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

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