Mercurial > repos > iuc > meningotype

annotate meningotype.xml @ 0:2d21809749f2 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
author iuc
date Tue, 13 Jun 2023 11:04:13 +0000
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2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
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1 <tool id="meningotype" name="Meningotype" version="@TOOL_VERSION@+galaxy0" profile="21.05">
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2 <description>assign sequence type to Neisseria meningitidis genome assemblies</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.8.5</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">meningotype</requirement>
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8 <!-- coreutils dep added because of a bug in the meningotype 0.8.5 container - it doesn't have `file` -->
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9 <requirement type="package" version="9.0">coreutils</requirement>
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10 </requirements>
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11 <version_command>meningotype --version</version_command>
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12 <command detect_errors="aggressive"><![CDATA[
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13 #if $db_source == 'network'
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14 python3 '$__tool_directory__/update_db.py' &&
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
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15 #end if
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16 #if $input.source == "single"
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17 #set $input_data = "'" + $input.fasta.element_identifier.replace(' uncompressed', '') + "'"
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
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18 ln -s '$input.fasta' $input_data &&
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
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19 #else
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20 #set $input_data = ""
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
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21 #for $el in $input.fastas
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22 #set $name = $el.element_identifier.replace(' uncompressed', '')
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
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23 ln -s '$el' '$name' &&
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24
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25 #set $input_data = $input_data + " '" + $name + "'"
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26 #end for
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27 #end if
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28 meningotype
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29 #if $db_source == "network"
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30 --db ./db
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31 #end if
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32 $input_data
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33 --cpus \${GALAXY_SLOTS:-1}
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34 #if "mlst" in $typing
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35 --mlst
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36 #end if
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37 #if "finetype" in $typing
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38 --finetype
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39 #end if
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40 #if "porb" in $typing
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41 --porB
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42 #end if
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43 #if "bast" in $typing
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44 --bast
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45 #end if
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46 #if $write_allele_sequences
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47 --printseq allele_sequences
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48 #end if
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49 #if not $include_header
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50 | python3 '$__tool_directory__/strip_header.py'
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51 #end if
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52 >'$output_tsv' &&
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53 python3 '$__tool_directory__/check_output.py' '$output_tsv'
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54 ]]></command>
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55 <inputs>
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56 <conditional name="input">
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57 <param type="select" name="source" label="Input type">
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58 <option value="collection" selected="true">Dataset collection</option>
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59 <option value="single">Single dataset</option>
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60 </param>
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61 <when value="collection">
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62 <param name="fastas" type="data_collection" format="fasta" collection_type="list" label="N. meningtidis genomes in FASTA format" />
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63 </when>
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64 <when value="single">
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65 <param type="data" format="fasta" name="fasta" label="Input FASTA" help="N. meningitidis genome in FASTA format" />
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66 </when>
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67 </conditional>
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68 <param type="select" name="db_source" label="Database source">
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69 <!-- the latest version of the DBs are stored on PubMLST. -->
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70 <option value="network" selected="true">Network</option>
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71 <option value="builtin">Built-in</option>
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72 </param>
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73 <param type="select" multiple="true" name="typing" label="Typing to perform">
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74 <option value="mlst" selected="true">MLST</option>
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75 <option value="finetype" selected="true">porA and fetA fine typing</option>
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76 <option value="bast" selected="true">Bexsero antigen sequence typing (BAST)</option>
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77 <option value="porb" selected="true">porB (NEIS2020) sequence typing</option>
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78 </param>
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79 <param type="boolean" name="include_header" checked="false" label="Include header in output" />
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80 <param type="boolean" name="write_allele_sequences" checked="false" label="Output sequences of porA, fetA, portB and BAST alleles" />
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81 </inputs>
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82 <outputs>
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83 <data format="tabular" name="output_tsv" label="Meningotype on ${on_string}">
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84 <actions>
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85 <action name="column_names" type="metadata" default="Sample_ID,Serogroup,ctrA,MLST,porA,fetA,porB,fHbp,NHBA,NadA,BAST" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
86 </actions>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
87 </data>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
88 <collection format="fasta" type="list" name="output_allele_sequences" label="Meningotype allele sequences on ${on_string}">
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
89 <discover_datasets pattern="__name_and_ext__" directory="allele_sequences" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
90 <filter>write_allele_sequences</filter>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
91 </collection>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
92 </outputs>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
93 <tests>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
94 <test expect_num_outputs="1"> <!-- test1: basic functionality -->
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
95 <conditional name="input">
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
96 <param name="source" value="single" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
97 <param name="fasta" value="input.fasta.gz" ftype="fasta.gz"/>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
98 </conditional>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
99 <param name="db_source" value="builtin" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
100 <param name="typing" value="mlst,finetype,bast,porb" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
101 <output name="output_tsv">
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
102 <assert_contents>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
103 <has_n_columns n="11" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
104 <has_text text="9367" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
105 <has_text text="21-15,16" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
106 <has_text text="F1-7" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
107 <has_text text="NEIS2020_506" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
108 <has_text text="27" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
109 <has_text text="798" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
110 <has_text text="0" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
111 </assert_contents>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
112 </output>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
113 </test>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
114 <test expect_num_outputs="1"> <!-- test2: test with header included -->
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
115 <conditional name="input">
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
116 <param name="source" value="single" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
117 <param name="fasta" value="input.fasta.gz" ftype="fasta.gz"/>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
118 </conditional>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
119 <param name="db_source" value="builtin" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
120 <param name="typing" value="mlst,finetype,bast,porb" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
121 <param name="include_header" value="true" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
122 <output name="output_tsv">
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
123 <assert_contents>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
124 <has_n_columns n="11" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
125 <has_text text="SAMPLE_ID" /> <!-- the header -->
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
126 <has_text text="9367" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
127 <has_text text="21-15,16" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
128 <has_text text="F1-7" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
129 <has_text text="NEIS2020_506" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
130 <has_text text="27" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
131 <has_text text="798" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
132 <has_text text="0" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
133 </assert_contents>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
134 </output>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
135 </test>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
136 <test expect_num_outputs="2"> <!-- test 3: test allele sequence output -->
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
137 <conditional name="input">
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
138 <param name="source" value="single" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
139 <param name="fasta" value="input.fasta.gz" ftype="fasta.gz"/>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
140 </conditional>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
141 <param name="db_source" value="builtin" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
142 <param name="typing" value="mlst,finetype,bast,porb" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
143 <param name="write_allele_sequences" value="true" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
144 <output name="output_tsv">
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
145 <assert_contents>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
146 <has_n_columns n="11" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
147 <has_text text="9367" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
148 <has_text text="21-15,16" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
149 <has_text text="F1-7" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
150 <has_text text="NEIS2020_506" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
151 <has_text text="27" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
152 <has_text text="798" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
153 <has_text text="0" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
154 </assert_contents>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
155 </output>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
156 <output_collection name="output_allele_sequences">
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
157 <element name="NHBA_seqs" file="NHBA_seqs.fasta" ftype="fasta" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
158 <element name="NadA_seqs" file="NadA_seqs.fasta" ftype="fasta" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
159 <element name="fHbp_seqs" file="fHbp_seqs.fasta" ftype="fasta" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
160 <element name="fetA_seqs" file="fetA_seqs.fasta" ftype="fasta" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
161 <element name="porA_seqs" file="porA_seqs.fasta" ftype="fasta" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
162 <element name="porB_seqs" file="porB_seqs.fasta" ftype="fasta" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
163 </output_collection>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
164 </test>
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
165 <test expect_num_outputs="1"> <!-- test4: test input collection -->
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
166 <conditional name="input">
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
167 <param name="source" value="collection" />
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
168 <param name="fastas">
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
diff changeset
169 <collection type="list">
2d21809749f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
iuc
parents:
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170 <element name="input1" value="input.fasta.gz" ftype="fasta.gz" />
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171 <element name="input2" value="input2.fasta.gz" ftype="fasta.gz" />
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172 </collection>
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173 </param>
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174 </conditional>
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175 <param name="db_source" value="builtin" />
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176 <param name="typing" value="mlst,finetype,bast,porb" />
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177 <output name="output_tsv">
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178 <assert_contents>
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179 <has_n_columns n="11" />
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180 <has_n_lines n="2" />
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181 <has_text text="9367" />
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182 <has_text text="21-15,16" />
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183 <has_text text="F1-7" />
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184 <has_text text="NEIS2020_506" />
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185 <has_text text="27" />
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186 <has_text text="798" />
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187 <has_text text="0" />
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188 </assert_contents>
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189 </output>
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190 </test>
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191 </tests>
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192 <help><![CDATA[
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193 meningotype_: In silico typing of Neisseria meningitidis contigs
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194
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195 * Serotyping
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196
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197 * MLST
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198
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199 * Finetyping (porA, fetA, porB)
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200
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201 * Bexsero antigen sequence typing (BAST) (fHbp, NHBA, NadA, PorA)
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202
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203 The databases used in the tool are sourced from PubMLST_. The default behaviour is to download updated
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204 copies of the databases before running the tool. While this can be ineffecient for e.g. typing a single
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205 isolate, the databases built-in to the tool are not the most recent versions.
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206
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207 If many isolates are being typed, they can be provided as a dataset collection. The output of the tool
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208 will contain one line of data for each isolate.
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209
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210 By default the header line is not included in the tool output (to make concatenation of results easier).
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211
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212 If output of matched alleles is requested, FASTA files are produced for each matching allele, with information
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213 on which dataset was matched in the FASTA header.
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214
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215 .. _meningotype: https://github.com/MDU-PHL/meningotype
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216 .. _PubMLST: https://pubmlst.org/
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217 ]]></help>
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218 <citations>
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219 <citation type="bibtex">
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220 <![CDATA[
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221 @misc{Kwong2018,
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222 author = {Kwong, J.C. and Gonçalves da Silva, A. and Stinear, T. P. and Howden, B. P. and Seemann, T.},
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223 title = {meningotype: in silico typing for Neisseria meningitidis.},
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224 year = {2018},
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225 publisher = {GitHub},
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226 journal = {GitHub repository},
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227 howpublished = {\url{https://github.com/MDU-PHL/meningotype}},
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228 commit = {aece5c9851c7ffc8357306a33a369307dddb726f}
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229 }
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230 ]]>
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231 </citation>
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232 </citations>
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233 </tool>