Mercurial > repos > iuc > ppanggolin_msa

comparison macros.xml @ 4:2da61c5e8aac draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
author iuc
date Tue, 16 Sep 2025 13:11:09 +0000
parents f5611e0df98c
children 579d7907524d
comparison
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3:f5611e0df98c 4:2da61c5e8aac
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">2.2.3</token> 2 <token name="@TOOL_VERSION@">2.2.5</token>
3 <token name="@VERSION_SUFFIX@">0</token> 3 <token name="@VERSION_SUFFIX@">0</token>
4 <xml name="citation"> 4 <xml name="citation">
5 <citations> 5 <citations>
6 <citation type="doi">10.1371/journal.pcbi.1007732</citation> 6 <citation type="doi">10.1371/journal.pcbi.1007732</citation>
7 <citation type="doi">10.1093/bioinformatics/btaa792</citation> 7 <citation type="doi">10.1093/bioinformatics/btaa792</citation>
15 <xml name="xrefs"> 15 <xml name="xrefs">
16 <xrefs> 16 <xrefs>
17 <xref type="bio.tools">ppanggolin</xref> 17 <xref type="bio.tools">ppanggolin</xref>
18 </xrefs> 18 </xrefs>
19 </xml> 19 </xml>
20 <token name="@ORGANISM_LIST@"><![CDATA[
21 touch ./tmp_ppanggolin/organism_list/organism.list &&
22 #set extension_input_files = ""
23 #for $counter_input_files, $file in enumerate($genomes):
24 #if $counter_input_files == 0:
25 #set extension_input_files = $file.ext
26 #else:
27 #if $file.ext != $extension_input_files:
28 #raise Exception("All the genome files must be of the same datatype, either all genbank files or all fasta files.")
29 #end if
30 #end if
31
32 #set base_name = re.sub('[^\w\-_\.]', '_', str($file.element_identifier))
33 echo -e '${base_name}\t${file}' >> ./tmp_ppanggolin/organism_list/organism.list &&
34 #end for
35 ]]></token>
36 <xml name="inputs_identity_coverage_do_defrag">
37 <param argument="--identity" type="float" value="0.8" min="0" max="1" label="Minimum alignment identity"/>
38 <param argument="--coverage" type="float" value="0.8" min="0" max="1" label="Minimum alignment coverage"/>
39 <param name="do_defrag" type="boolean" checked="true" label="Gene family defragmentation" truevalue="" falsevalue="--no_defrag" help="Realign gene families to link fragments with their non-fragmented gene family. (--no_defrag)"/>
40 </xml>
41 <xml name="inputs_nb_of_partitions">
42 <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.">
43 <validator type="expression" message="Value needs to be empty or an integer between 2 and 20">value == "" or int(value) >= 2</validator>
44 </param>
45 </xml>
46 <xml name="inputs_translation_table">
47 <param argument="--translation_table" type="select" label="Translation table">
48 <option value="1" selected="true">1 - Standard Code</option>
49 <option value="2">2 - Vertebrate Mitochondrial</option>
50 <option value="3">3 - Yeast Mitochondrial</option>
51 <option value="4">4 - Mold, Protozoan, and Coelenterate Mitochondrial</option>
52 <option value="5">5 - Invertebrate Mitochondrial</option>
53 <option value="6">6 - Ciliate Nuclear</option>
54 <option value="9">9 - Echinoderm Mitochondrial</option>
55 <option value="10">10 - Euplotid Nuclear</option>
56 <option value="11">11 - Bacterial and Plant Plastid</option>
57 <option value="12">12 - Alternative Yeast Nuclear</option>
58 <option value="13">13 - Ascidian Mitochondrial</option>
59 <option value="14">14 - Flatworm Mitochondrial</option>
60 <option value="15">15 - Blepharisma Nuclear</option>
61 <option value="16">16 - Chlorophycean Mitochondrial</option>
62 <option value="21">21 - Trematode Mitochondrial</option>
63 <option value="22">22 - Scenedesmus obliquus Mitochondrial</option>
64 <option value="23">23 - Thraustochytrium Mitochondrial</option>
65 <option value="24">24 - Pterobranchia Mitochondrial</option>
66 <option value="25">25 - Candidate Division SR1 and Gracilibacteria</option>
67 <option value="26">26 - Pachysolen tannophilus Nuclear</option>
68 <option value="27">27 - Karyorelict Nuclear</option>
69 <option value="28">28 - Condylostoma Nuclear</option>
70 <option value="29">29 - Mesodinium Nuclear</option>
71 <option value="30">30 - Peritrich Nuclear</option>
72 <option value="31">31 - Blastocrithidia Nuclear</option>
73 <option value="32">32 - Balanophoraceae Plastid</option>
74 <option value="33">33 - Cephalodiscidae Mitochondrial</option>
75 </param>
76 </xml>
77 <xml name="inputs_pangenome">
78 <param argument="--pangenome" name="pangenome_h5" type="data" format="h5" label="Input pangenome h5 file"/>
79 </xml>
80 <xml name="inputs_soft_core">
81 <param argument="--soft_core" type="float" value="0.95" min="0" max="1" label="Soft core threshold used when generating general statistics on the projected genome" help="Default=0.95 .This threshold does not influence PPanGGOLiN's partitioning. The value determines the minimum fraction of genomes that must possess a gene family for it to be considered part of the soft core."/>
82 </xml>
83 <xml name="inputs_genomes" token_min="1" token_extratexthelp="">
84 <param name="genomes" type="data" multiple="true" min="@MIN@" label="Genome files" format="fasta,genbank" help="All the genome files must be of the same format, either all genbank files or all fasta files. A minimum of @MIN@ genome file(s) is mandatory.@EXTRATEXTHELP@ Special characters and spaces are replaced by underscore."/>
85 </xml>
20 </macros> 86 </macros>