Mercurial > repos > thanhlv > kmerfinder

annotate kmerfinder.xml @ 0:b868a5fd2653 draft default tip

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"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
author thanhlv
date Thu, 18 Nov 2021 18:00:28 +0000
parents
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
b868a5fd2653 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
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1 <tool id="kmerfinder" name="Kmerfinder" version="@VERSION@+galaxy0">
b868a5fd2653 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
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2 <description> Species identification using kmer</description>
b868a5fd2653 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
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3 <macros>
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4 <token name="@VERSION@">3.0.2</token>
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5 </macros>
b868a5fd2653 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
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6 <requirements>
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7 <requirement type="package" version="@VERSION@">kmerfinder</requirement>
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8 <!-- <container type="singularity">kmerfinder.sif</container> -->
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9 </requirements>
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10 <version_command>echo "3.0.2"</version_command>
b868a5fd2653 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
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11 <command detect_errors="exit_code"><![CDATA[
b868a5fd2653 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
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12 #import re
b868a5fd2653 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
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13 #if $input.is_of_type('fastqsanger', 'fastq'):
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14 #set $ext = 'fastq'
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15 #elif $input.is_of_type('fastqsanger.gz'):
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16 #set $ext = 'fastq.gz'
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17 #elif $input.is_of_type('fastq'):
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18 #set $ext = 'fastq'
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19 #elif $input.is_of_type('fastq.gz'):
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20 #set $ext = 'fastq.gz'
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21 #elif $input.is_of_type('fasta.gz'):
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22 #set $ext = 'fasta.gz'
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23 #elif $input.is_of_type('fasta'):
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24 #set $ext = 'fasta'
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25 #end if
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26 #set $safename = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
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27 ln -fs '$input' $safename.$ext &&
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28
b868a5fd2653 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
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29 kmerfinder.py
b868a5fd2653 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
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30 -i '$safename.$ext'
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31 -db '${kmerfinder_databases.fields.path}.ATG'
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32 -tax '${kmerfinder_databases.fields.path}.tax'
b868a5fd2653 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
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33 -o output
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34 ]]> </command>
b868a5fd2653 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
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35 <inputs>
b868a5fd2653 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
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36 <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" multiple="false" label="Sequence files" help="Fasta for Fastq"/>
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37 <!-- DATABASE INPUT-->
b868a5fd2653 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
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38 <param label="Select a database" name="kmerfinder_databases" type="select">
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39 <options from_data_table="kmerfinder_databases">
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40 <validator message="No database is available" type="no_options" />
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41 </options>
b868a5fd2653 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
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42 </param>
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43 </inputs>
b868a5fd2653 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
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44 <outputs>
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45 <data name="results" format="tabular" label="${tool.name} on ${on_string} Results" from_work_dir="output/results.txt"/>
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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="input" value="test.fastq.gz" ftype="fastqsanger.gz"/>
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50 <param name="kmerfinder_databases" value="pseudomonas"/>
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51 <output name="results">
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52 <assert_contents>
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53 <has_text text="Pseudomonas aeruginosa genome assembly PAO1OR" />
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54 <has_text text="NZ_LN871187.1" />
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55 </assert_contents>
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56 </output>
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57 </test>
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58 </tests>
b868a5fd2653 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
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59 <help><![CDATA[
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60 Kmerfinder finds the best match (species identification) to the reads in one or more fastq files or one fasta file in a (kmer) database produced using the KMA program. The method outputs the best matches, along with additional taxonomic information, if that option is selected.
b868a5fd2653 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
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61
b868a5fd2653 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
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62 _`Document`: https://bitbucket.org/genomicepidemiology/kmerfinder
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63
b868a5fd2653 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
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64 ]]></help>
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65 <citations>
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66 <citation type="doi">10.1128/JCM.02981-13</citation>
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67 <citation type="doi">10.1128/JCM.02452-13</citation>
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68 <citation type="doi">10.1186/s12859-018-2336-6</citation>
b868a5fd2653 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
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69 </citations>
b868a5fd2653 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
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70
b868a5fd2653 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
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71 </tool>