, S,...etc)
56 - NCBI taxonomic ID
57 - name of level
58
59 Output file format (tab-delimited)
60 - percentage of total reads (for summed reads)
61 - combined number of reads (including reads within subtree)
62 - combined number of reads (only at this level)
63 - S1_all_reads, S1_lvl_reads, S2_all_reads, S2_lvl_reads, ...etc.
64 - taxonomic classification level (U, D, P, C, O, F, G, S,...etc)
65 - NCBI taxonomic ID
66 - name of level
67
68 ]]></help>
69 <expand macro="citations"/>
70 </tool>