Mercurial > repos > iuc > ppanggolin_all

annotate ppanggolin_all.xml @ 7:72179c3fa871 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ppanggolin commit 29098ae57dcc42db8f9adf321d31ed37fb999d17
author iuc
date Mon, 24 Nov 2025 12:55:56 +0000
parents d2b0073ef8d6
children
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6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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1 <tool id="ppanggolin_all" name="PPanGGOLiN all" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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2 <description>generates a partitioned pangenome</description>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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3 <macros>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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4 <import>macros.xml</import>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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5 </macros>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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6 <expand macro="xrefs"/>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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7 <expand macro="requirements"/>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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9 <command detect_errors="exit_code"><![CDATA[
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d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
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10 #import re
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6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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11
5
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
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12 mkdir -p ./tmp_ppanggolin/all &&
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
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13 mkdir -p ./tmp_ppanggolin/organism_list &&
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
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d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
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15 @ORGANISM_LIST@
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6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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17 ppanggolin all
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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19 #if $extension_input_files == "fasta":
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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20 --fasta
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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21 #elif $extension_input_files == "genbank":
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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22 --anno
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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23 #end if
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d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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24 ./tmp_ppanggolin/organism_list/organism.list
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6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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25
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d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
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26 --output ./tmp_ppanggolin/all
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6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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27 --force
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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28 --cpu "\${GALAXY_SLOTS:-4}"
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d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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29 --disable_prog_bar
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6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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31 --coverage $coverage
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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32 --identity $identity
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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33 --translation_table $translation_table
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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36 #if str($nb_of_partitions) != "":
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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37 --nb_of_partitions $nb_of_partitions
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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38 #end if
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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39
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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40 $do_defrag
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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41
5
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
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43 && ppanggolin info
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
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44 --pangenome ./tmp_ppanggolin/all/pangenome.h5
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
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45 > ./tmp_ppanggolin/all/ppanggolin_info.txt
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
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46
0
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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47
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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48 #if "output_functional_modules" in $advanced_pangenome_optional_files:
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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49 && cat ./tmp_ppanggolin/all/functional_modules.tsv > '${functional_modules}'
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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50 #end if
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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51 #if "output_modules_RGP_lists" in $advanced_pangenome_optional_files:
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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52 && cat ./tmp_ppanggolin/all/modules_RGP_lists.tsv > '${modules_RGP_lists}'
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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53 #end if
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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54 #if "output_modules_spots" in $advanced_pangenome_optional_files:
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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55 && cat ./tmp_ppanggolin/all/modules_spots.tsv > '${modules_spots}'
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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56 #end if
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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57 #if "output_modules_in_genomes" in $advanced_pangenome_optional_files:
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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58 && cat ./tmp_ppanggolin/all/modules_in_genomes.tsv > '${modules_in_genomes}'
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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59 #end if
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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60 #if "output_modules_summary" in $advanced_pangenome_optional_files:
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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61 && cat ./tmp_ppanggolin/all/modules_summary.tsv > '${modules_summary}'
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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62 #end if
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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63 #if "output_spot_borders" in $advanced_pangenome_optional_files:
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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64 && cat ./tmp_ppanggolin/all/spot_borders.tsv > '${spot_borders}'
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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65 #end if
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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66 #if "output_spots" in $advanced_pangenome_optional_files:
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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67 && cat ./tmp_ppanggolin/all/spots.tsv > '${spots}'
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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68 #end if
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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69 #if "output_summarize_spots" in $advanced_pangenome_optional_files:
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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70 && cat ./tmp_ppanggolin/all/summarize_spots.tsv > '${summarize_spots}'
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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71 #end if
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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72 #if "output_border_protein_genes" in $advanced_pangenome_optional_files:
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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73 && cat ./tmp_ppanggolin/all/border_protein_genes.fasta > '${border_protein_genes}'
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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74 #end if
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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75
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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76 #if "output_tile_plot" in $advanced_pangenome_optional_files:
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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77 && cat ./tmp_ppanggolin/all/tile_plot.html > '${tile_plot}'
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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78 #end if
5
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
parents: 0
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79 #if "output_Ushaped_plot" in $advanced_pangenome_optional_files:
0
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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80 && cat ./tmp_ppanggolin/all/Ushaped_plot.html > '${Ushaped_plot}'
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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81 #end if
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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83 #if "output_pangenomeGraph_json" in $advanced_pangenome_optional_files:
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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84 && cat ./tmp_ppanggolin/all/pangenomeGraph.json > '${pangenomeGraph_json}'
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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85 #end if
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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86 #if "output_pangenomeGraph_gexf" in $advanced_pangenome_optional_files:
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
87 && cat ./tmp_ppanggolin/all/pangenomeGraph.gexf > '${pangenomeGraph_gexf}'
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
88 #end if
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
89 #if "output_pangenomeGraph_light_gexf" in $advanced_pangenome_optional_files:
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
90 && cat ./tmp_ppanggolin/all/pangenomeGraph_light.gexf > '${pangenomeGraph_light_gexf}'
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
91 #end if
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
92
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
93 #if "output_matrix" in $advanced_pangenome_optional_files:
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
94 && cat ./tmp_ppanggolin/all/matrix.csv > '${matrix}'
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
95 #end if
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
96 #if "output_mean_persistent_duplication" in $advanced_pangenome_optional_files:
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
97 && cat ./tmp_ppanggolin/all/mean_persistent_duplication.tsv > '${mean_persistent_duplication}'
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
98 #end if
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
99 #if "output_gene_families" in $advanced_pangenome_optional_files:
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
100 && cat ./tmp_ppanggolin/all/gene_families.tsv > '${gene_families}'
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
101 #end if
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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102 #if "output_gene_presence_absence" in $advanced_pangenome_optional_files:
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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103 && cat ./tmp_ppanggolin/all/gene_presence_absence.Rtab > '${gene_presence_absence}'
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
104 #end if
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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105
5
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
parents: 0
diff changeset
106 && cat ./tmp_ppanggolin/all/ppanggolin_info.txt > '${ppanggolin_info}'
0
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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107 && cat ./tmp_ppanggolin/all/regions_of_genomic_plasticity.tsv > '${regions_of_genomic_plasticity}'
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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108 && cat ./tmp_ppanggolin/all/pangenome.h5 > '${pangenome_h5}'
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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109 && cat ./tmp_ppanggolin/all/genomes_statistics.tsv > '${genomes_statistics}'
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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parents:
diff changeset
110
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
111
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
112 ]]></command>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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113
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
114 <inputs>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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115
5
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
parents: 0
diff changeset
116 <expand macro="inputs_genomes" min="2" extratexthelp=" Processing of at least 15 genomes files is recommended." />
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
parents: 0
diff changeset
117
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
parents: 0
diff changeset
118 <expand macro="inputs_identity_coverage_do_defrag"/>
0
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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119
5
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
parents: 0
diff changeset
120 <expand macro="inputs_nb_of_partitions"/>
0
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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121
5
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
parents: 0
diff changeset
122 <expand macro="inputs_translation_table"/>
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
parents: 0
diff changeset
123
0
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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124 <param name="advanced_pangenome_optional_files" type="select" label="Add the following pangenome output files in the Galaxy history" multiple="true" optional="true" display="checkboxes" >
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
125 <!-- Basic files -->
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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126 <option value="output_gene_presence_absence" selected="true">Gene presence absence</option>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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127 <option value="output_gene_families" selected="true">Gene families</option>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
128 <option value="output_mean_persistent_duplication" selected="true">Mean persistent duplication</option>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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129 <option value="output_matrix" selected="true">Matrix</option>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
130 <!-- plot files -->
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
131 <option value="output_Ushaped_plot" selected="true">Ushaped plot</option>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
132 <option value="output_tile_plot" selected="true">Tile plot</option>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
133 <!-- graph files -->
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
134 <option value="output_pangenomeGraph_light_gexf" selected="true">PanGenome Graph Light (Gexf)</option>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
135 <option value="output_pangenomeGraph_gexf" selected="true">PanGenome Graph (Gexf)</option>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
136 <option value="output_pangenomeGraph_json" selected="true">PanGenome Graph (Json)</option>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
137 <!-- advanced files -->
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
138 <option value="output_summarize_spots" selected="true">Summarize spots</option>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
139 <option value="output_spots" selected="true">Spots</option>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
140 <option value="output_spot_borders" selected="true">Spot borders</option>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
141 <option value="output_border_protein_genes" selected="true">Border protein genes</option>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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142 <option value="output_modules_summary" selected="true">Modules summary</option>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
143 <option value="output_modules_in_genomes" selected="true">Modules in genomes</option>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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144 <option value="output_modules_spots" selected="true">Modules spots</option>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
145 <option value="output_modules_RGP_lists" selected="true">Modules RGP lists</option>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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146 <option value="output_functional_modules" selected="true">Functional modules</option>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
147 </param>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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parents:
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148
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
149 </inputs>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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parents:
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150
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
151 <outputs>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
152
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
153 <data name="functional_modules" format="tsv" label="PPanGGOLiN all on ${on_string}: Functional modules" >
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
154 <filter>advanced_pangenome_optional_files and "output_functional_modules" in advanced_pangenome_optional_files</filter>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
155 </data>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
156 <data name="modules_RGP_lists" format="tsv" label="PPanGGOLiN all on ${on_string}: Modules RGP lists" >
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
157 <filter>advanced_pangenome_optional_files and "output_modules_RGP_lists" in advanced_pangenome_optional_files</filter>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
158 </data>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
159 <data name="modules_spots" format="tsv" label="PPanGGOLiN all on ${on_string}: Modules spots" >
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
160 <filter>advanced_pangenome_optional_files and "output_modules_spots" in advanced_pangenome_optional_files</filter>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
161 </data>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
162 <data name="modules_in_genomes" format="tsv" label="PPanGGOLiN all on ${on_string}: Modules in genomes" >
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
163 <filter>advanced_pangenome_optional_files and "output_modules_in_genomes" in advanced_pangenome_optional_files</filter>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
164 </data>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
165 <data name="modules_summary" format="tsv" label="PPanGGOLiN all on ${on_string}: Modules summary" >
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
166 <filter>advanced_pangenome_optional_files and "output_modules_summary" in advanced_pangenome_optional_files</filter>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
167 </data>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
168 <data name="border_protein_genes" format="fasta" label="PPanGGOLiN all on ${on_string}: Border protein genes" >
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
169 <filter>advanced_pangenome_optional_files and "output_border_protein_genes" in advanced_pangenome_optional_files</filter>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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170 </data>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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171 <data name="spot_borders" format="tsv" label="PPanGGOLiN all on ${on_string}: Spot borders" >
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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172 <filter>advanced_pangenome_optional_files and "output_spot_borders" in advanced_pangenome_optional_files</filter>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
173 </data>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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174 <data name="spots" format="tsv" label="PPanGGOLiN all on ${on_string}: Spots" >
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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diff changeset
175 <filter>advanced_pangenome_optional_files and "output_spots" in advanced_pangenome_optional_files</filter>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
176 </data>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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177 <data name="summarize_spots" format="tsv" label="PPanGGOLiN all on ${on_string}: Summarized spots" >
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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178 <filter>advanced_pangenome_optional_files and "output_summarize_spots" in advanced_pangenome_optional_files</filter>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
179 </data>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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180
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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diff changeset
181 <data name="pangenomeGraph_json" format="json" label="PPanGGOLiN all on ${on_string}: PanGenome Graph (JSON)" >
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
182 <filter>advanced_pangenome_optional_files and "output_pangenomeGraph_json" in advanced_pangenome_optional_files</filter>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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183 </data>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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diff changeset
184 <data name="pangenomeGraph_gexf" format="xml" label="PPanGGOLiN all on ${on_string}: PanGenome Graph (GEXF)" >
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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diff changeset
185 <filter>advanced_pangenome_optional_files and "output_pangenomeGraph_gexf" in advanced_pangenome_optional_files</filter>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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186 </data>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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187 <data name="pangenomeGraph_light_gexf" format="xml" label="PPanGGOLiN all on ${on_string}: PanGenome Graph Light (GEXF)" >
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
188 <filter>advanced_pangenome_optional_files and "output_pangenomeGraph_light_gexf" in advanced_pangenome_optional_files</filter>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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diff changeset
189 </data>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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190
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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diff changeset
191
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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192 <data name="tile_plot" format="html" label="PPanGGOLiN all on ${on_string}: Tile plot" >
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
193 <filter>advanced_pangenome_optional_files and "output_tile_plot" in advanced_pangenome_optional_files</filter>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
194 </data>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
195 <data name="Ushaped_plot" format="html" label="PPanGGOLiN all on ${on_string}: U-shaped plot" >
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
196 <filter>advanced_pangenome_optional_files and "output_Ushaped_plot" in advanced_pangenome_optional_files</filter>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
197 </data>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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diff changeset
198
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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diff changeset
199 <data name="matrix" format="csv" label="PPanGGOLiN all on ${on_string}: Matrix" >
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
200 <filter>advanced_pangenome_optional_files and "output_matrix" in advanced_pangenome_optional_files</filter>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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diff changeset
201 </data>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
202 <data name="mean_persistent_duplication" format="tsv" label="PPanGGOLiN all on ${on_string}: Mean persistent duplication" >
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
203 <filter>advanced_pangenome_optional_files and "output_mean_persistent_duplication" in advanced_pangenome_optional_files</filter>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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diff changeset
204 </data>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
205 <data name="gene_families" format="tsv" label="PPanGGOLiN all on ${on_string}: Gene families" >
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
206 <filter>advanced_pangenome_optional_files and "output_gene_families" in advanced_pangenome_optional_files</filter>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
207 </data>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
208 <data name="gene_presence_absence" format="tsv" label="PPanGGOLiN all on ${on_string}: Gene presence/absence matrix" >
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
209 <filter>advanced_pangenome_optional_files and "output_gene_presence_absence" in advanced_pangenome_optional_files</filter>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
210 </data>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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diff changeset
211
5
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
parents: 0
diff changeset
212 <data name="ppanggolin_info" format="txt" label="PPanGGOLiN all on ${on_string}: PPanGGOLiN info" />
0
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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diff changeset
213 <data name="regions_of_genomic_plasticity" format="tsv" label="PPanGGOLiN all on ${on_string}: Regions of genomic plasticity" />
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
214 <data name="pangenome_h5" format="h5" label="PPanGGOLiN all on ${on_string}: PanGenome HDF5 file" />
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
215 <data name="genomes_statistics" format="tsv" label="PPanGGOLiN all on ${on_string}: Genome statistics" />
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
216
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
217 </outputs>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
218
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
219 <tests>
5
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
parents: 0
diff changeset
220 <test expect_num_outputs="22">
0
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
221 <param name="nb_of_partitions" value="3"/>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
222 <param name="coverage" value="0.8"/>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
223 <param name="identity" value="0.8"/>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
224 <param name="translation_table" value="1"/>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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diff changeset
225 <param name="genomes" value="fasta/AP028611_984801_1194801.fasta.gz,fasta/CP107038_1022972_1232972.fasta.gz,fasta/CP113115_1290693_1440693.fasta.gz,fasta/LN831051_1254175_1464175.fasta.gz,fasta/NC_012467_959209_1169209.fasta.gz" ftype="fasta"/>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
226 <output name="genomes_statistics" >
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
227 <assert_contents>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
228 <has_text text="#soft_core=" />
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
229 <has_text text="#duplication_margin=" />
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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diff changeset
230 </assert_contents>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
231 </output>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
232 <output name="regions_of_genomic_plasticity" >
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
233 <assert_contents>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
234 <has_text text="region" />
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
235 </assert_contents>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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diff changeset
236 </output>
5
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
parents: 0
diff changeset
237 <output name="ppanggolin_info" >
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
parents: 0
diff changeset
238 <assert_contents>
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
parents: 0
diff changeset
239 <has_text text="Content:" />
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
parents: 0
diff changeset
240 </assert_contents>
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
parents: 0
diff changeset
241 </output>
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
parents: 0
diff changeset
242 <output name="Ushaped_plot" >
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
parents: 0
diff changeset
243 <assert_contents>
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
parents: 0
diff changeset
244 <has_text text="html" />
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
parents: 0
diff changeset
245 </assert_contents>
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
parents: 0
diff changeset
246 </output>
0
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
247 </test>
5
d2b0073ef8d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
parents: 0
diff changeset
248 <test expect_num_outputs="22">
0
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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diff changeset
249 <param name="nb_of_partitions" value="3"/>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
250 <param name="coverage" value="0.8"/>
6fdee3720de7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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251 <param name="identity" value="0.8"/>
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252 <param name="translation_table" value="1"/>
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253 <param name="genomes" value="genbank/AP028611_984801_1194801.gb.gz,genbank/CP107038_1022972_1232972.gb.gz,genbank/CP113115_1290693_1440693.gb.gz,genbank/LN831051_1254175_1464175.gb.gz,genbank/NC_012467_959209_1169209.gb.gz" ftype="genbank"/>
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254 <output name="genomes_statistics" >
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255 <assert_contents>
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256 <has_text text="#soft_core=" />
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257 <has_text text="#duplication_margin=" />
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258 </assert_contents>
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259 </output>
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260 <output name="regions_of_genomic_plasticity" >
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261 <assert_contents>
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262 <has_text text="region" />
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263 </assert_contents>
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264 </output>
5
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265 <output name="ppanggolin_info" >
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266 <assert_contents>
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267 <has_text text="Content:" />
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268 </assert_contents>
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269 </output>
0
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270 </test>
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271 <test expect_failure="true">
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272 <param name="nb_of_partitions" value="3"/>
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273 <param name="coverage" value="0.8"/>
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274 <param name="identity" value="0.8"/>
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275 <param name="translation_table" value="1"/>
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276 <param name="genomes" value="genbank/AP028611_984801_1194801.gb.gz,genbank/CP107038_1022972_1232972.gb.gz,genbank/CP113115_1290693_1440693.gb.gz,fasta/AP028611_984801_1194801.fasta.gz,fasta/CP107038_1022972_1232972.fasta.gz,fasta/CP113115_1290693_1440693.fasta.gz" ftype="genbank"/>
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277 </test>
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278 </tests>
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279
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280 <help><![CDATA[
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281
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282 PPanGGOLiN_ (Gautreau et al. 2020) is a software suite used to create and manipulate prokaryotic pangenomes from a set of either assembled
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283 genomic DNA sequences or provided genome annotations. PPanGGOLiN builds pangenomes through a graphical model and a statistical method to partition gene
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284 families in persistent, shell and cloud genomes. It integrates both information on protein-coding genes and their genomic neighborhood to build a graph
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285 of gene families where each node is a gene family, and each edge is a relation of genetic contiguity.
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286
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287 The `ppanggolin all` command generates a partitioned pangenome graph with predicted RGP, spots and modules. Please see the documentation_ on how parameters can be tuned for this command.
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288
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289 .. _PPanGGOLiN: https://github.com/labgem/PPanGGOLiN
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290 .. _documentation: https://ppanggolin.readthedocs.io/en/latest/user/QuickUsage/quickAnalyses.html
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291
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292 ]]></help>
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293
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294 <expand macro="citation"/>
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295
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296 </tool>