annotate screen_abricate_report.xml @ 3:1c1c680c70a0 draft default tip

"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467-dirty"
author dfornika
date Thu, 02 Jan 2020 21:04:04 +0000
parents 378696e5f81c
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1 <tool id="screen_abricate_report" name="Screen Abricate Report" version="0.3.0">
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2 <description>Screens an abricate report for genes of interest</description>
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3 <requirements>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 '${__tool_directory__}/screen_abricate_report.py'
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7 '${abricate_report}'
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8 #if str( $screening_file_source.screening_file_source_selector ) == "tool_data_table":
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9 #set $input_screening_file = str( $screening_file_source.screening_file.fields.path )
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10 #else:
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11 #set $input_screening_file = str( $screening_file_source.screening_file )
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12 #end if
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13 --screening_file '${input_screening_file}'
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14 --screened_report '${screened_report}'
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15 --gene_detection_status '${gene_detection_status}'
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16 --min_coverage '${min_coverage}'
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17 --min_identity '${min_identity}' &&
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18 cp '${input_screening_file}' '${output_screening_file}'
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19 ]]></command>
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20 <inputs>
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21 <conditional name="screening_file_source">
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22 <param name="screening_file_source_selector" type="select" label="Select a gene screening file from your history or use one from a tool data table?"
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23 help="Screening files must be stored in the 'abricate_report_screening_files' tool data table">
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24 <option value="tool_data_table">From tool data table</option>
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25 <option value="history">From history</option>
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26 </param>
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27 <when value="tool_data_table">
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28 <param name="screening_file" type="select" format="tabular">
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29 <options from_data_table="abricate_report_screening_files">
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30 <validator type="no_options" message="No abricate report screening files are available" />
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31 </options>
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32 </param>
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33 </when>
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34 <when value="history">
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35 <param name="screening_file" type="data" format="tabular" label="Gene screening file" help="A two-column tab-delimited file with gene names and regular expressions" />
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36 </when>
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37 </conditional>
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38 <param name="abricate_report" type="data" format="tabular" />
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39 <param name="min_coverage" type="float" min="0.0" value="90.0" max="100.0" />
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40 <param name="min_identity" type="float" min="0.0" value="90.0" max="100.0" />
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41 </inputs>
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42 <outputs>
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43 <data name="screened_report" format="tabular" label="Screened Abricate Report" />
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44 <data name="gene_detection_status" format="tabular" label="Gene Detection Status" />
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45 <data name="output_screening_file" format="tabular" />
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46 </outputs>
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47 <tests>
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48 <test>
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49 <param name="screening_file_source.screening_file_source_selector" value="tool_data_table" />
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50 <param name="screening_file_source.screening_file" value="test_entry"/>
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51 <param name="abricate_report" value="SAMN13042171_abricate_report.tsv"/>
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52 <output name="screened_report" file="SAMN13042171_abricate_report_screened.tsv" ftype="tabular"/>
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53 <output name="gene_detection_status" file="SAMN13042171_gene_detection_status.tsv" ftype="tabular"/>
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54 </test>
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55 <test>
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56 <param name="screening_file_source.screening_file_source_selector" value="history" />
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57 <param name="screening_file_source.screening_file" value="screening_file.tsv"/>
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58 <param name="abricate_report" value="SAMN13042171_abricate_report.tsv"/>
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59 <output name="screened_report" file="SAMN13042171_abricate_report_screened.tsv" ftype="tabular"/>
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60 <output name="gene_detection_status" file="SAMN13042171_gene_detection_status.tsv" ftype="tabular"/>
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61 </test>
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62 </tests>
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63 <help><![CDATA[
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64 This tool is used to filter (ie. 'screen') an abricate report to only include
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65 specific genes of interest.
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66
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67 A list of genes is supplied in a 'screening file', which is a two-column .tsv
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68 with headers 'gene_name' and 'regex'. The first column gives the name of the
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69 gene of interest, and the second column is a regular expression that can be used
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70 to identify examples of that gene in the 'GENE' column of the abricate report.
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71
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72 For example, one might use the regex '^KPC-\d+$' to identify all alleles of the
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73 KPC gene (KPC-2, KPC-3, KPC-4, ..., KPC-10, ...)
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74 ]]></help>
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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75 <citations>
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
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76 </citations>
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
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77 </tool>