Mercurial > repos > nml > sistr_cmd

annotate sistr_cmd.xml @ 0:1f6159dc3598 draft default tip

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planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
author nml
date Fri, 20 Dec 2024 18:33:49 +0000
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0
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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1 <tool id="sistr_cmd" name="sistr_cmd" version="@VERSION@+galaxy0">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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2 <description>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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3 Salmonella In Silico Typing Resource command-line tool for serovar prediction
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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4 </description>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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5 <macros>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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6 <token name="@VERSION@">1.1.3</token>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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7 </macros>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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8 <xrefs>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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9 <xref type="bio.tools">SISTR</xref>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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10 </xrefs>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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11 <requirements>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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12 <requirement type="package" version="@VERSION@">sistr_cmd</requirement>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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13 </requirements>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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14 <stdio>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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15 <exit_code range="1:" />
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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16 </stdio>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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17 <command><![CDATA[
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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18
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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19 sistr
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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20 #for $fasta in $input_fastas
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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21 -i '$fasta' '${$fasta.element_identifier.replace("." + $fasta.ext, "")}'
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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22 #end for
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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23 -f $output_format
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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24 -o sistr-report.$output_format
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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25 -p $cgmlst_profiles
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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26 -n $novel_alleles
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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27 -a $alleles_output
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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28 $use_full_cgmlst_db
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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29 $no_cgmlst
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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30 $run_mash
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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31 $qc
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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32 #if $serovar_list.selection_mode == "default"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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33 --list-of-serovars
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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34 #elif $serovar_list.selection_mode == "custom"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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35 --list-of-serovars $serovar_list.custom_list_of_serovars_file
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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36 #end if
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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37 --threads "\${GALAXY_SLOTS:-1}"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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38 -T "\${TMPDIR:-/tmp}"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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39 $keep_tmp
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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40 $more_output
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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41 $verbosity
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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42 ]]></command>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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43 <inputs>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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44 <param
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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45 name="input_fastas"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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46 type="data"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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47 label="Input Genome(s)"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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48 optional="false"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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49 multiple="true"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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50 format="fasta"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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51 />
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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52 <param
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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53 name="output_format"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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54 type="select"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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55 label="Results output format"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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56 multiple="false">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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57 <option value="tab" selected="true">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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58 Tabular (tab-delimited values)
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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59 </option>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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60 <option value="csv">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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61 CSV (Comma Separated Values)
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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62 </option>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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63 <option value="json">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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64 JSON (JavaScript Object Notation)
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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65 </option>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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66 </param>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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67 <param
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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68 name="use_full_cgmlst_db"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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69 type="boolean"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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70 checked="false"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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71 truevalue="--use-full-cgmlst-db"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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72 falsevalue=""
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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73 label="Use full cgMLST database for serovar prediction. About 10X slower with equivalent results to reduced centroid allele database."
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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74 />
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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75 <param
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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76 name="run_mash"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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77 type="boolean"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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78 checked="true"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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79 truevalue="--run-mash"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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80 falsevalue=""
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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81 label="Run Mash MinHash-based serovar prediction"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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82 />
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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83 <param
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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84 name="no_cgmlst"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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85 type="boolean"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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86 checked="false"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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87 truevalue="--no-cgmlst"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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88 falsevalue=""
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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89 label="Skip running cgMLST-based serovar prediction"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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90 />
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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91 <param
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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92 name="qc"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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93 type="boolean"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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94 checked="true"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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95 truevalue="--qc"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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96 falsevalue=""
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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97 label="Basic QC of results"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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98 />
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
99 <conditional name="serovar_list">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
100 <param label="Check predicted SISTR serovar against the list of serovars?" name="selection_mode" type="select">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
101 <option value="none">Not selected</option>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
102 <option selected="true" value="default">Use the default list</option>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
103 <option value="custom">Use a custom list</option>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
104 </param>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
105 <when value="none"/>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
106 <when value="default"/>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
107 <when value="custom">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
108 <param name="custom_list_of_serovars_file" type="data" format="text" optional="true" label="Custom list of serovars (optional)"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
109 help="if no file selected, the default one is used available at https://raw.githubusercontent.com/phac-nml/sistr_cmd/v1.1.3/sistr/data/serovar-list.txt"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
110 />
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
111 </when>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
112 </conditional>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
113 <param
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
114 name="more_output"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
115 type="select"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
116 label="Results verbosity">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
117 <option value="" selected="true">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
118 Basic results only
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
119 </option>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
120 <option value="-M">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
121 Report top antigen BLAST results
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
122 </option>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
123 <option value="-MM" >
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
124 Report all antigen BLAST results
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
125 </option>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
126 </param>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
127 <param
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
128 name="keep_tmp"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
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129 type="boolean"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
130 checked="false"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
131 falsevalue=""
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
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132 truevalue="--keep-tmp"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
133 label="Keep temporary analysis directory"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
134 />
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
135 <param
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
136 name="verbosity"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
137 type="select"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
138 label="Logging verbosity">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
139 <option value="">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
140 Error messages only
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
141 </option>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
142 <option value="-v">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
143 Show warning messages
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
144 </option>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
145 <option value="-vv" selected="true">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
146 Show info messages
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
147 </option>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
148 <option value="-vvv">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
149 Show debug messages
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
150 </option>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
151 </param>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
152 </inputs>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
153 <outputs>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
154 <data
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
155 name="output_prediction_csv"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
156 format="csv"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
157 label="${tool.name} on ${input_fastas[0].element_identifier}: Main Report (csv)"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
158 from_work_dir="sistr-report.csv">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
159 <filter>output_format == "csv"</filter>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
160 </data>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
161 <data
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
162 name="output_prediction_json"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
163 format="json"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
164 label="${tool.name} on ${input_fastas[0].element_identifier}: Main Report (json)"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
165 from_work_dir="sistr-report.json">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
166 <filter>output_format == "json"</filter>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
167 </data>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
168 <data
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
169 name="output_prediction_tab"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
170 format="tabular"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
171 label="${tool.name} on ${input_fastas[0].element_identifier}: Main Report (tab)"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
172 from_work_dir="sistr-report.tab">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
173 <filter>output_format == "tab"</filter>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
174 </data>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
175 <data
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
176 name="cgmlst_profiles"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
177 format="csv"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
178 label="${tool.name} on ${input_fastas[0].element_identifier}: cgMLST allele match results (csv)" />
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
179 <data
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
180 name="novel_alleles"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
181 format="fasta"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
182 label="${tool.name} on ${input_fastas[0].element_identifier}: Novel cgMLST alleles (fasta)" />
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
183 <data
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
184 name="alleles_output"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
185 format="json"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
186 label="${tool.name} on ${input_fastas[0].element_identifier}: cgMLST allele match results (json)" />
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
187 </outputs>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
188 <tests>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
189 <test expect_num_outputs="4">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
190 <param name="input_fastas" value="AE014613-699860.fasta" ftype="fasta"/>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
191 <param name="output_format" value="tab"/>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
192 <param name="selection_mode" value="none"/>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
193 <output
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
nml
parents:
diff changeset
194 name="cgmlst_profiles"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
diff changeset
195 value="cgmlst-profiles-AE014613.csv"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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parents:
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196 ftype="csv"
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197 compare="diff">
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198 </output>
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199 <output name="output_prediction_tab"
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200 ftype="tabular"
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201 value="sistr-results-AE014613-699860.tabular"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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202 compare="sim_size">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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203 <assert_contents>
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204 <has_text text="AE014613-699860" />
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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205 <has_text text="Typhi" />
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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206 <has_text text="enterica" />
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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207 <has_text_matching expression="FAIL\t-\t-:-:-\t-:-:-"/>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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208 <has_text text="2014-LET-0419"/>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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209 <has_n_columns n="23" />
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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210 </assert_contents>
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211 </output>
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212 <output
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213 name="alleles_output"
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214 value="alleles-output-AE014613.json"
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215 ftype="json"
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216 compare="sim_size">
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217 <assert_contents>
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218 <has_text text="NZ_AOXE01000059.1"/>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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219 <has_text text="Salmonella enterica subsp. enterica serovar Typhi Ty2"/>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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220 <has_text text="NZ_AOXE01000033.1"/>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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221 <has_text text="NZ_AOXE01000052.1"/>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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222 </assert_contents>
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223 </output>
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224 </test>
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225 <test expect_num_outputs="4">
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226 <param name="input_fastas" value="13-1101-Paratyphi_B_varJava.fasta" ftype="fasta"/>
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227 <param name="output_format" value="tab"/>
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228 <output
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229 name="novel_alleles"
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230 value="novel-alleles-13-1101.fasta"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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231 ftype="fasta"
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232 compare="sim_size"/>
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233 <output
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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234 name="cgmlst_profiles"
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235 value="cgmlst-profiles-13-1101.csv"
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236 ftype="csv"
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237 compare="diff">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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238 </output>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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239 <output
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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240 name="output_prediction_tab"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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241 value="sistr-results-13-1101.tabular"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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242 ftype="tabular"
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243 compare="sim_size">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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244 <assert_contents>
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245 <has_text text="13-1101-Paratyphi_B"/>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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246 <has_text text="Paratyphi B var. Java"/>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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247 <has_text text="enterica"/>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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248 <has_text text="1,4,[5],12"/>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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249 <has_text text="1,4,[5],12:b:1,2"/>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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250 <has_text text="FAIL"/>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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251 <has_text text="Y"/>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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252 <has_n_columns n="24"/>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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253 </assert_contents>
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254 </output>
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255 <output
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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256 name="alleles_output"
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257 value="alleles-output-13-1101.json"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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258 ftype="json"
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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259 compare="sim_size">
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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260 <assert_contents>
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261 <has_text text="13-1101-Paratyphi_B"/>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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262 <has_text text="NZ_AOXE01000059.1"/>
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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263 </assert_contents>
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264 </output>
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265 </test>
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266 </tests>
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267 <help>
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268 <![CDATA[
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269
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270 Usage::
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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271
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272 usage: sistr_cmd [-h] [-i fasta_path genome_name] [-f OUTPUT_FORMAT]
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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273 [-o OUTPUT_PREDICTION] [-M] [-p CGMLST_PROFILES]
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274 [-n NOVEL_ALLELES] [-a ALLELES_OUTPUT] [-T TMP_DIR] [-K]
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275 [--use-full-cgmlst-db] [--no-cgmlst] [-m] [--qc] [-t THREADS]
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276 [-v] [-V]
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277 [F [F ...]]
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278
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279 SISTR (Salmonella In Silico Typing Resource) Command-line Tool
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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280 ==============================================================
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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281 Serovar predictions from whole-genome sequence assemblies by determination of antigen gene and cgMLST gene alleles using BLAST.
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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282
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283 Note about using the "--use-full-cgmlst-db" flag:
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284 The "centroid" allele database is ~10% the size of the full set so analysis is much quicker with the "centroid" vs "full" set of alleles.
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285 Results between 2 cgMLST allele sets should not differ.
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286
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287 If you find this program useful in your research, please cite as:
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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288 The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies.
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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289 Catherine Yoshida, Peter Kruczkiewicz, Chad R. Laing, Erika J. Lingohr, Victor P.J. Gannon, John H.E. Nash, Eduardo N. Taboada.
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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290 PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101
1f6159dc3598 planemo upload for repository https://github.com/phac-nml/sistr_cmd commit 4a9d0e766264aab4b92d8971b70112f84e28e8cd
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291
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292 positional arguments:
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293 F Input genome FASTA file
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294
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295 optional arguments:
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296 -h, --help show this help message and exit
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297 -i fasta_path genome_name, --input-fasta-genome-name fasta_path genome_name
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298 fasta file path to genome name pair
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299 -f OUTPUT_FORMAT, --output-format OUTPUT_FORMAT
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300 Output format (json, csv, pickle)
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301 -o OUTPUT_PREDICTION, --output-prediction OUTPUT_PREDICTION
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302 SISTR serovar prediction output path
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303 -M, --more-results Output more detailed results (-M) and all antigen
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304 search blastn results (-MM)
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305 -p CGMLST_PROFILES, --cgmlst-profiles CGMLST_PROFILES
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306 Output CSV file destination for cgMLST allelic
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307 profiles
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308 -n NOVEL_ALLELES, --novel-alleles NOVEL_ALLELES
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309 Output FASTA file destination of novel cgMLST alleles
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310 from input genomes
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311 -a ALLELES_OUTPUT, --alleles-output ALLELES_OUTPUT
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312 Output path of allele sequences and info to JSON
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313 -T TMP_DIR, --tmp-dir TMP_DIR
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314 Base temporary working directory for intermediate
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315 analysis files.
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316 -K, --keep-tmp Keep temporary analysis files.
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317 --use-full-cgmlst-db Use the full set of cgMLST alleles which can include
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318 highly similar alleles. By default the smaller
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319 "centroid" alleles or representative alleles are used
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320 for each marker.
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321 --no-cgmlst Do not run cgMLST serovar prediction
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322 -m, --run-mash Determine Mash MinHash genomic distances to Salmonella
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323 genomes with trusted serovar designations. Mash binary
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324 must be in accessible via $PATH (e.g. /usr/bin).
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325 --qc Perform basic QC to provide level of confidence in
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326 serovar prediction results.
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327 -t THREADS, --threads THREADS
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328 Number of parallel threads to run sistr_cmd analysis.
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329 -l [LIST_OF_SEROVARS], --list-of-serovars [LIST_OF_SEROVARS]
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330 A path to a single column text file containing list of
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331 serovars to check SISTR serovar prediction against.
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332 Result reported in the "predicted_serovar_in_list"
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333 field as Y (present) or N (absent) value.
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334 -v, --verbose Logging verbosity level (-v == show warnings; -vvv ==
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335 show debug info)
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336 -V, --version show program's version number and exit
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337 ]]>
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338
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339 </help>
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340 <citations>
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341 <!-- Citation for SISTR PLOS ONE paper -->
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342 <citation type="doi">10.1371/journal.pone.0147101</citation>
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343 </citations>
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344 </tool>