Mercurial > repos > iuc > bracken

annotate est-abundance.xml @ 5:19035a7b1106 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/bracken commit 004793bd31d2b4dcc065fb1fe3ad40fa98190c56
author iuc
date Wed, 06 Jul 2022 14:47:54 +0000
parents e1d4cab2daea
children 79450f7fd718
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
19035a7b1106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 004793bd31d2b4dcc065fb1fe3ad40fa98190c56
iuc
parents: 3
diff changeset
1 <tool id="est_abundance" name="Estimate Abundance at Taxonomic Level" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
0
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
2 <description>Bayesian Reestimation of Abundance with KrakEN</description>
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>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
6 <edam_topics>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
7 <edam_topic>topic_3174</edam_topic>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
8 <edam_topic>topic_3697</edam_topic>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
9 </edam_topics>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
10 <edam_operations>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
11 <edam_operation>operation_2238</edam_operation>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
12 </edam_operations>
5
19035a7b1106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 004793bd31d2b4dcc065fb1fe3ad40fa98190c56
iuc
parents: 3
diff changeset
13 <xrefs>
19035a7b1106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 004793bd31d2b4dcc065fb1fe3ad40fa98190c56
iuc
parents: 3
diff changeset
14 <xref type="bio.tools">bracken</xref>
19035a7b1106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 004793bd31d2b4dcc065fb1fe3ad40fa98190c56
iuc
parents: 3
diff changeset
15 </xrefs>
0
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
16 <expand macro="requirements" />
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
17 <command detect_errors="exit_code"><![CDATA[
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
18 est_abundance.py
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
19 -i '$input'
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
20 -k '$kmer_distr.fields.path'
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
21 -l $level
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
22 -t $threshold
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
23 -o '$report'
5
19035a7b1106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 004793bd31d2b4dcc065fb1fe3ad40fa98190c56
iuc
parents: 3
diff changeset
24 ## --out-report needs to be set always, since it is written next to the input file
19035a7b1106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 004793bd31d2b4dcc065fb1fe3ad40fa98190c56
iuc
parents: 3
diff changeset
25 --out-report bracken.report
0
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
26 ]]>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
27 </command>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
28 <inputs>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
29 <param name="input" type="data" format="tabular" label="Kraken report file" />
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">
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
32 <validator message="No database is available" type="no_options" />
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>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
35 <param name="level" type="select" label="Level" help="Level to push all reads to" >
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
36 <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
37 <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
38 <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
39 <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
40 <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
41 <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
42 <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
43 </param>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
44 <param name="threshold" type="integer" value="10" label="Number of mismatches allowed when matching tag"
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
45 help="Threshold for the minimum number of reads kraken must assign to a classification for that
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
46 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
47 <param argument="--out-report" type="boolean" checked="false" label="Produce Kraken-Style Bracken report"/>
0
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
48 </inputs>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
49 <outputs>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
50 <data name="report" format="tabular" label="${tool.name} on ${on_string}: Report" />
5
19035a7b1106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 004793bd31d2b4dcc065fb1fe3ad40fa98190c56
iuc
parents: 3
diff changeset
51 <data name="kraken_report" format="tabular" from_work_dir="bracken.report" label="${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
52 <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
53 </data>
0
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
54 </outputs>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
55 <tests>
5
19035a7b1106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 004793bd31d2b4dcc065fb1fe3ad40fa98190c56
iuc
parents: 3
diff changeset
56 <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
57 <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
58 <param name="level" value="S" />
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
59 <param name="bracken_database" value="test_entry"/>
3
e1d4cab2daea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2e8d990fa8b6de085046195464071020b467ce5a"
iuc
parents: 2
diff changeset
60 <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
61 </test>
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="2">
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_011750.1_simulated_kraken_report.txt" ftype="tabular"/>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
64 <param name="level" value="S" />
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
65 <param name="bracken_database" 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
66 <param name="out_report" 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
67 <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
68 <output name="kraken_report" file="NC_011750.1_simulated_kraken_style_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
69 </test>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
70 </tests>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
71 <help>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
72 <![CDATA[
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
73 Documentation can be found at `site <http://ccb.jhu.edu/software/bracken/index.shtml?t=manual>`_.
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
74 ]]></help>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
75 <expand macro="citations" />
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
diff changeset
76 </tool>