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comparison est-abundance.xml @ 6:79450f7fd718 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit c396abec691d64fc4cb7f205f54c01b1be7fd649
author iuc
date Fri, 26 Aug 2022 07:21:39 +0000
parents 19035a7b1106
children 978ae4147c29
comparison
equal deleted inserted replaced
5:19035a7b1106 6:79450f7fd718
1 <tool id="est_abundance" name="Estimate Abundance at Taxonomic Level" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="est_abundance" name="Estimate Abundance at Taxonomic Level" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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 <expand macro="edam" />
7 <edam_topic>topic_3174</edam_topic> 7 <expand macro="xref" />
8 <edam_topic>topic_3697</edam_topic> 8 <expand macro="requirements" />
9 </edam_topics>
10 <edam_operations>
11 <edam_operation>operation_2238</edam_operation>
12 </edam_operations>
13 <xrefs>
14 <xref type="bio.tools">bracken</xref>
15 </xrefs>
16 <expand macro="requirements" />
17 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
18 est_abundance.py 10 est_abundance.py
19 -i '$input' 11 -i '$input'
20 -k '$kmer_distr.fields.path' 12 -k '$kmer_distr.fields.path'
21 -l $level 13 -l $level
22 -t $threshold 14 -t $threshold
23 -o '$report' 15 -o '$report'
24 ## --out-report needs to be set always, since it is written next to the input file 16 ## --out-report needs to be set always, since it is written next to the input file
25 --out-report bracken.report 17 --out-report bracken.report
18 #if $logfile_output == "True"
19 | tee '$logfile'
20 #end if
26 ]]> 21 ]]>
27 </command> 22 </command>
28 <inputs> 23 <inputs>
29 <param name="input" type="data" format="tabular" label="Kraken report file" /> 24 <param name="input" type="data" format="tabular" label="Kraken report file" />
30 <param label="Select a Kmer distribution" name="kmer_distr" type="select"> 25 <param label="Select a Kmer distribution" name="kmer_distr" type="select">
31 <options from_data_table="bracken_databases"> 26 <options from_data_table="bracken_databases">
32 <validator message="No database is available" type="no_options" /> 27 <validator message="No database is available" type="no_options" />
40 <option value="C">Class</option> 35 <option value="C">Class</option>
41 <option value="P">Phylum</option> 36 <option value="P">Phylum</option>
42 <option value="D">Domain</option> 37 <option value="D">Domain</option>
43 </param> 38 </param>
44 <param name="threshold" type="integer" value="10" label="Number of mismatches allowed when matching tag" 39 <param name="threshold" type="integer" value="10" label="Number of mismatches allowed when matching tag"
45 help="Threshold for the minimum number of reads kraken must assign to a classification for that 40 help="Threshold for the minimum number of reads kraken must assign to a classification for that
46 classification to be considered in the final abundance estimation." /> 41 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 <param argument="--out-report" type="boolean" checked="false" label="Produce Kraken-Style Bracken report"/>
43 <param name="logfile_output" type="boolean" truevalue="True" falsevalue="False" label="Add log file output"/>
48 </inputs> 44 </inputs>
49 <outputs> 45 <outputs>
50 <data name="report" format="tabular" label="${tool.name} on ${on_string}: Report" /> 46 <data name="report" format="tabular" label="${tool.name} on ${on_string}: Report" />
51 <data name="kraken_report" format="tabular" from_work_dir="bracken.report" label="${tool.name} on ${on_string}: Kraken style report"> 47 <data name="kraken_report" format="tabular" from_work_dir="bracken.report" label="${tool.name} on ${on_string}: Kraken style report">
52 <filter>out_report</filter> 48 <filter>out_report</filter>
53 </data> 49 </data>
50 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file">
51 <filter> logfile_output == True </filter>
52 </data>
54 </outputs> 53 </outputs>
55 <tests> 54 <tests>
56 <test expect_num_outputs="1"> 55 <test expect_num_outputs="1">
57 <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/> 56 <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/>
58 <param name="level" value="S" /> 57 <param name="level" value="S" />
59 <param name="bracken_database" value="test_entry"/> 58 <param name="kmer_distr" value="test_entry"/>
59 <param name="logfile_output" value="False"/>
60 <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"/>
61 </test> 61 </test>
62 <test expect_num_outputs="2"> 62 <test expect_num_outputs="3">
63 <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"/>
64 <param name="level" value="S" /> 64 <param name="level" value="S" />
65 <param name="bracken_database" value="test_entry"/> 65 <param name="kmer_distr" value="test_entry"/>
66 <param name="out_report" value="true"/> 66 <param name="out_report" value="true"/>
67 <param name="logfile_output" value="True"/>
67 <output name="report" file="NC_011750.1_simulated_bracken_report.txt" ftype="tabular"/> 68 <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"/> 69 <output name="kraken_report" file="NC_011750.1_simulated_kraken_style_bracken_report.txt" ftype="tabular"/>
70 <output name="logfile" file="test2.log" lines_diff="8" />
69 </test> 71 </test>
70 </tests> 72 </tests>
71 <help> 73 <help>
72 <![CDATA[ 74 <![CDATA[
73 Documentation can be found at `site <http://ccb.jhu.edu/software/bracken/index.shtml?t=manual>`_. 75 Documentation can be found at `site <http://ccb.jhu.edu/software/bracken/index.shtml?t=manual>`
74 ]]></help> 76 ]]></help>
75 <expand macro="citations" /> 77 <expand macro="citations" />
76 </tool> 78 </tool>