Mercurial > repos > iuc > seqsero2
annotate seqsero2.xml @ 0:e13b5be2de4e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
author | iuc |
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date | Tue, 07 Nov 2023 19:18:04 +0000 |
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children | 5a9a6074d99b |
rev | line source |
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0
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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1 <tool id="seqsero2" name="SeqSero2" version="@TOOL_VERSION@+galaxy0" profile="21.05"> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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changeset
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2 <description>Salmonella serotype prediction</description> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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3 <macros> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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changeset
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4 <import>macros.xml</import> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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5 </macros> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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changeset
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6 <expand macro="requirements" /> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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7 <version_command>SeqSero2_package.py -v</version_command> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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8 <command detect_errors="exit_code"><![CDATA[ |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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9 #import re |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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changeset
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10 #set $seqsero_t_value = '' |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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changeset
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11 #set $seqsero_workflow_type = '' |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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12 |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
diff
changeset
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13 #if str($input_type_cond.input_type) in ['single', 'paired', 'assembly', 'nanopore']: |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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changeset
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14 #set read1 = $input_type_cond.read1 |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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15 |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
diff
changeset
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16 #if str($input_type_cond.input_type) in ['assembly', 'nanopore']: |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
diff
changeset
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17 #set ext = '.fasta' |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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changeset
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18 #else: |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
diff
changeset
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19 #set ext = '.fastq' |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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changeset
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20 #end if |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
diff
changeset
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21 #if $read1.ext.endswith('.gz'): |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
diff
changeset
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22 #set ext = $ext+'.gz' |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
diff
changeset
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23 #end if |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
diff
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24 |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
diff
changeset
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25 #if str($input_type_cond.input_type) == 'paired': |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
diff
changeset
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26 #set read1_file = re.sub('[^\w\-\.]', '_', str($read1.element_identifier)) + '_forward' + $ext |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
diff
changeset
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27 #set read2 = $input_type_cond.read2 |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
diff
changeset
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28 #set read2_file = re.sub('[^\w\-\.]', '_', str($read2.element_identifier)) + '_reverse' + $ext |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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29 ln -s '$read2' '$read2_file' && |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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30 #else: |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
diff
changeset
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31 #set read1_file = re.sub('[^\w\-\.]', '_', str($read1.element_identifier)) + $ext |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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32 #end if |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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33 |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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34 ln -s '$read1' '$read1_file' && |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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35 #else: |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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36 #set read1 = $input_type_cond.input_collection.forward |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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37 |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
diff
changeset
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38 #set ext = '.fastq' |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
diff
changeset
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39 #if $read1.ext.endswith('.gz'): |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
diff
changeset
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40 #set ext = $ext+'.gz' |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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41 #end if |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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42 |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
diff
changeset
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43 #set read1_file = re.sub('[^\w\-\.]', '_', str($read1.element_identifier)) + $ext |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
diff
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44 ln -s '$read1' '$read1_file' && |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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45 |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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46 #set read2 = $input_type_cond.input_collection.reverse |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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47 #set read2_file = re.sub('[^\w\-\.]', '_', str($read2.element_identifier)) + $ext |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
diff
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48 ln -s '$read2' '$read2_file' && |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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49 |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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50 #end if |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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51 |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
diff
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52 #if str($input_type_cond.input_type) in ['paired', 'collection']: |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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53 #set $seqsero_t_value = '2' |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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54 #elif str($input_type_cond.input_type) == 'assembly': |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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55 #set $seqsero_t_value = '4' |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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56 #elif str($input_type_cond.input_type) == 'single': |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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57 #set $seqsero_t_value = '3' |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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58 #elif str($input_type_cond.input_type) == 'nanopore': |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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59 #set $seqsero_t_value = '5' |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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60 #end if |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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61 |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
diff
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62 #if str($input_type_cond.input_type) in ['assembly', 'nanopore']: |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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63 #set $seqsero_workflow_type = 'k' |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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64 #else: |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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65 #set $seqsero_workflow_type = $input_type_cond.workflow |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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66 #end if |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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67 |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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68 SeqSero2_package.py |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
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69 -m '$seqsero_workflow_type' |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
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70 -t '$seqsero_t_value' |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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71 -i '$read1_file' |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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72 #if str($input_type_cond.input_type) in ['paired', 'collection']: |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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73 '$read2_file' |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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74 #end if |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
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75 -p \${GALAXY_SLOTS:-4} |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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76 -d output |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
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77 ]]> </command> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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78 <inputs> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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79 <conditional name="input_type_cond"> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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80 <param name="input_type" type="select" label="Input type" help="Select 'paired end' reads or 'sequence' for genomes/contigs"> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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81 <option value="paired">Paired End</option> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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changeset
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82 <option value="collection">Collection</option> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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changeset
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83 <option value="assembly">Contigs</option> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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changeset
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84 <option value="single">Interleaved</option> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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85 <option value="nanopore">Nanopore reads</option> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
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86 </param> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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87 <when value="paired"> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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88 <param name="read1" type="data" format="fastqsanger,fastqsanger.gz" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
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89 <param name="read2" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
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90 <expand macro="select_workflow_type" /> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
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91 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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92 <when value="collection"> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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93 <param name="input_collection" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Paired collection"/> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
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changeset
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94 <expand macro="select_workflow_type" /> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
parents:
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95 </when> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
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changeset
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96 <when value="single"> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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changeset
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97 <param name="read1" type="data" format="fastqsanger,fastqsanger.gz" multiple="false" label="Interleaved" /> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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98 <expand macro="select_workflow_type" /> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
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99 </when> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
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100 <when value="nanopore"> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
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101 <param name="read1" type="data" format="fasta" multiple="false" label="Nanopore reads" /> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
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102 </when> |
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iuc
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103 <when value="assembly"> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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104 <param name="read1" type="data" format="fasta" multiple="false" label="Contigs/genomes" /> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
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105 </when> |
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iuc
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106 </conditional> |
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107 <section name="output_options" title="Output options"> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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108 <param argument="logfile" type="boolean" checked="false" truevalue="true" falsevalue="" label="Include log as output file."/> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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109 </section> |
e13b5be2de4e
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110 </inputs> |
e13b5be2de4e
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111 <outputs> |
e13b5be2de4e
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112 <data name="results" format="tabular" label="${tool.name} on ${on_string} Results" from_work_dir="output/SeqSero_result.tsv"/> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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113 <data name="log" format="txt" label="${tool.name} on ${on_string} Log" from_work_dir="output/SeqSero_log.txt"> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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114 <filter>output_options['logfile']</filter> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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115 </data> |
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116 </outputs> |
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117 <tests> |
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iuc
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118 <test expect_num_outputs="2"> |
e13b5be2de4e
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119 <param name="input_type" value="assembly" /> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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120 <param name="read1" value="CP009102.1.fasta" ftype="fasta" /> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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121 <param name="logfile" value="true" /> |
e13b5be2de4e
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iuc
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122 <output name="results"> |
e13b5be2de4e
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iuc
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123 <assert_contents> |
e13b5be2de4e
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124 <has_text text="Salmonella enterica subspecies enterica (subspecies I)" /> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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125 <has_text text="Typhimurium" /> |
e13b5be2de4e
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126 </assert_contents> |
e13b5be2de4e
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127 </output> |
e13b5be2de4e
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128 <output name="log"> |
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129 <assert_contents> |
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130 <has_n_lines n="104" /> |
e13b5be2de4e
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131 <has_text text="O_scores" /> |
e13b5be2de4e
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132 <has_text text="H_scores" /> |
e13b5be2de4e
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133 <has_text text="Special_scores" /> |
e13b5be2de4e
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134 </assert_contents> |
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135 </output> |
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136 </test> |
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137 <test expect_num_outputs="1"> |
e13b5be2de4e
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138 <param name="input_type" value="paired" /> |
e13b5be2de4e
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139 <param name="workflow" value="a" /> |
e13b5be2de4e
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140 <param name="read1" value="SRR10859038_R1.fastq.gz" ftype="fastqsanger.gz" /> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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141 <param name="read2" value="SRR10859038_R2.fastq.gz" ftype="fastqsanger.gz" /> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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142 <output name="results"> |
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143 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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144 <has_text text="The input genome cannot be identified as Salmonella." /> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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145 </assert_contents> |
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146 </output> |
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147 </test> |
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148 <test expect_num_outputs="1"> |
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149 <param name="input_type" value="collection" /> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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150 <param name="workflow" value="k" /> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
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151 <param name="input_collection"> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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152 <collection type="paired"> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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153 <element name="forward" value="SRR10859038_R1.fastq.gz" ftype="fastqsanger.gz" /> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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154 <element name="reverse" value="SRR10859038_R2.fastq.gz" ftype="fastqsanger.gz" /> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
iuc
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155 </collection> |
e13b5be2de4e
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156 </param> |
e13b5be2de4e
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157 <output name="results"> |
e13b5be2de4e
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158 <assert_contents> |
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159 <has_text text="The input genome cannot be identified as Salmonella." /> |
e13b5be2de4e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 commit 2268c10b0cf71b1a1967ce84720137f01db24c3b
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160 </assert_contents> |
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161 </output> |
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162 </test> |
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163 <test expect_num_outputs="1"> |
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164 <param name="input_type" value="single" /> |
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165 <param name="workflow" value="a" /> |
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166 <param name="read1" value="SRR10859038_R1.fastq.gz" ftype="fastqsanger.gz" /> |
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167 <output name="results"> |
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168 <assert_contents> |
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169 <has_text text="The input genome cannot be identified as Salmonella" /> |
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170 </assert_contents> |
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171 </output> |
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172 </test> |
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173 <test expect_num_outputs="1"> |
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174 <param name="input_type" value="nanopore" /> |
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175 <param name="read1" value="CP009102.1.fasta" ftype="fasta" /> |
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176 <output name="results"> |
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177 <assert_contents> |
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178 <has_text text="Salmonella enterica subspecies enterica (subspecies I)" /> |
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179 <has_text text="Typhimurium" /> |
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180 </assert_contents> |
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181 </output> |
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182 </test> |
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183 </tests> |
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184 <help><![CDATA[ |
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185 **What is SeqSero2** |
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186 |
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187 SeqSero2 is a pipeline for Salmonella serotype prediction from raw sequencing reads or genome assemblies. |
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188 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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189 |
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190 **Workflows** |
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191 |
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192 * 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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193 * 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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194 * 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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195 |
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196 **Extra parameter information.** |
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197 |
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198 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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199 |
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200 * -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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201 |
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202 ----- |
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203 |
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204 _`Document`: https://github.com/denglab/SeqSero2 |
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205 |
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206 ]]></help> |
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207 <expand macro="citations"/> |
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208 </tool> |