Mercurial > repos > thanhlv > kaptive

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"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kaptive commit f07ab842192ee3d9d1cc46c1de3c542213152a31-dirty"
author thanhlv
date Tue, 19 Oct 2021 09:32:23 +0000
parents 62f30507967c
children
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3e11d50307ce "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kaptive commit fbfc04c5de0c8a92a69b30fdaec4929f95e8cc3d-dirty"
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1 <tool id="kaptive" name="kaptive" version="@VERSION@">
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2 <description> reports surface polysaccharide loci for Klebsiella and Acinetobacter baumannii genome assemblies</description>
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3 <macros>
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4 <token name="@VERSION@">0.7.3</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@VERSION@">kaptive</requirement>
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8 </requirements>
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9 <version_command>kaptive.py --version</version_command>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #import re
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12 #for $counter, $input in enumerate($assemblies):
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13 #set $name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
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14 ln -s '$input' ${name}.fasta &&
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15 #end for
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16 kaptive.py
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17 --verbose
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18 -a *.fasta
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19 -k '$ref'
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20 #if $allelic_typing:
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21 -g '$allelic_typing'
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22 #end if
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23 -t \${GALAXY_SLOTS:-4}
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24 $no_seq_out
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25 $no_json
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26 --start_end_margin '$start_end_margin'
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27 --min_gene_cov '$min_gene_cov'
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28 --min_gene_id '$min_gene_id'
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29 --low_gene_id '$low_gene_id'
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30 --min_assembly_piece '$min_assembly_piece'
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31 --gap_fill_size '$gap_fill_size'
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32 #if $locus_label:
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33 --locus_label '$locus_label'
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34 #end if
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35 > $output
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36 ]]> </command>
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37
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38 <inputs>
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39 <param name="assemblies" type="data" format="fasta" multiple="true" label="Assembly"/>
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40 <param name="ref" type="data" format="genbank" label="Reference" help="Genbank format"/>
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41 <param name="allelic_typing" type="data" format="fasta" optional="true" label="Allelic Typing input" help="Optional"/>
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42 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="True" label="Suppress output files of sequences matching locus" />
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43 <param argument="--no_seq_out" type="boolean" truevalue="--no_seq_out" falsevalue="" checked="False" label="Suppress output files of sequences matching locus" />
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44 <param argument="--no_json" type="boolean" truevalue="--no_json" falsevalue="" checked="True" label="Suppress output of JSON file" />
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45 <param argument="--start_end_margin" type="integer" value="10" label="Missing bases at the ends of locus allowed in a perfect match" />
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46 <param argument="--min_gene_cov" type="float" value="90.0" max="100.0" label="Minimum required percent coverage for genes" />
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47 <param argument="--min_gene_id" type="float" value="80.0" max="100.0" label="Minimum required percent identity for genes" />
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48 <param argument="--low_gene_id" type="float" value="95.0" max="100.0" label="Genes with a percent identity below this value will be flagged as low identity" />
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49 <param argument="--min_assembly_piece" type="integer" value="100" label="Minimum locus matching assembly piece to return" />
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50 <param argument="--gap_fill_size" type="integer" value="100" label="Gap fill size" help="When separate parts of the assembly are found within this distance, they will be merged" />
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51 <param argument="--locus_label" type="text" label="Locus label" optional="true" help="In the Genbank file, the source feature must have a note identifying the locus name, starting with this label followed by a colon (e.g. /note='K locus: K1')" />
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52 </inputs>
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53
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54 <outputs>
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55 <data name="output" format="txt" label="${tool.name} on ${on_string} Log"/>
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56 <data name="results_table" format="tabular" from_work_dir="kaptive_results_table.txt" label="${tool.name} on ${on_string} Result table"/>
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57 <data name="results_json" format="json" from_work_dir="kaptive_results_table.txt" label="${tool.name} on ${on_string} Result json">
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58 <filter>no_json is False</filter>
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59 </data>
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60 <collection name="list_fasta" type="list" label="Locus matching sequences">
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61 <filter>no_seq_out is False</filter>
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62 <discover_datasets pattern="kaptive_results(?P&lt;designation&gt;[a-zA-Z0-9\-\_]+)\.fasta$" ext="fasta" directory="./" />
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63 </collection>
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64 </outputs>
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65 <tests>
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66 <test>
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67 <param name="assemblies" value="exact_match" />
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68 <param name="ref" value="Klebsiella_o_locus_primary_reference.gbk" />
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69 <param name="allelic_typing" value="wzi_wzc_db.fasta" />
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70 <output name="output" file="output.txt" ftype="txt" />
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71 <output name="results_table" file="kaptive_results_table.txt" ftype="tabular" />
3e11d50307ce "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kaptive commit fbfc04c5de0c8a92a69b30fdaec4929f95e8cc3d-dirty"
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72 </test>
3e11d50307ce "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kaptive commit fbfc04c5de0c8a92a69b30fdaec4929f95e8cc3d-dirty"
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73 </tests>
3e11d50307ce "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kaptive commit fbfc04c5de0c8a92a69b30fdaec4929f95e8cc3d-dirty"
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74 <help><![CDATA[
3e11d50307ce "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kaptive commit fbfc04c5de0c8a92a69b30fdaec4929f95e8cc3d-dirty"
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75 ]]> </help>
2
62f30507967c "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kaptive commit f07ab842192ee3d9d1cc46c1de3c542213152a31-dirty"
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76 <citations>
62f30507967c "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kaptive commit f07ab842192ee3d9d1cc46c1de3c542213152a31-dirty"
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77 <citation type="doi">10.1099/mgen.0.000102</citation>
62f30507967c "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kaptive commit f07ab842192ee3d9d1cc46c1de3c542213152a31-dirty"
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78 <yield />
62f30507967c "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kaptive commit f07ab842192ee3d9d1cc46c1de3c542213152a31-dirty"
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79 </citations>
0
3e11d50307ce "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kaptive commit fbfc04c5de0c8a92a69b30fdaec4929f95e8cc3d-dirty"
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80 </tool>