annotate est-abundance.xml @ 8:1d4bd12f01cf draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2d68ebc8d29e6046811970c6ef04f683e9916857
author iuc
date Thu, 18 Jan 2024 15:38:05 +0000
parents 978ae4147c29
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
1 <tool id="est_abundance" name="Bracken" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
2 <description>to re-estimate abundance at a taxonomic level from kraken output</description>
0
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
3 <macros>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
5 </macros>
7
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
6 <expand macro="edam"/>
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
7 <expand macro="xref"/>
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
8 <expand macro="requirements"/>
0
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
7
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
10 ## Prevent logfile pipe below from quenching the raised error.
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
11 set -o pipefail &&
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
12
6
79450f7fd718 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit c396abec691d64fc4cb7f205f54c01b1be7fd649
iuc
parents: 5
diff changeset
13 est_abundance.py
7
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
14 -i '$input'
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
15 -k '$kmer_distr.fields.path'
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
16 -l $level
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
17 -t $threshold
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
18 -o '$report'
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
19
6
79450f7fd718 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit c396abec691d64fc4cb7f205f54c01b1be7fd649
iuc
parents: 5
diff changeset
20 ## --out-report needs to be set always, since it is written next to the input file
79450f7fd718 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit c396abec691d64fc4cb7f205f54c01b1be7fd649
iuc
parents: 5
diff changeset
21 --out-report bracken.report
7
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
22
6
79450f7fd718 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit c396abec691d64fc4cb7f205f54c01b1be7fd649
iuc
parents: 5
diff changeset
23 #if $logfile_output == "True"
79450f7fd718 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit c396abec691d64fc4cb7f205f54c01b1be7fd649
iuc
parents: 5
diff changeset
24 | tee '$logfile'
79450f7fd718 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit c396abec691d64fc4cb7f205f54c01b1be7fd649
iuc
parents: 5
diff changeset
25 #end if
0
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
26 ]]>
6
79450f7fd718 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit c396abec691d64fc4cb7f205f54c01b1be7fd649
iuc
parents: 5
diff changeset
27 </command>
0
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
28 <inputs>
7
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
29 <param name="input" type="data" format="tabular" label="Kraken report file"/>
0
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
30 <param label="Select a Kmer distribution" name="kmer_distr" type="select">
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
31 <options from_data_table="bracken_databases">
7
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
32 <validator message="No database is available" type="no_options"/>
0
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
33 </options>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
34 </param>
7
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
35 <param name="level" type="select" label="Level" help="Level to push all reads to">
8
1d4bd12f01cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2d68ebc8d29e6046811970c6ef04f683e9916857
iuc
parents: 7
diff changeset
36 <option value="S2">Subspecies 2</option>
1d4bd12f01cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2d68ebc8d29e6046811970c6ef04f683e9916857
iuc
parents: 7
diff changeset
37 <option value="S1">Subspecies 1</option>
0
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
38 <option value="S" selected="true">Species</option>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
39 <option value="G">Genus</option>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
40 <option value="F">Family</option>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
41 <option value="O">Order</option>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
42 <option value="C">Class</option>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
43 <option value="P">Phylum</option>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
44 <option value="D">Domain</option>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
45 </param>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
46 <param name="threshold" type="integer" value="10" label="Number of mismatches allowed when matching tag"
6
79450f7fd718 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit c396abec691d64fc4cb7f205f54c01b1be7fd649
iuc
parents: 5
diff changeset
47 help="Threshold for the minimum number of reads kraken must assign to a classification for that
7
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
48 classification to be considered in the final abundance estimation."/>
5
19035a7b1106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 004793bd31d2b4dcc065fb1fe3ad40fa98190c56
iuc
parents: 3
diff changeset
49 <param argument="--out-report" type="boolean" checked="false" label="Produce Kraken-Style Bracken report"/>
6
79450f7fd718 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit c396abec691d64fc4cb7f205f54c01b1be7fd649
iuc
parents: 5
diff changeset
50 <param name="logfile_output" type="boolean" truevalue="True" falsevalue="False" label="Add log file output"/>
0
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
51 </inputs>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
52 <outputs>
7
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
53 <data name="report" format="tabular" label="${tool.name} on ${on_string}: Report"/>
5
19035a7b1106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 004793bd31d2b4dcc065fb1fe3ad40fa98190c56
iuc
parents: 3
diff changeset
54 <data name="kraken_report" format="tabular" from_work_dir="bracken.report" label="${tool.name} on ${on_string}: Kraken style report">
19035a7b1106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 004793bd31d2b4dcc065fb1fe3ad40fa98190c56
iuc
parents: 3
diff changeset
55 <filter>out_report</filter>
19035a7b1106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 004793bd31d2b4dcc065fb1fe3ad40fa98190c56
iuc
parents: 3
diff changeset
56 </data>
6
79450f7fd718 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit c396abec691d64fc4cb7f205f54c01b1be7fd649
iuc
parents: 5
diff changeset
57 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file">
79450f7fd718 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit c396abec691d64fc4cb7f205f54c01b1be7fd649
iuc
parents: 5
diff changeset
58 <filter> logfile_output == True </filter>
79450f7fd718 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit c396abec691d64fc4cb7f205f54c01b1be7fd649
iuc
parents: 5
diff changeset
59 </data>
0
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
60 </outputs>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
61 <tests>
5
19035a7b1106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 004793bd31d2b4dcc065fb1fe3ad40fa98190c56
iuc
parents: 3
diff changeset
62 <test expect_num_outputs="1">
0
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
63 <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/>
7
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
64 <param name="level" value="S"/>
6
79450f7fd718 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit c396abec691d64fc4cb7f205f54c01b1be7fd649
iuc
parents: 5
diff changeset
65 <param name="kmer_distr" value="test_entry"/>
79450f7fd718 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit c396abec691d64fc4cb7f205f54c01b1be7fd649
iuc
parents: 5
diff changeset
66 <param name="logfile_output" value="False"/>
3
e1d4cab2daea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2e8d990fa8b6de085046195464071020b467ce5a"
iuc
parents: 2
diff changeset
67 <output name="report" file="NC_003198.1_simulated_bracken_report.txt" ftype="tabular"/>
0
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
68 </test>
6
79450f7fd718 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit c396abec691d64fc4cb7f205f54c01b1be7fd649
iuc
parents: 5
diff changeset
69 <test expect_num_outputs="3">
0
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
70 <param name="input" value="NC_011750.1_simulated_kraken_report.txt" ftype="tabular"/>
7
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
71 <param name="level" value="S"/>
6
79450f7fd718 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit c396abec691d64fc4cb7f205f54c01b1be7fd649
iuc
parents: 5
diff changeset
72 <param name="kmer_distr" value="test_entry"/>
5
19035a7b1106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 004793bd31d2b4dcc065fb1fe3ad40fa98190c56
iuc
parents: 3
diff changeset
73 <param name="out_report" value="true"/>
6
79450f7fd718 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit c396abec691d64fc4cb7f205f54c01b1be7fd649
iuc
parents: 5
diff changeset
74 <param name="logfile_output" value="True"/>
3
e1d4cab2daea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2e8d990fa8b6de085046195464071020b467ce5a"
iuc
parents: 2
diff changeset
75 <output name="report" file="NC_011750.1_simulated_bracken_report.txt" ftype="tabular"/>
5
19035a7b1106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 004793bd31d2b4dcc065fb1fe3ad40fa98190c56
iuc
parents: 3
diff changeset
76 <output name="kraken_report" file="NC_011750.1_simulated_kraken_style_bracken_report.txt" ftype="tabular"/>
7
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
77 <output name="logfile" file="test2.log" lines_diff="8"/>
0
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
78 </test>
8
1d4bd12f01cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2d68ebc8d29e6046811970c6ef04f683e9916857
iuc
parents: 7
diff changeset
79 <test expect_num_outputs="1">
1d4bd12f01cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2d68ebc8d29e6046811970c6ef04f683e9916857
iuc
parents: 7
diff changeset
80 <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/>
1d4bd12f01cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2d68ebc8d29e6046811970c6ef04f683e9916857
iuc
parents: 7
diff changeset
81 <param name="level" value="S1"/>
1d4bd12f01cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2d68ebc8d29e6046811970c6ef04f683e9916857
iuc
parents: 7
diff changeset
82 <param name="kmer_distr" value="test_entry"/>
1d4bd12f01cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2d68ebc8d29e6046811970c6ef04f683e9916857
iuc
parents: 7
diff changeset
83 <param name="logfile_output" value="False"/>
1d4bd12f01cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2d68ebc8d29e6046811970c6ef04f683e9916857
iuc
parents: 7
diff changeset
84 <output name="report" file="NC_003198.1_simulated_bracken_report_S1.txt" ftype="tabular"/>
1d4bd12f01cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2d68ebc8d29e6046811970c6ef04f683e9916857
iuc
parents: 7
diff changeset
85 </test>
1d4bd12f01cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2d68ebc8d29e6046811970c6ef04f683e9916857
iuc
parents: 7
diff changeset
86 <test expect_num_outputs="1">
1d4bd12f01cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2d68ebc8d29e6046811970c6ef04f683e9916857
iuc
parents: 7
diff changeset
87 <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/>
1d4bd12f01cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2d68ebc8d29e6046811970c6ef04f683e9916857
iuc
parents: 7
diff changeset
88 <param name="level" value="S2"/>
1d4bd12f01cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2d68ebc8d29e6046811970c6ef04f683e9916857
iuc
parents: 7
diff changeset
89 <param name="kmer_distr" value="test_entry"/>
1d4bd12f01cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2d68ebc8d29e6046811970c6ef04f683e9916857
iuc
parents: 7
diff changeset
90 <param name="logfile_output" value="False"/>
1d4bd12f01cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2d68ebc8d29e6046811970c6ef04f683e9916857
iuc
parents: 7
diff changeset
91 <output name="report" file="NC_003198.1_simulated_bracken_report_S2.txt" ftype="tabular"/>
1d4bd12f01cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2d68ebc8d29e6046811970c6ef04f683e9916857
iuc
parents: 7
diff changeset
92 </test>
0
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
93 </tests>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
94 <help>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
95 <![CDATA[
7
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
96 Bracken relies on Bayesian probabilities that derive from the knowledge about the Kraken classification of each read-length kmer from all genomes within the provided Kraken database. It takes the tabular report output of kraken/kraken2 representing abundance of all detected taxa and provides as output a table representing the re-estimated abundances of different taxa at the taxonomy level pre-determined by the user. For more information about the operation behind the scene, visit http://ccb.jhu.edu/software/bracken/index.shtml?t=manual.
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
97
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
98 Prior to abundance estimation with bracken, we must divide each genome in the Kraken database into read-length kmers, classify each of those kmers and store as a data structure. This indexing step has already been performed for you and it suffices to select the name of the correct kraken DB that you used for read classification.
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
99
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
100 Bracken output file format (tabular):
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
101 * Taxon name
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
102 * Taxonomy ID
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
103 * Level ID (S=Species, G=Genus, O=Order, F=Family, P=Phylum, K=Kingdom)
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
104 * Kraken assigned reads
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
105 * Added reads with abundance re-estimation
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
106 * Total reads after abundance re-estimation
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
107 * Fraction of total reads
0
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
108 ]]></help>
7
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
parents: 6
diff changeset
109 <expand macro="citations"/>
0
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
110 </tool>