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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta commit 6adea21f21f7445e92568579096b7c7ea4781e50
author iuc
date Wed, 22 Oct 2025 15:47:16 +0000
parents 137d00a9a598
children
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72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
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1 <tool id="panta" name="PanTA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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2 <description>Efficient inference of large prokaryotic pangenomes with PanTA</description>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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3 <macros>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
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4 <import>macros.xml</import>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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5 </macros>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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6 <expand macro="requirements"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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7
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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8 <command detect_errors="exit_code"><![CDATA[
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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9 mkdir out &&
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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10 #import re, os
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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11 #set input_directory = 'input_directory'
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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12 mkdir $input_directory &&
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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13
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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14 #if $input_type.input_type_selector == "gff":
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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15 #for gff in $input_type.input_gff
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137d00a9a598 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 55ba2c9616d6567fe7e6a798103c28885ca754dd
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16 #set $filename = '%s.gff' % re.sub('[^\w_-]', '_', str($gff.element_identifier))
137d00a9a598 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 55ba2c9616d6567fe7e6a798103c28885ca754dd
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17 cp '$gff' '$input_directory/$filename' &&
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72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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18 #end for
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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19 #elif $input_type.input_type_selector == "tsv":
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137d00a9a598 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 55ba2c9616d6567fe7e6a798103c28885ca754dd
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20 #set $filename = '%s.tsv' % re.sub('[^\w_-]', '_', str($input_type.input_tsv.element_identifier))
137d00a9a598 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 55ba2c9616d6567fe7e6a798103c28885ca754dd
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21 cp '$input_type.input_tsv' '$input_directory/$filename' &&
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72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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22 #end if
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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23
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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24 #if $mode.select_mode == "main":
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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25 panta main
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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26 #if $input_type.input_type_selector == "gff":
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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27 -g $input_directory/*.gff
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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28 #elif $input_type.input_type_selector == "tsv":
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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29 -f $input_directory/*.tsv
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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30 #end if
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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31 -o out
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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32 $dont_split
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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33 --blast '$blast'
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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34 --identity '$identity'
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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35 --LD '$LD'
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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36 --AL '$AL'
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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37 --AS '$AS'
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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38 --evalue '$evalue'
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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39 --threads "\${GALAXY_SLOTS:-8}"
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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40 --table '$table'
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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41 #if $alignment != 'None':
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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42 --alignment '$alignment'
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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43 #end if
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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44 && tar -czf collection_dir.tar.gz -C out .
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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45
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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46 #elif $mode.select_mode == "add":
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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47 mkdir -p extracted_dir &&
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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48 ln -s $collection_dir collection_dir.tar.gz &&
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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49 tar --strip-components=1 -xzf collection_dir.tar.gz -C extracted_dir &&
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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50 panta add
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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51 #if $input_type.input_type_selector == "gff":
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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52 -g $input_directory/*.gff
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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53 #elif $input_type.input_type_selector == "tsv":
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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54 -f $input_directory/*.tsv
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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55 #end if
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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56 -c extracted_dir
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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57 $dont_split
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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58 --blast '$blast'
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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59 --identity '$identity'
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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60 --LD '$LD'
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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61 --AL '$AL'
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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62 --AS '$AS'
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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63 --evalue '$evalue'
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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64 --threads "\${GALAXY_SLOTS:-8}"
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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65 --table '$table'
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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66 #if $alignment != 'None':
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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67 --alignment '$alignment'
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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68 #end if
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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69 && cp -r extracted_dir/* out
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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70 #end if
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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71 ]]></command>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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72
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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73 <inputs>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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74 <conditional name="mode">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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75 <param label="Select mode" name="select_mode" type="select">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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76 <option selected="true" value="main">Use PanTA main</option>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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77 <option value="add">Use PanTA add</option>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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78 </param>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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79 <when value="main"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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80 <when value="add">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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81 <param name="collection_dir" type="data" format="tar,tar.gz" label="Previous collection directory"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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82 </when>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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83 </conditional>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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84 <conditional name="input_type">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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85 <param name="input_type_selector" type="select" label="Choose the input format">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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86 <option value="gff" selected="true">GFF File</option>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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87 <option value="tsv">TSV File</option>
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88 </param>
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89 <when value="gff">
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90 <param type="data_collection" name="input_gff" format="gff3" collection_type="list" label="Select input files to analyze" help="Select the files you wish to analyze with PanTA"/>
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91 </when>
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92 <when value="tsv">
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93 <param type="data" name="input_tsv" format="tsv,tabular" multiple="false" label="Select input file to analyze" help="Select the file you wish to analyze with PanTA"/>
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94 </when>
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95 </conditional>
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96 <param argument="--dont-split" type="boolean" truevalue="--dont-split" falsevalue="" label="Dont split" help="Decide for or against splitting paralog clusters"/>
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97 <param argument="--blast" type="select" label="Alignment method" help="Method for all-against-all alignment (default: diamond)">
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98 <option value="diamond" selected="True">Diamond</option>
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99 <option value="blast">Blast</option>
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100 </param>
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101 <param argument="--identity" type="float" value="0.7" label="Minimum percentage identity" help="Set the minimum percentage identity"/>
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102 <param argument="--LD" type="float" value="0.7" label="Length difference cutoff" help="Set the length difference cutoff between two sequences"/>
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103 <param argument="--AL" type="float" value="0" label="Alignment coverage for the longer sequence" help="Set the alignment coverage for the longer sequence"/>
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104 <param argument="--AS" type="float" value="0" label="Alignment coverage for the shorter sequence" help="Set the alignment coverage for the shorter sequence"/>
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105 <param argument="--evalue" type="float" value="1e-06" label="Blast evalue" help="Maximum expected value for reporting hits and lower values are stricter"/>
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106 <param argument="--table" type="integer" value="" label="Codon table" help="Set the codon table"/>
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107 <param argument="--alignment" type="select" label="Run alignment for each gene cluster">
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108 <option value="None" selected="True">None</option>
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109 <option value="nucleotide">Nucleotide</option>
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110 <option value="protein">Protein</option>
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111 </param>
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112 </inputs>
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113
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114 <outputs>
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115 <!--Basic PanTA main outputs -->
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116 <data format="json" name="annotated_clusters" label="${tool.name} on ${on_string} : Annotated Clusters" from_work_dir="out/annotated_clusters.json"/>
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117 <data format="tsv" name="blast_output" label="${tool.name} on ${on_string} : BLAST" from_work_dir="out/blast.tsv"/>
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118 <data format="json" name="clusters" label="${tool.name} on ${on_string} : Clusters" from_work_dir="out/clusters.json"/>
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119 <data format="csv" name="gene_annotation" label="${tool.name} on ${on_string} : Gene Annotation" from_work_dir="out/gene_annotation.csv"/>
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120 <data format="csv" name="gene_position" label="${tool.name} on ${on_string} : Gene Position" from_work_dir="out/gene_position.csv"/>
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121 <data format="csv" name="gene_presence_absence" label="${tool.name} on ${on_string} : Gene Presence Absence" from_work_dir="out/gene_presence_absence.csv"/>
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122 <data format="txt" name="gene_presence_absence_Rtab" label="${tool.name} on ${on_string} : Gene Presence Absence Rtab" from_work_dir="out/gene_presence_absence.Rtab"/>
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123 <data format="fasta" name="representative_clusters_nucl" label="${tool.name} on ${on_string} : Representative Clusters Nucl" from_work_dir="out/representative_clusters_nucl.fasta"/>
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124 <data format="fasta" name="representative_clusters_prot" label="${tool.name} on ${on_string} : Representative Clusters Prot" from_work_dir="out/representative_clusters_prot.fasta"/>
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125 <data format="fasta" name="representative" label="${tool.name} on ${on_string} : Representative FASTA" from_work_dir="out/representative.fasta"/>
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126 <data format="json" name="samples" label="${tool.name} on ${on_string} : Samples" from_work_dir="out/samples.json"/>
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127 <data format="txt" name="summary_statistics" label="${tool.name} on ${on_string} : Summary Statistics" from_work_dir="out/summary_statistics.txt"/>
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128
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129 <!--Alignment outputs -->
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130 <data format="fasta" name="core_gene_alignment" label="${tool.name} on ${on_string} : Core Gene Alignment" from_work_dir="out/core_gene_alignment.aln.gz">
0
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131 <filter> ['alignment'] != 'None' </filter>
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132 </data>
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133 <data format="fasta" name="pan_genome_reference" label="${tool.name} on ${on_string} : Pan Genome Reference" from_work_dir="out/pan_genome_reference.fna">
0
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134 <filter> ['alignment'] != 'None' </filter>
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135 </data>
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136 </outputs>
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137
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138 <tests>
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139 <!--Test 01: Basic PanTA main test for gff files: Tests the basic command for PanTA main -->
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140 <test expect_num_outputs="14">
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141 <conditional name="mode">
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142 <param name="select_mode" value="main"/>
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143 </conditional>
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144 <conditional name="input_type">
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145 <param name="input_type_selector" value="gff"/>
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146 <param name="input_gff">
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147 <collection type="list">
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148 <element name="GCA_021342655.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021342655.1.gff"/>
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149 <element name="GCA_021534865.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021534865.1.gff"/>
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150 <element name="GCA_021697815.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021697815.1.gff"/>
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151 <element name="GCA_021890555.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021890555.1.gff"/>
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152 </collection>
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153 </param>
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154 </conditional>
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155 <param name="table" value="10"/>
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156 <output name="annotated_clusters" ftype="json">
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157 <assert_contents>
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158 <has_text text="GCA_021342655.1-NZ_JAJTPH010000093.1-5475-cds-WP_000557454.1"/>
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159 <has_n_lines n="96508" delta='3'/>
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160 </assert_contents>
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161 </output>
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162 <output name="blast_output" ftype="tsv">
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163 <assert_contents>
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164 <has_text text="GCA_021342655.1-NZ_JAJTPH010000101.1-3-cds-WP_233337042.1"/>
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165 <has_n_lines n="30680" delta='3'/>
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166 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
167 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
168 <output name="clusters" ftype="json">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
169 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
170 <has_text text="GCA_021890555.1-NZ_JAKLOD010000002.1-4878-cds-L3T02_RS24235"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
171 <has_n_lines n="24266" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
172 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
173 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
174 <output name="gene_annotation" ftype="csv">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
175 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
176 <has_text text="IclR family transcriptional regulator,6"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
177 <has_n_lines n="19712" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
178 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
179 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
180 <output name="gene_position" ftype="csv">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
181 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
182 <has_text text="1-NZ_JAJTPH010000010.1-23-cds-LXO36_RS13380"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
183 <has_n_lines n="195" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
184 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
185 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
186 <output name="gene_presence_absence" ftype="csv">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
187 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
188 <has_n_lines n="7682" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
189 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
190 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
191 <output name="gene_presence_absence_Rtab" ftype="txt">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
192 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
193 <has_n_lines n="7682" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
194 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
195 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
196 <output name="representative_clusters_nucl" ftype="fasta">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
197 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
198 <has_text text="GGTCTGCCCCACCGGCATCGACATTCGCGACGGCCTGCAGATCGAGTGCATTGGTTGCGC"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
199 <has_n_lines n="124180" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
200 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
201 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
202 <output name="representative_clusters_prot" ftype="fasta">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
203 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
204 <has_text text="GLPHRHRHSRRPADRVHWLRRLHRCLRQHHGQDGLPQGPDQLHNRTQSFRTEDPSAAPTP"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
205 <has_n_lines n="49014" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
206 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
207 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
208 <output name="representative" ftype="fasta">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
209 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
210 <has_text text="RIEGSVWPKSIRGSTPKVRGTCQIERAASESPHFMRFHVACPHCGEEQYLKFGDKETPFGLKWTPDDPSSVFYLCEHNACVIRQQELDFTDARYICEKTGIWTRDGILWFSSSGEEIEPPDSVTFHIWTAYSPFTTWVQIVKDWMKTKGDTGKRKTFVNTTLGETWEAKIGERPDAEVMAERKEHYSAPVPDRVAYLTAGIDSQLDRYEMRVWGWGPGEESWLIDRQIIMGRHDDEQTLLRVDEAINKTYTRRNGAEMS"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
211 <has_n_lines n="18795" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
212 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
213 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
214 <output name="samples" ftype="json">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
215 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
216 <has_n_lines n="22" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
217 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
218 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
219 <output name="summary_statistics" ftype="txt">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
220 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
221 <has_text text="Soft core genes"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
222 <has_n_lines n="6" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
223 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
224 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
225 </test>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
226
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
227 <!--Test 2: PanTA main test for gff files: Tests the 'dont_split' parameter -->
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
228 <test expect_num_outputs="14">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
229 <conditional name="mode">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
230 <param name="select_mode" value="main"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
231 </conditional>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
232 <conditional name="input_type">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
233 <param name="input_type_selector" value="gff"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
234 <param name="input_gff">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
235 <collection type="list">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
236 <element name="GCA_021342655.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021342655.1.gff"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
237 <element name="GCA_021534865.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021534865.1.gff"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
238 <element name="GCA_021697815.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021697815.1.gff"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
239 <element name="GCA_021890555.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021890555.1.gff"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
240 </collection>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
241 </param>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
242 </conditional>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
243 <param name="table" value="10"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
244 <param name="dont_split" value="true"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
245 <output name="annotated_clusters" ftype="json">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
246 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
247 <has_text text="GCA_021342655.1-NZ_JAJTPH010000093.1-5475-cds-WP_000557454.1"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
248 <has_n_lines n="90588" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
249 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
250 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
251 <output name="blast_output" ftype="tsv">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
252 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
253 <has_text text="GCA_021342655.1-NZ_JAJTPH010000101.1-3-cds-WP_233337042.1"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
254 <has_n_lines n="30680" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
255 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
256 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
257 <output name="clusters" ftype="json">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
258 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
259 <has_text text="GCA_021890555.1-NZ_JAKLOD010000002.1-4878-cds-L3T02_RS24235"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
260 <has_n_lines n="24266" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
261 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
262 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
263 <output name="gene_annotation" ftype="csv">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
264 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
265 <has_text text="IclR family transcriptional regulator,6"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
266 <has_n_lines n="19712" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
267 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
268 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
269 <output name="gene_position" ftype="csv">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
270 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
271 <has_text text="1-NZ_JAJTPH010000010.1-23-cds-LXO36_RS13380"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
272 <has_n_lines n="195" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
273 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
274 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
275 <output name="gene_presence_absence" ftype="csv">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
276 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
277 <has_n_lines n="7089" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
278 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
279 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
280 <output name="gene_presence_absence_Rtab" ftype="txt">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
281 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
282 <has_n_lines n="7089" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
283 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
284 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
285 <output name="representative_clusters_nucl" ftype="fasta">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
286 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
287 <has_text text="GGTCTGCCCCACCGGCATCGACATTCGCGACGGCCTGCAGATCGAGTGCATTGGTTGCGC"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
288 <has_n_lines n="115793" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
289 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
290 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
291 <output name="representative_clusters_prot" ftype="fasta">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
292 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
293 <has_text text="GLPHRHRHSRRPADRVHWLRRLHRCLRQHHGQDGLPQGPDQLHNRTQSFRTEDPSAAPTP"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
294 <has_n_lines n="45624" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
295 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
296 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
297 <output name="representative" ftype="fasta">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
298 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
299 <has_text text="RIEGSVWPKSIRGSTPKVRGTCQIERAASESPHFMRFHVACPHCGEEQYLKFGDKETPFGLKWTPDDPSSVFYLCEHNACVIRQQELDFTDARYICEKTGIWTRDGILWFSSSGEEIEPPDSVTFHIWTAYSPFTTWVQIVKDWMKTKGDTGKRKTFVNTTLGETWEAKIGERPDAEVMAERKEHYSAPVPDRVAYLTAGIDSQLDRYEMRVWGWGPGEESWLIDRQIIMGRHDDEQTLLRVDEAINKTYTRRNGAEMS"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
300 <has_n_lines n="18795" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
301 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
302 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
303 <output name="samples" ftype="json">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
304 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
305 <has_n_lines n="22" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
306 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
307 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
308 <output name="summary_statistics" ftype="txt">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
309 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
310 <has_text text="Soft core genes"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
311 <has_n_lines n="6" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
312 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
313 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
314 </test>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
315
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
316 <!--Test 3: PanTA main test for gff files: The 'alignment' parameter -->
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
317 <test expect_num_outputs="14">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
318 <conditional name="mode">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
319 <param name="select_mode" value="main"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
320 </conditional>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
321 <conditional name="input_type">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
322 <param name="input_type_selector" value="gff"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
323 <param name="input_gff">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
324 <collection type="list">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
325 <element name="GCA_021342655.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021342655.1.gff"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
326 <element name="GCA_021534865.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021534865.1.gff"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
327 <element name="GCA_021697815.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021697815.1.gff"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
328 <element name="GCA_021890555.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021890555.1.gff"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
329 </collection>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
330 </param>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
331 </conditional>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
332 <param name="table" value="10"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
333 <param name="alignment" value="nucleotide"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
334 <output name="annotated_clusters" ftype="json">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
335 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
336 <has_text text="GCA_021342655.1-NZ_JAJTPH010000093.1-5475-cds-WP_000557454.1"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
337 <has_n_lines n="96508" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
338 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
339 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
340 <output name="blast_output" ftype="tsv">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
341 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
342 <has_text text="GCA_021342655.1-NZ_JAJTPH010000101.1-3-cds-WP_233337042.1"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
343 <has_n_lines n="30680" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
344 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
345 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
346 <output name="clusters" ftype="json">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
347 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
348 <has_text text="GCA_021890555.1-NZ_JAKLOD010000002.1-4878-cds-L3T02_RS24235"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
349 <has_n_lines n="24266" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
350 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
351 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
352 <output name="gene_annotation" ftype="csv">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
353 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
354 <has_text text="IclR family transcriptional regulator,6"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
355 <has_n_lines n="19712" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
356 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
357 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
358 <output name="gene_position" ftype="csv">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
359 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
360 <has_text text="1-NZ_JAJTPH010000010.1-23-cds-LXO36_RS13380"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
361 <has_n_lines n="195" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
362 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
363 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
364 <output name="gene_presence_absence" ftype="csv">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
365 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
366 <has_n_lines n="7681" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
367 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
368 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
369 <output name="gene_presence_absence_Rtab" ftype="txt">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
370 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
371 <has_n_lines n="7681" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
372 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
373 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
374 <output name="representative_clusters_nucl" ftype="fasta">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
375 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
376 <has_text text="GGTCTGCCCCACCGGCATCGACATTCGCGACGGCCTGCAGATCGAGTGCATTGGTTGCGC"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
377 <has_n_lines n="124180" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
378 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
379 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
380 <output name="representative_clusters_prot" ftype="fasta">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
381 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
382 <has_text text="GLPHRHRHSRRPADRVHWLRRLHRCLRQHHGQDGLPQGPDQLHNRTQSFRTEDPSAAPTP"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
383 <has_n_lines n="49014" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
384 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
385 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
386 <output name="representative" ftype="fasta">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
387 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
388 <has_text text="RIEGSVWPKSIRGSTPKVRGTCQIERAASESPHFMRFHVACPHCGEEQYLKFGDKETPFGLKWTPDDPSSVFYLCEHNACVIRQQELDFTDARYICEKTGIWTRDGILWFSSSGEEIEPPDSVTFHIWTAYSPFTTWVQIVKDWMKTKGDTGKRKTFVNTTLGETWEAKIGERPDAEVMAERKEHYSAPVPDRVAYLTAGIDSQLDRYEMRVWGWGPGEESWLIDRQIIMGRHDDEQTLLRVDEAINKTYTRRNGAEMS"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
389 <has_n_lines n="18795" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
390 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
391 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
392 <output name="samples" ftype="json">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
393 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
394 <has_n_lines n="22" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
395 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
396 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
397 <output name="summary_statistics" ftype="txt">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
398 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
399 <has_text text="Soft core genes"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
400 <has_n_lines n="6" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
401 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
402 </output>
3
1de68b7a1e3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta commit 6adea21f21f7445e92568579096b7c7ea4781e50
iuc
parents: 2
diff changeset
403 <output name="core_gene_alignment" ftype="fasta">
0
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
404 <assert_contents>
2
137d00a9a598 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 55ba2c9616d6567fe7e6a798103c28885ca754dd
iuc
parents: 1
diff changeset
405 <has_n_lines n="96130" delta='3'/>
0
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
406 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
407 </output>
3
1de68b7a1e3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta commit 6adea21f21f7445e92568579096b7c7ea4781e50
iuc
parents: 2
diff changeset
408 <output name="pan_genome_reference" ftype="fasta">
0
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
409 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
410 <has_text text="AAAGGCGTTTGGTATATAACGATGCCAG"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
411 <has_n_lines n="84292" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
412 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
413 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
414 </test>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
415
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
416 <!--Test 4: Basic PanTA add test for gff files: Tests the basic command for PanTA add -->
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
417 <test expect_num_outputs="14">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
418 <conditional name="mode">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
419 <param name="select_mode" value="add"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
420 <param name="collection_dir" location="https://zenodo.org/records/16568442/files/collection_dir.tar.gz" ftype="tar.gz"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
421 </conditional>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
422 <conditional name="input_type">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
423 <param name="input_type_selector" value="gff"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
424 <param name="input_gff">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
425 <collection type="list">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
426 <element name="GCA_021342735.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021342735.1.gff"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
427 <element name="GCA_021725855.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021725855.1.gff"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
428 <element name="GCA_021890695.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021890695.1.gff"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
429 </collection>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
430 </param>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
431 </conditional>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
432 <param name="table" value="10"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
433 <output name="annotated_clusters" ftype="json">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
434 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
435 <has_text text="GCA_021342655.1-NZ_JAJTPH010000093.1-5475-cds-WP_000557454.1"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
436 <has_n_lines n="118811" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
437 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
438 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
439 <output name="blast_output" ftype="tsv">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
440 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
441 <has_text text="GCA_021342655.1-NZ_JAJTPH010000101.1-3-cds-WP_233337042.1"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
442 <has_n_lines n="38245" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
443 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
444 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
445 <output name="clusters" ftype="json">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
446 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
447 <has_text text="GCA_021890555.1-NZ_JAKLOD010000002.1-4878-cds-L3T02_RS24235"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
448 <has_n_lines n="39790" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
449 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
450 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
451 <output name="gene_annotation" ftype="csv">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
452 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
453 <has_text text="IclR family transcriptional regulator,6"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
454 <has_n_lines n="33564" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
455 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
456 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
457 <output name="gene_position" ftype="csv">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
458 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
459 <has_text text="1-NZ_JAJTPH010000010.1-23-cds-LXO36_RS13380"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
460 <has_n_lines n="363" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
461 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
462 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
463 <output name="gene_presence_absence" ftype="csv">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
464 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
465 <has_n_lines n="8523" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
466 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
467 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
468 <output name="gene_presence_absence_Rtab" ftype="txt">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
469 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
470 <has_n_lines n="8523" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
471 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
472 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
473 <output name="representative_clusters_nucl" ftype="fasta">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
474 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
475 <has_text text="GGTCTGCCCCACCGGCATCGACATTCGCGACGGCCTGCAGATCGAGTGCATTGGTTGCGC"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
476 <has_n_lines n="136572" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
477 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
478 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
479 <output name="representative_clusters_prot" ftype="fasta">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
480 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
481 <has_text text="GLPHRHRHSRRPADRVHWLRRLHRCLRQHHGQDGLPQGPDQLHNRTQSFRTEDPSAAPTP"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
482 <has_n_lines n="53952" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
483 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
484 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
485 <output name="representative" ftype="fasta">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
486 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
487 <has_text text="RIEGSVWPKSIRGSTPKVRGTCQIERAASESPHFMRFHVACPHCGEEQYLKFGDKETPFGLKWTPDDPSSVFYLCEHNACVIRQQELDFTDARYICEKTGIWTRDGILWFSSSGEEIEPPDSVTFHIWTAYSPFTTWVQIVKDWMKTKGDTGKRKTFVNTTLGETWEAKIGERPDAEVMAERKEHYSAPVPDRVAYLTAGIDSQLDRYEMRVWGWGPGEESWLIDRQIIMGRHDDEQTLLRVDEAINKTYTRRNGAEMS"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
488 <has_n_lines n="29001" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
489 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
490 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
491 <output name="samples" ftype="json">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
492 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
493 <has_n_lines n="37" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
494 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
495 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
496 <output name="summary_statistics" ftype="txt">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
497 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
498 <has_text text="Soft core genes"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
499 <has_n_lines n="6" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
500 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
501 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
502 </test>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
503
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
504 <!--Test 5: Basic PanTA add test for gff files: Tests the 'dont_split' parameter -->
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
505 <test expect_num_outputs="14">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
506 <conditional name="mode">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
507 <param name="select_mode" value="add"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
508 <param name="collection_dir" location="https://zenodo.org/records/16568442/files/collection_dir.tar.gz" ftype="tar.gz"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
509 </conditional>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
510 <conditional name="input_type">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
511 <param name="input_type_selector" value="gff"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
512 <param name="input_gff">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
513 <collection type="list">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
514 <element name="GCA_021342735.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021342735.1.gff"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
515 <element name="GCA_021725855.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021725855.1.gff"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
516 <element name="GCA_021890695.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021890695.1.gff"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
517 </collection>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
518 </param>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
519 </conditional>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
520 <param name="table" value="10"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
521 <param name="dont_split" value="true"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
522 <output name="annotated_clusters" ftype="json">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
523 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
524 <has_text text="GCA_021342655.1-NZ_JAJTPH010000093.1-5475-cds-WP_000557454.1"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
525 <has_n_lines n="111811" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
526 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
527 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
528 <output name="blast_output" ftype="tsv">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
529 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
530 <has_text text="GCA_021342655.1-NZ_JAJTPH010000101.1-3-cds-WP_233337042.1"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
531 <has_n_lines n="38245" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
532 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
533 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
534 <output name="clusters" ftype="json">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
535 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
536 <has_text text="GCA_021890555.1-NZ_JAKLOD010000002.1-4878-cds-L3T02_RS24235"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
537 <has_n_lines n="39790" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
538 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
539 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
540 <output name="gene_annotation" ftype="csv">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
541 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
542 <has_text text="IclR family transcriptional regulator,6"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
543 <has_n_lines n="33564" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
544 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
545 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
546 <output name="gene_position" ftype="csv">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
547 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
548 <has_text text="1-NZ_JAJTPH010000010.1-23-cds-LXO36_RS13380"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
549 <has_n_lines n="363" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
550 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
551 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
552 <output name="gene_presence_absence" ftype="csv">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
553 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
554 <has_n_lines n="7825" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
555 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
556 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
557 <output name="gene_presence_absence_Rtab" ftype="txt">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
558 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
559 <has_n_lines n="7825" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
560 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
561 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
562 <output name="representative_clusters_nucl" ftype="fasta">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
563 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
564 <has_text text="GGTCTGCCCCACCGGCATCGACATTCGCGACGGCCTGCAGATCGAGTGCATTGGTTGCGC"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
565 <has_n_lines n="126631" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
566 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
567 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
568 <output name="representative_clusters_prot" ftype="fasta">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
569 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
570 <has_text text="GLPHRHRHSRRPADRVHWLRRLHRCLRQHHGQDGLPQGPDQLHNRTQSFRTEDPSAAPTP"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
571 <has_n_lines n="49946" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
572 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
573 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
574 <output name="representative" ftype="fasta">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
575 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
576 <has_text text="RIEGSVWPKSIRGSTPKVRGTCQIERAASESPHFMRFHVACPHCGEEQYLKFGDKETPFGLKWTPDDPSSVFYLCEHNACVIRQQELDFTDARYICEKTGIWTRDGILWFSSSGEEIEPPDSVTFHIWTAYSPFTTWVQIVKDWMKTKGDTGKRKTFVNTTLGETWEAKIGERPDAEVMAERKEHYSAPVPDRVAYLTAGIDSQLDRYEMRVWGWGPGEESWLIDRQIIMGRHDDEQTLLRVDEAINKTYTRRNGAEMS"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
577 <has_n_lines n="29001" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
578 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
579 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
580 <output name="samples" ftype="json">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
581 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
582 <has_n_lines n="37" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
583 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
584 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
585 <output name="summary_statistics" ftype="txt">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
586 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
587 <has_text text="Soft core genes"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
588 <has_n_lines n="6" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
589 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
590 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
591 </test>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
592
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
593 <!--Test 6: Basic PanTA add test for gff files: Tests the 'alignment' parameter -->
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
594 <test expect_num_outputs="14">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
595 <conditional name="mode">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
596 <param name="select_mode" value="add"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
597 <param name="collection_dir" location="https://zenodo.org/records/16568442/files/collection_dir.tar.gz" ftype="tar.gz"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
598 </conditional>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
599 <conditional name="input_type">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
600 <param name="input_type_selector" value="gff"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
601 <param name="input_gff">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
602 <collection type="list">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
603 <element name="GCA_021342735.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021342735.1.gff"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
604 <element name="GCA_021725855.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021725855.1.gff"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
605 <element name="GCA_021890695.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021890695.1.gff"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
606 </collection>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
607 </param>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
608 </conditional>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
609 <param name="table" value="10"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
610 <param name="alignment" value="nucleotide"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
611 <output name="annotated_clusters" ftype="json">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
612 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
613 <has_text text="GCA_021342655.1-NZ_JAJTPH010000093.1-5475-cds-WP_000557454.1"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
614 <has_n_lines n="118811" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
615 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
616 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
617 <output name="blast_output" ftype="tsv">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
618 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
619 <has_text text="GCA_021342655.1-NZ_JAJTPH010000101.1-3-cds-WP_233337042.1"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
620 <has_n_lines n="38245" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
621 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
622 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
623 <output name="clusters" ftype="json">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
624 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
625 <has_text text="GCA_021890555.1-NZ_JAKLOD010000002.1-4878-cds-L3T02_RS24235"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
626 <has_n_lines n="39790" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
627 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
628 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
629 <output name="gene_annotation" ftype="csv">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
630 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
631 <has_text text="IclR family transcriptional regulator,6"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
632 <has_n_lines n="33564" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
633 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
634 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
635 <output name="gene_position" ftype="csv">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
636 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
637 <has_text text="1-NZ_JAJTPH010000010.1-23-cds-LXO36_RS13380"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
638 <has_n_lines n="363" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
639 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
640 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
641 <output name="gene_presence_absence" ftype="csv">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
642 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
643 <has_n_lines n="8523" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
644 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
645 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
646 <output name="gene_presence_absence_Rtab" ftype="txt">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
647 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
648 <has_n_lines n="8523" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
649 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
650 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
651 <output name="representative_clusters_nucl" ftype="fasta">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
652 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
653 <has_text text="GGTCTGCCCCACCGGCATCGACATTCGCGACGGCCTGCAGATCGAGTGCATTGGTTGCGC"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
654 <has_n_lines n="136572" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
655 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
656 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
657 <output name="representative_clusters_prot" ftype="fasta">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
658 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
659 <has_text text="GLPHRHRHSRRPADRVHWLRRLHRCLRQHHGQDGLPQGPDQLHNRTQSFRTEDPSAAPTP"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
660 <has_n_lines n="53952" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
661 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
662 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
663 <output name="representative" ftype="fasta">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
664 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
665 <has_text text="RIEGSVWPKSIRGSTPKVRGTCQIERAASESPHFMRFHVACPHCGEEQYLKFGDKETPFGLKWTPDDPSSVFYLCEHNACVIRQQELDFTDARYICEKTGIWTRDGILWFSSSGEEIEPPDSVTFHIWTAYSPFTTWVQIVKDWMKTKGDTGKRKTFVNTTLGETWEAKIGERPDAEVMAERKEHYSAPVPDRVAYLTAGIDSQLDRYEMRVWGWGPGEESWLIDRQIIMGRHDDEQTLLRVDEAINKTYTRRNGAEMS"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
666 <has_n_lines n="29001" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
667 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
668 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
669 <output name="samples" ftype="json">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
670 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
671 <has_n_lines n="37" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
672 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
673 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
674 <output name="summary_statistics" ftype="txt">
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
iuc
parents:
diff changeset
675 <assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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676 <has_text text="Soft core genes"/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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677 <has_n_lines n="6" delta='3'/>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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678 </assert_contents>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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679 </output>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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680 </test>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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681 </tests>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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682 <help><![CDATA[
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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683
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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684 PanTA builds the pangenome of a large collection of genomes and adds a set of new genomes to an existing pangenome without rebuilding the accumulated pangenome from scratch. PanTA takes as input a list of genome assemblies and their annotations. It extracts the protein-coding regions as specified by the annotations and translates them into protein sequences. PanTA then generates output reports according to the standards set out by Roary, which include a spreadsheet detailing the presence and absence of each gene in each isolate as well as a summary of pangenome statistics.
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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685
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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686 **INPUTS**
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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687
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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688 - A collection of gff3 files or a tsv file.
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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689
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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690 **OUTPUTS**
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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691
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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692 - annotated_clusters.json
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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693 - blast.tsv
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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694 - clusters.json
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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695 - gene_annotation.csv
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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696 - gene_position.csv
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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697 - gene_presence_absence.csv
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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698 - gene_presence_absence.Rtab
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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699 - representative_clusters_nucl.fasta
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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700 - representative_clusters_prot.fasta
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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701 - representative.fasta
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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702 - samples.json
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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703 - summary_statistics.txt
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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704 - core_gene_alignment.aln.gz (requires alignment option)
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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705 - pan_genome_reference.fna (requires alignment option)
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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706
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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707 ]]></help>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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708 <citations>
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709 <citation type="doi">10.6084/m9.figshare.23724705</citation>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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710 </citations>
72296762b4f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
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711 <expand macro="creator"/>
2
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712 </tool>