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comparison est-abundance.xml @ 5:19035a7b1106 draft

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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
comparison
equal deleted inserted replaced
4:b08ac10aed96 5:19035a7b1106
1 <tool id="est_abundance" name="Estimate Abundance at Taxonomic Level" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="est_abundance" name="Estimate Abundance at Taxonomic Level" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>Bayesian Reestimation of Abundance with KrakEN</description> 2 <description>Bayesian Reestimation of Abundance with KrakEN</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <edam_topics> 6 <edam_topics>
8 <edam_topic>topic_3697</edam_topic> 8 <edam_topic>topic_3697</edam_topic>
9 </edam_topics> 9 </edam_topics>
10 <edam_operations> 10 <edam_operations>
11 <edam_operation>operation_2238</edam_operation> 11 <edam_operation>operation_2238</edam_operation>
12 </edam_operations> 12 </edam_operations>
13 <xrefs>
14 <xref type="bio.tools">bracken</xref>
15 </xrefs>
13 <expand macro="requirements" /> 16 <expand macro="requirements" />
14 <command detect_errors="exit_code"><![CDATA[ 17 <command detect_errors="exit_code"><![CDATA[
15 est_abundance.py 18 est_abundance.py
16 -i '$input' 19 -i '$input'
17 -k '$kmer_distr.fields.path' 20 -k '$kmer_distr.fields.path'
18 -l $level 21 -l $level
19 -t $threshold 22 -t $threshold
20 -o '$report' 23 -o '$report'
24 ## --out-report needs to be set always, since it is written next to the input file
25 --out-report bracken.report
21 ]]> 26 ]]>
22 </command> 27 </command>
23 <inputs> 28 <inputs>
24 <param name="input" type="data" format="tabular" label="Kraken report file" /> 29 <param name="input" type="data" format="tabular" label="Kraken report file" />
25 <param label="Select a Kmer distribution" name="kmer_distr" type="select"> 30 <param label="Select a Kmer distribution" name="kmer_distr" type="select">
37 <option value="D">Domain</option> 42 <option value="D">Domain</option>
38 </param> 43 </param>
39 <param name="threshold" type="integer" value="10" label="Number of mismatches allowed when matching tag" 44 <param name="threshold" type="integer" value="10" label="Number of mismatches allowed when matching tag"
40 help="Threshold for the minimum number of reads kraken must assign to a classification for that 45 help="Threshold for the minimum number of reads kraken must assign to a classification for that
41 classification to be considered in the final abundance estimation." /> 46 classification to be considered in the final abundance estimation." />
47 <param argument="--out-report" type="boolean" checked="false" label="Produce Kraken-Style Bracken report"/>
42 </inputs> 48 </inputs>
43 <outputs> 49 <outputs>
44 <data name="report" format="tabular" label="${tool.name} on ${on_string}: Report" /> 50 <data name="report" format="tabular" label="${tool.name} on ${on_string}: Report" />
51 <data name="kraken_report" format="tabular" from_work_dir="bracken.report" label="${tool.name} on ${on_string}: Kraken style report">
52 <filter>out_report</filter>
53 </data>
45 </outputs> 54 </outputs>
46 <tests> 55 <tests>
47 <test> 56 <test expect_num_outputs="1">
48 <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/> 57 <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/>
49 <param name="level" value="S" /> 58 <param name="level" value="S" />
50 <param name="bracken_database" value="test_entry"/> 59 <param name="bracken_database" value="test_entry"/>
51 <output name="report" file="NC_003198.1_simulated_bracken_report.txt" ftype="tabular"/> 60 <output name="report" file="NC_003198.1_simulated_bracken_report.txt" ftype="tabular"/>
52 </test> 61 </test>
53 <test> 62 <test expect_num_outputs="2">
54 <param name="input" value="NC_011750.1_simulated_kraken_report.txt" ftype="tabular"/> 63 <param name="input" value="NC_011750.1_simulated_kraken_report.txt" ftype="tabular"/>
55 <param name="level" value="S" /> 64 <param name="level" value="S" />
56 <param name="bracken_database" value="test_entry"/> 65 <param name="bracken_database" value="test_entry"/>
66 <param name="out_report" value="true"/>
57 <output name="report" file="NC_011750.1_simulated_bracken_report.txt" ftype="tabular"/> 67 <output name="report" file="NC_011750.1_simulated_bracken_report.txt" ftype="tabular"/>
68 <output name="kraken_report" file="NC_011750.1_simulated_kraken_style_bracken_report.txt" ftype="tabular"/>
58 </test> 69 </test>
59 </tests> 70 </tests>
60 <help> 71 <help>
61 <![CDATA[ 72 <![CDATA[
62 Documentation can be found at `site <http://ccb.jhu.edu/software/bracken/index.shtml?t=manual>`_. 73 Documentation can be found at `site <http://ccb.jhu.edu/software/bracken/index.shtml?t=manual>`_.