Mercurial > repos > iuc > seqsero2

annotate seqsero2.xml @ 0:f7f22f0db880 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
author iuc
date Mon, 06 Oct 2025 14:53:34 +0000
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f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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1 <tool id="seqsero2" name="SeqSero2" version="@TOOL_VERSION@+galaxy0" profile="21.05">
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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2 <description>Salmonella serotype prediction</description>
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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3 <macros>
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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4 <import>macros.xml</import>
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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5 </macros>
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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6 <expand macro="xrefs" />
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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7 <expand macro="requirements" />
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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8 <version_command>SeqSero2_package.py -v</version_command>
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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9 <command detect_errors="exit_code"><![CDATA[
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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10 #import re
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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11 #set $seqsero_t_value = ''
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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12 #set $seqsero_workflow_type = ''
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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13
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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14 #if str($input_type_cond.input_type) in ['single', 'paired', 'assembly', 'nanopore']:
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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15 #set read1 = $input_type_cond.read1
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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16
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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17 #if str($input_type_cond.input_type) in ['assembly', 'nanopore']:
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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18 #set ext = '.fasta'
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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19 #else:
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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20 #set ext = '.fastq'
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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21 #end if
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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22 #if $read1.ext.endswith('.gz'):
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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23 #set ext = $ext+'.gz'
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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24 #end if
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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25
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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26 #if str($input_type_cond.input_type) == 'paired':
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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27 #set read1_file = re.sub('[^\w\-\.]', '_', str($read1.element_identifier)) + '_forward' + $ext
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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28 #set read2 = $input_type_cond.read2
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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29 #set read2_file = re.sub('[^\w\-\.]', '_', str($read2.element_identifier)) + '_reverse' + $ext
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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30 ln -s '$read2' '$read2_file' &&
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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31 #else:
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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32 #set read1_file = re.sub('[^\w\-\.]', '_', str($read1.element_identifier)) + $ext
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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33 #end if
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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34
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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35 ln -s '$read1' '$read1_file' &&
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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36 #else:
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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37 #set read1 = $input_type_cond.input_collection.forward
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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38
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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39 #set ext = '.fastq'
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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40 #if $read1.ext.endswith('.gz'):
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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41 #set ext = $ext+'.gz'
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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42 #end if
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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43
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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44 #set read1_file = re.sub('[^\w\-\.]', '_', str($read1.element_identifier)) + $ext
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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45 ln -s '$read1' '$read1_file' &&
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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46
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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47 #set read2 = $input_type_cond.input_collection.reverse
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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48 #set read2_file = re.sub('[^\w\-\.]', '_', str($read2.element_identifier)) + $ext
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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49 ln -s '$read2' '$read2_file' &&
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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50
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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51 #end if
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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52
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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53 #if str($input_type_cond.input_type) in ['paired', 'collection']:
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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54 #set $seqsero_t_value = '2'
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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55 #elif str($input_type_cond.input_type) == 'assembly':
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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56 #set $seqsero_t_value = '4'
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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57 #elif str($input_type_cond.input_type) == 'single':
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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58 #set $seqsero_t_value = '3'
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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59 #elif str($input_type_cond.input_type) == 'nanopore':
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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60 #set $seqsero_t_value = '5'
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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61 #end if
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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62
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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63 #if str($input_type_cond.input_type) in ['assembly', 'nanopore']:
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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64 #set $seqsero_workflow_type = 'k'
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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65 #else:
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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66 #set $seqsero_workflow_type = $input_type_cond.workflow
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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67 #end if
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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68
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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69 SeqSero2_package.py
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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70 -m '$seqsero_workflow_type'
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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71 -t '$seqsero_t_value'
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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72 -i '$read1_file'
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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73 #if str($input_type_cond.input_type) in ['paired', 'collection']:
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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74 '$read2_file'
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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75 #end if
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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76 -p \${GALAXY_SLOTS:-4}
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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77 -d output
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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78 ]]> </command>
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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79 <inputs>
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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80 <conditional name="input_type_cond">
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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81 <param name="input_type" type="select" label="Input type" help="Select 'paired end' reads or 'sequence' for genomes/contigs">
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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82 <option value="paired">Paired End</option>
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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83 <option value="collection">Collection</option>
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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84 <option value="assembly">Contigs</option>
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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85 <option value="single">Interleaved</option>
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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86 <option value="nanopore">Nanopore reads</option>
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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87 </param>
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88 <when value="paired">
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89 <param name="read1" type="data" format="fastqsanger,fastqsanger.gz" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/>
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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90 <param name="read2" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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91 <expand macro="select_workflow_type" />
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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92 </when>
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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93 <when value="collection">
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94 <param name="input_collection" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Paired collection"/>
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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95 <expand macro="select_workflow_type" />
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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96 </when>
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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97 <when value="single">
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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98 <param name="read1" type="data" format="fastqsanger,fastqsanger.gz" multiple="false" label="Interleaved" />
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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99 <expand macro="select_workflow_type" />
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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100 </when>
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101 <when value="nanopore">
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102 <param name="read1" type="data" format="fasta" multiple="false" label="Nanopore reads" />
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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103 </when>
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104 <when value="assembly">
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105 <param name="read1" type="data" format="fasta" multiple="false" label="Contigs/genomes" />
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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106 </when>
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107 </conditional>
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108 <section name="output_options" title="Output options">
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109 <param argument="logfile" type="boolean" checked="false" truevalue="true" falsevalue="" label="Include log as output file."/>
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110 </section>
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111 </inputs>
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112 <outputs>
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113 <data name="results" format="tabular" label="${tool.name} on ${on_string} Results" from_work_dir="output/SeqSero_result.tsv"/>
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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114 <data name="log" format="txt" label="${tool.name} on ${on_string} Log" from_work_dir="output/SeqSero_log.txt">
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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115 <filter>output_options['logfile']</filter>
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116 </data>
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117 </outputs>
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118 <tests>
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iuc
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119 <test expect_num_outputs="2">
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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120 <param name="input_type" value="assembly" />
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121 <param name="read1" value="CP009102.1.fasta" ftype="fasta" />
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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122 <param name="logfile" value="true" />
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iuc
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123 <output name="results">
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124 <assert_contents>
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iuc
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125 <has_text text="Salmonella enterica subspecies enterica (subspecies I)" />
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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126 <has_text text="Typhimurium" />
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127 </assert_contents>
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128 </output>
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129 <output name="log">
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130 <assert_contents>
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131 <has_n_lines n="103" />
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132 <has_text text="O_scores" />
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133 <has_text text="H_scores" />
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134 <has_text text="Special_scores" />
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135 </assert_contents>
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136 </output>
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137 </test>
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138 <test expect_num_outputs="1">
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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139 <param name="input_type" value="paired" />
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140 <param name="workflow" value="a" />
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diff changeset
141 <param name="read1" value="SRR10859038_R1.fastq.gz" ftype="fastqsanger.gz" />
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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142 <param name="read2" value="SRR10859038_R2.fastq.gz" ftype="fastqsanger.gz" />
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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143 <output name="results">
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144 <assert_contents>
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145 <has_text text="The input genome cannot be identified as Salmonella." />
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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146 </assert_contents>
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147 </output>
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148 </test>
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149 <test expect_num_outputs="1">
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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150 <param name="input_type" value="collection" />
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151 <param name="workflow" value="k" />
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iuc
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diff changeset
152 <param name="input_collection">
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iuc
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153 <collection type="paired">
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iuc
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154 <element name="forward" value="SRR10859038_R1.fastq.gz" ftype="fastqsanger.gz" />
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iuc
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155 <element name="reverse" value="SRR10859038_R2.fastq.gz" ftype="fastqsanger.gz" />
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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156 </collection>
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157 </param>
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iuc
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158 <output name="results">
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159 <assert_contents>
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iuc
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160 <has_text text="The input genome cannot be identified as Salmonella." />
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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161 </assert_contents>
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162 </output>
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163 </test>
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164 <test expect_num_outputs="1">
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165 <param name="input_type" value="single" />
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166 <param name="workflow" value="a" />
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iuc
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diff changeset
167 <param name="read1" value="SRR10859038_R1.fastq.gz" ftype="fastqsanger.gz" />
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
iuc
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diff changeset
168 <output name="results">
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169 <assert_contents>
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iuc
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170 <has_text text="The input genome cannot be identified as Salmonella" />
f7f22f0db880 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit eaa07f4ff143aeba209c9efdf5f6ffb292119eb0
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171 </assert_contents>
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172 </output>
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173 </test>
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174 <test expect_num_outputs="1">
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175 <param name="input_type" value="nanopore" />
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176 <param name="read1" value="CP009102.1.fasta" ftype="fasta" />
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177 <output name="results">
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178 <assert_contents>
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179 <has_text text="Salmonella enterica subspecies enterica (subspecies I)" />
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180 <has_text text="Typhimurium" />
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181 </assert_contents>
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182 </output>
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183 </test>
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184 </tests>
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185 <help><![CDATA[
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186 **What is SeqSero2**
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187
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188 SeqSero2 is a pipeline for Salmonella serotype prediction from raw sequencing reads or genome assemblies.
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189 SeqSero is based on curated databases of Salmonella serotype determinants (rfb gene cluster, fliC and fljB alleles) and is predicted to determine serotype rapidly and accurately for nearly the full spectrum of Salmonella serotypes (more than 2,300 serotypes), from both raw sequencing reads and genome assemblies.
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190
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191 **Workflows**
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192
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193 * Allele micro-assembly (workflow: allele). This workflow takes raw reads as input and performs targeted assembly of serotype determinant alleles. Assembled alleles are used to predict serotype and flag potential inter-serotype contamination in sequencing data (i.e., presence of reads from multiple serotypes due to, for example, cross or carryover contamination during sequencing).
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194 * Raw reads k-mer (workflow: k-mer). This workflow takes raw reads as input and performs rapid serotype prediction based on unique k-mers of serotype determinants.
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195 * Genome assembly k-mer (input type: contigs). This workflow takes genome assemblies as input and the rest of the workflow largely overlaps with the raw reads k-mer workflow.
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196
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197 **Extra parameter information.**
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198
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199 The '-t' parameter is automatically determined using the input files, and therefore not customizable by the user. The logic used is based on the tool's parameter description:
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200
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201 * -t {1,2,3,4,5} <int>: '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore reads (fasta/fastq)
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202
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203 -----
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204
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205 _`Document`: https://github.com/denglab/SeqSero2
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206
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207 ]]></help>
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208 <expand macro="citations"/>
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209 </tool>