Mercurial > repos > iuc > ppanggolin_all

annotate ppanggolin_all.xml @ 0:5366cac57e83 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
author iuc
date Wed, 22 Jan 2025 10:34:21 +0000
parents
children b0601fae2212
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5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
1 <tool id="ppanggolin_all" name="PPanGGOLiN all" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
5366cac57e83 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>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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3 <macros>
5366cac57e83 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>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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5 </macros>
5366cac57e83 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"/>
5366cac57e83 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"/>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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8
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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9 <command detect_errors="exit_code"><![CDATA[
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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11 mkdir -p "./tmp_ppanggolin/all" &&
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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12 mkdir -p "./tmp_ppanggolin/organism_list" &&
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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13 mkdir -p "./tmp_ppanggolin/ln_input_genomes" &&
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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15 touch "./tmp_ppanggolin/organism_list/organism.list" &&
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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17 #set extension_input_files = ""
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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18 #for $counter_input_files, $file in enumerate($genomes):
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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19 #if $counter_input_files == 0:
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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20 #set extension_input_files = $file.ext
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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21 #else:
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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22 #if $file.ext != $extension_input_files:
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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23 #raise Exception("All the genome files must be of the same datatype, either all genbank files or all fasta files.")
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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24 #end if
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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25 #end if
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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26
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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27 #set base_name = str($file.element_identifier).replace(" ", "_")
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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28 echo -e '${base_name}\t${file}' >> "./tmp_ppanggolin/organism_list/organism.list" &&
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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29
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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30 #end for
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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31
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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32 ppanggolin all
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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33
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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34 #if $extension_input_files == "fasta":
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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35 --fasta
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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36 #elif $extension_input_files == "genbank":
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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37 --anno
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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38 #end if
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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39 "./tmp_ppanggolin/organism_list/organism.list"
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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40
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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41 -o ./tmp_ppanggolin/all
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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42 --force
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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43 --cpu "\${GALAXY_SLOTS:-4}"
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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44
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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45 --coverage $coverage
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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46 --identity $identity
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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47 --translation_table $translation_table
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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48
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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49
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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50 #if str($nb_of_partitions) != "":
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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51 --nb_of_partitions $nb_of_partitions
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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52 #end if
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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53
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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54 $do_defrag
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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55
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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56
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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57 #if "output_functional_modules" in $advanced_pangenome_optional_files:
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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58 && cat ./tmp_ppanggolin/all/functional_modules.tsv > '${functional_modules}'
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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59 #end if
5366cac57e83 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_RGP_lists" in $advanced_pangenome_optional_files:
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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61 && cat ./tmp_ppanggolin/all/modules_RGP_lists.tsv > '${modules_RGP_lists}'
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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62 #end if
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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63 #if "output_modules_spots" in $advanced_pangenome_optional_files:
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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64 && cat ./tmp_ppanggolin/all/modules_spots.tsv > '${modules_spots}'
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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65 #end if
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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66 #if "output_modules_in_genomes" in $advanced_pangenome_optional_files:
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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67 && cat ./tmp_ppanggolin/all/modules_in_genomes.tsv > '${modules_in_genomes}'
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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68 #end if
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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69 #if "output_modules_summary" in $advanced_pangenome_optional_files:
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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70 && cat ./tmp_ppanggolin/all/modules_summary.tsv > '${modules_summary}'
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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71 #end if
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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72 #if "output_spot_borders" in $advanced_pangenome_optional_files:
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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73 && cat ./tmp_ppanggolin/all/spot_borders.tsv > '${spot_borders}'
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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74 #end if
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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75 #if "output_spots" in $advanced_pangenome_optional_files:
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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76 && cat ./tmp_ppanggolin/all/spots.tsv > '${spots}'
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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77 #end if
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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78 #if "output_summarize_spots" in $advanced_pangenome_optional_files:
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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79 && cat ./tmp_ppanggolin/all/summarize_spots.tsv > '${summarize_spots}'
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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80 #end if
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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81 #if "output_border_protein_genes" in $advanced_pangenome_optional_files:
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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82 && cat ./tmp_ppanggolin/all/border_protein_genes.fasta > '${border_protein_genes}'
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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83 #end if
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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84
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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85 #if "output_tile_plot" in $advanced_pangenome_optional_files:
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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86 && cat ./tmp_ppanggolin/all/tile_plot.html > '${tile_plot}'
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
87 #end if
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
88 #if "output_ushaped_plot" in $advanced_pangenome_optional_files:
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
89 && cat ./tmp_ppanggolin/all/Ushaped_plot.html > '${Ushaped_plot}'
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
90 #end if
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
91
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
92 #if "output_pangenomeGraph_json" in $advanced_pangenome_optional_files:
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
93 && cat ./tmp_ppanggolin/all/pangenomeGraph.json > '${pangenomeGraph_json}'
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
94 #end if
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
95 #if "output_pangenomeGraph_gexf" in $advanced_pangenome_optional_files:
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
96 && cat ./tmp_ppanggolin/all/pangenomeGraph.gexf > '${pangenomeGraph_gexf}'
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
97 #end if
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
98 #if "output_pangenomeGraph_light_gexf" in $advanced_pangenome_optional_files:
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
99 && cat ./tmp_ppanggolin/all/pangenomeGraph_light.gexf > '${pangenomeGraph_light_gexf}'
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
100 #end if
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
101
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
102 #if "output_matrix" in $advanced_pangenome_optional_files:
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
103 && cat ./tmp_ppanggolin/all/matrix.csv > '${matrix}'
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
104 #end if
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
105 #if "output_mean_persistent_duplication" in $advanced_pangenome_optional_files:
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
106 && cat ./tmp_ppanggolin/all/mean_persistent_duplication.tsv > '${mean_persistent_duplication}'
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
107 #end if
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
108 #if "output_gene_families" in $advanced_pangenome_optional_files:
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
109 && cat ./tmp_ppanggolin/all/gene_families.tsv > '${gene_families}'
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
110 #end if
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
111 #if "output_gene_presence_absence" in $advanced_pangenome_optional_files:
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
112 && cat ./tmp_ppanggolin/all/gene_presence_absence.Rtab > '${gene_presence_absence}'
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
113 #end if
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
114
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
115
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
116 && cat ./tmp_ppanggolin/all/regions_of_genomic_plasticity.tsv > '${regions_of_genomic_plasticity}'
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
117 && cat ./tmp_ppanggolin/all/pangenome.h5 > '${pangenome_h5}'
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
118 && cat ./tmp_ppanggolin/all/genomes_statistics.tsv > '${genomes_statistics}'
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
119
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
120
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
121 ]]></command>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
122
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
123 <inputs>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
124
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
125 <param name="genomes" type="data" multiple="true" min="2" label="Select genome files" format="fasta,genbank" help="All the genome files must be of similar format, either all genbank files or all fasta files. Processing of at least 15 genomes files is recommended, a minimum of 2 genomes files is mandatory. Space is not allowed in filename.">
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
126 </param>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
127
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
128 <param argument="--identity" type="float" value="0.8" min="0" max="1" label="Minimum alignment identity"/>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
129 <param argument="--coverage" type="float" value="0.8" min="0" max="1" label="Minimum alignment coverage"/>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
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diff changeset
130
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
131 <param argument="--nb_of_partitions" type="integer" max="20" label="Number of classes used to partition the pangenome" optional="true" help="If empty value (default), it will be automatically determined. Otherwise, the value needs to be between 2 and 20 and it is advised to set a value of 3. See the link for the documentation in the help section for more details.">
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
132 <validator type="expression" message="Value needs to be empty or an integer between 2 and 20">value == "" or int(value) >= 2</validator>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
133 </param>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
134
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
135 <param argument="--translation_table" type="select" label="Translation table">
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
136 <option value="1">1 - Standard Code</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
137 <option value="2">2 - Vertebrate Mitochondrial</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
138 <option value="3">3 - Yeast Mitochondrial</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
139 <option value="4">4 - Mold, Protozoan, and Coelenterate Mitochondrial</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
140 <option value="5">5 - Invertebrate Mitochondrial</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
141 <option value="6">6 - Ciliate Nuclear</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
142 <option value="9">9 - Echinoderm Mitochondrial</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
143 <option value="10">10 - Euplotid Nuclear</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
144 <option value="11">11 - Bacterial and Plant Plastid</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
145 <option value="12">12 - Alternative Yeast Nuclear</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
146 <option value="13">13 - Ascidian Mitochondrial</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
147 <option value="14">14 - Flatworm Mitochondrial</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
148 <option value="15">15 - Blepharisma Nuclear</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
149 <option value="16">16 - Chlorophycean Mitochondrial</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
150 <option value="21">21 - Trematode Mitochondrial</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
151 <option value="22">22 - Scenedesmus obliquus Mitochondrial</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
152 <option value="23">23 - Thraustochytrium Mitochondrial</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
153 <option value="24">24 - Pterobranchia Mitochondrial</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
154 <option value="25">25 - Candidate Division SR1 and Gracilibacteria</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
155 <option value="26">26 - Pachysolen tannophilus Nuclear</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
156 <option value="27">27 - Karyorelict Nuclear</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
157 <option value="28">28 - Condylostoma Nuclear</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
158 <option value="29">29 - Mesodinium Nuclear</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
159 <option value="30">30 - Peritrich Nuclear</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
160 <option value="31">31 - Blastocrithidia Nuclear</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
161 <option value="32">32 - Balanophoraceae Plastid</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
162 <option value="33">33 - Cephalodiscidae Mitochondrial</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
163 </param>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
164 <param name="do_defrag" type="boolean" checked="true" label="Gene family defragmentation" truevalue="" falsevalue="--no_defrag"/>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
165
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
166
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
167 <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" >
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
168 <!-- Basic files -->
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
169 <option value="output_gene_presence_absence" selected="true">Gene presence absence</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
170 <option value="output_gene_families" selected="true">Gene families</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
171 <option value="output_mean_persistent_duplication" selected="true">Mean persistent duplication</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
172 <option value="output_matrix" selected="true">Matrix</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
173 <!-- plot files -->
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
174 <option value="output_Ushaped_plot" selected="true">Ushaped plot</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
175 <option value="output_tile_plot" selected="true">Tile plot</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
176 <!-- graph files -->
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
177 <option value="output_pangenomeGraph_light_gexf" selected="true">PanGenome Graph Light (Gexf)</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
178 <option value="output_pangenomeGraph_gexf" selected="true">PanGenome Graph (Gexf)</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
179 <option value="output_pangenomeGraph_json" selected="true">PanGenome Graph (Json)</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
180 <!-- advanced files -->
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
181 <option value="output_summarize_spots" selected="true">Summarize spots</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
182 <option value="output_spots" selected="true">Spots</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
183 <option value="output_spot_borders" selected="true">Spot borders</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
184 <option value="output_border_protein_genes" selected="true">Border protein genes</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
185 <option value="output_modules_summary" selected="true">Modules summary</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
186 <option value="output_modules_in_genomes" selected="true">Modules in genomes</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
187 <option value="output_modules_spots" selected="true">Modules spots</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
188 <option value="output_modules_RGP_lists" selected="true">Modules RGP lists</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
189 <option value="output_functional_modules" selected="true">Functional modules</option>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
190 </param>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
191
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
192 </inputs>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
193
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
194 <outputs>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
195
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
196 <data name="functional_modules" format="tsv" label="PPanGGOLiN all on ${on_string}: Functional modules" >
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
197 <filter>advanced_pangenome_optional_files and "output_functional_modules" in advanced_pangenome_optional_files</filter>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
198 </data>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
199 <data name="modules_RGP_lists" format="tsv" label="PPanGGOLiN all on ${on_string}: Modules RGP lists" >
5366cac57e83 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_modules_RGP_lists" in advanced_pangenome_optional_files</filter>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
201 </data>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
202 <data name="modules_spots" format="tsv" label="PPanGGOLiN all on ${on_string}: Modules spots" >
5366cac57e83 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_modules_spots" in advanced_pangenome_optional_files</filter>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
204 </data>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
205 <data name="modules_in_genomes" format="tsv" label="PPanGGOLiN all on ${on_string}: Modules in genomes" >
5366cac57e83 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_modules_in_genomes" in advanced_pangenome_optional_files</filter>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
207 </data>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
208 <data name="modules_summary" format="tsv" label="PPanGGOLiN all on ${on_string}: Modules summary" >
5366cac57e83 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_modules_summary" in advanced_pangenome_optional_files</filter>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
210 </data>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
211 <data name="border_protein_genes" format="fasta" label="PPanGGOLiN all on ${on_string}: Border protein genes" >
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
212 <filter>advanced_pangenome_optional_files and "output_border_protein_genes" in advanced_pangenome_optional_files</filter>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
213 </data>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
214 <data name="spot_borders" format="tsv" label="PPanGGOLiN all on ${on_string}: Spot borders" >
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
215 <filter>advanced_pangenome_optional_files and "output_spot_borders" in advanced_pangenome_optional_files</filter>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
216 </data>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
217 <data name="spots" format="tsv" label="PPanGGOLiN all on ${on_string}: Spots" >
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
218 <filter>advanced_pangenome_optional_files and "output_spots" in advanced_pangenome_optional_files</filter>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
219 </data>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
220 <data name="summarize_spots" format="tsv" label="PPanGGOLiN all on ${on_string}: Summarized spots" >
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
221 <filter>advanced_pangenome_optional_files and "output_summarize_spots" in advanced_pangenome_optional_files</filter>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
222 </data>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
223
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
224 <data name="pangenomeGraph_json" format="json" label="PPanGGOLiN all on ${on_string}: PanGenome Graph (JSON)" >
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
225 <filter>advanced_pangenome_optional_files and "output_pangenomeGraph_json" in advanced_pangenome_optional_files</filter>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
226 </data>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
227 <data name="pangenomeGraph_gexf" format="xml" label="PPanGGOLiN all on ${on_string}: PanGenome Graph (GEXF)" >
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
228 <filter>advanced_pangenome_optional_files and "output_pangenomeGraph_gexf" in advanced_pangenome_optional_files</filter>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
229 </data>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
230 <data name="pangenomeGraph_light_gexf" format="xml" label="PPanGGOLiN all on ${on_string}: PanGenome Graph Light (GEXF)" >
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
231 <filter>advanced_pangenome_optional_files and "output_pangenomeGraph_light_gexf" in advanced_pangenome_optional_files</filter>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
232 </data>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
233
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
234
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
235 <data name="tile_plot" format="html" label="PPanGGOLiN all on ${on_string}: Tile plot" >
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
236 <filter>advanced_pangenome_optional_files and "output_tile_plot" in advanced_pangenome_optional_files</filter>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
237 </data>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
238 <data name="Ushaped_plot" format="html" label="PPanGGOLiN all on ${on_string}: U-shaped plot" >
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
239 <filter>advanced_pangenome_optional_files and "output_Ushaped_plot" in advanced_pangenome_optional_files</filter>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
240 </data>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
241
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
242 <data name="matrix" format="csv" label="PPanGGOLiN all on ${on_string}: Matrix" >
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
243 <filter>advanced_pangenome_optional_files and "output_matrix" in advanced_pangenome_optional_files</filter>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
244 </data>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
245 <data name="mean_persistent_duplication" format="tsv" label="PPanGGOLiN all on ${on_string}: Mean persistent duplication" >
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
246 <filter>advanced_pangenome_optional_files and "output_mean_persistent_duplication" in advanced_pangenome_optional_files</filter>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
247 </data>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
diff changeset
248 <data name="gene_families" format="tsv" label="PPanGGOLiN all on ${on_string}: Gene families" >
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
iuc
parents:
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249 <filter>advanced_pangenome_optional_files and "output_gene_families" in advanced_pangenome_optional_files</filter>
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250 </data>
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251 <data name="gene_presence_absence" format="tsv" label="PPanGGOLiN all on ${on_string}: Gene presence/absence matrix" >
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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252 <filter>advanced_pangenome_optional_files and "output_gene_presence_absence" in advanced_pangenome_optional_files</filter>
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253 </data>
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254
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255
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256 <data name="regions_of_genomic_plasticity" format="tsv" label="PPanGGOLiN all on ${on_string}: Regions of genomic plasticity" />
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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257 <data name="pangenome_h5" format="h5" label="PPanGGOLiN all on ${on_string}: PanGenome HDF5 file" />
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258 <data name="genomes_statistics" format="tsv" label="PPanGGOLiN all on ${on_string}: Genome statistics" />
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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259
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260 </outputs>
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261
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262 <tests>
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263 <test expect_num_outputs="21">
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264 <param name="nb_of_partitions" value="3"/>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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265 <param name="coverage" value="0.8"/>
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266 <param name="identity" value="0.8"/>
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267 <param name="translation_table" value="1"/>
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268 <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"/>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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269 <output name="genomes_statistics" >
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270 <assert_contents>
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271 <has_text text="#soft_core=" />
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272 <has_text text="#duplication_margin=" />
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273 </assert_contents>
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274 </output>
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275 <output name="regions_of_genomic_plasticity" >
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276 <assert_contents>
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277 <has_text text="region" />
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278 </assert_contents>
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279 </output>
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280 </test>
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281 <test expect_num_outputs="21">
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282 <param name="nb_of_partitions" value="3"/>
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283 <param name="coverage" value="0.8"/>
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284 <param name="identity" value="0.8"/>
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285 <param name="translation_table" value="1"/>
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286 <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"/>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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287 <output name="genomes_statistics" >
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288 <assert_contents>
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289 <has_text text="#soft_core=" />
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290 <has_text text="#duplication_margin=" />
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291 </assert_contents>
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292 </output>
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293 <output name="regions_of_genomic_plasticity" >
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294 <assert_contents>
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295 <has_text text="region" />
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296 </assert_contents>
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297 </output>
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298 </test>
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299 <test expect_failure="true">
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300 <param name="nb_of_partitions" value="3"/>
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301 <param name="coverage" value="0.8"/>
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302 <param name="identity" value="0.8"/>
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303 <param name="translation_table" value="1"/>
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304 <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"/>
5366cac57e83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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305 </test>
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306 </tests>
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307
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308 <help><![CDATA[
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309
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310 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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311 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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312 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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313 of gene families where each node is a gene family, and each edge is a relation of genetic contiguity.
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314
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315 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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316
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317 .. _PPanGGOLiN: https://github.com/labgem/PPanGGOLiN
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318 .. _documentation: https://ppanggolin.readthedocs.io/en/latest/user/QuickUsage/quickAnalyses.html
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319
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320 ]]></help>
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321
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322 <expand macro="citation"/>
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323
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324 </tool>