Mercurial > repos > iuc > ppanggolin_msa

comparison ppanggolin_msa.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 6e3a117b43d5
children
comparison
equal deleted inserted replaced
3:f5611e0df98c 4:2da61c5e8aac
6 <expand macro="xrefs"/> 6 <expand macro="xrefs"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 8
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 10
11 mkdir -p "./tmp_ppanggolin/msa" && 11 mkdir -p ./tmp_ppanggolin/msa &&
12 mkdir -p "./tmp_ppanggolin/tmpdir_msa" && 12 mkdir -p ./tmp_ppanggolin/tmpdir_msa &&
13 13
14 ppanggolin msa 14 ppanggolin msa
15 --pangenome '$pangenome_h5' 15 --pangenome '$pangenome_h5'
16 --output ./tmp_ppanggolin/msa 16 --output ./tmp_ppanggolin/msa
17 --tmpdir ./tmp_ppanggolin/tmpdir_msa 17 --tmpdir ./tmp_ppanggolin/tmpdir_msa
44 44
45 ]]></command> 45 ]]></command>
46 46
47 <inputs> 47 <inputs>
48 48
49 <param argument="--pangenome" name="pangenome_h5" type="data" format="h5" label="Input pangenome h5 file"/> 49 <expand macro="inputs_pangenome"/>
50 50
51 <conditional name="input_choose_partition"> 51 <conditional name="input_choose_partition">
52 <param argument="--partition" name="choice_partition" type="select" label="Partition"> 52 <param argument="--partition" name="choice_partition" type="select" label="Partition">
53 <option value="core" selected="true">Core</option> 53 <option value="core" selected="true">Core</option>
54 <option value="persistent">Persistent</option> 54 <option value="persistent">Persistent</option>
61 <when value="core"/> 61 <when value="core"/>
62 <when value="persistent"/> 62 <when value="persistent"/>
63 <when value="shell"/> 63 <when value="shell"/>
64 <when value="cloud"/> 64 <when value="cloud"/>
65 <when value="softcore"> 65 <when value="softcore">
66 <param argument="--soft_core" name="choice_soft_core" type="float" value="0.95" min="0" max="1" label="Soft core threshold to use if 'softcore' partition is chosen"/> 66 <expand macro="inputs_soft_core"/>
67 </when> 67 </when>
68 <when value="accessory"/> 68 <when value="accessory"/>
69 <when value="all"/> 69 <when value="all"/>
70 </conditional> 70 </conditional>
71 71
75 </param> 75 </param>
76 76
77 <param argument="--phylo" name="do_phylo" type="boolean" checked="true" label="Writes a whole genome msa file for additional phylogenetic analysis (recommended)" truevalue="--phylo" falsevalue=""/> 77 <param argument="--phylo" name="do_phylo" type="boolean" checked="true" label="Writes a whole genome msa file for additional phylogenetic analysis (recommended)" truevalue="--phylo" falsevalue=""/>
78 78
79 <param argument="--single_copy" name="do_single_copy" type="boolean" checked="false" label="Report gene families that are considered 'single copy'" truevalue="--single_copy" falsevalue=""/> 79 <param argument="--single_copy" name="do_single_copy" type="boolean" checked="false" label="Report gene families that are considered 'single copy'" truevalue="--single_copy" falsevalue=""/>
80 80
81 <param argument="--translation_table" type="select" label="Translation table"> 81 <expand macro="inputs_translation_table"/>
82 <option value="1" selected="true">1 - Standard Code</option>
83 <option value="2">2 - Vertebrate Mitochondrial</option>
84 <option value="3">3 - Yeast Mitochondrial</option>
85 <option value="4">4 - Mold, Protozoan, and Coelenterate Mitochondrial</option>
86 <option value="5">5 - Invertebrate Mitochondrial</option>
87 <option value="6">6 - Ciliate Nuclear</option>
88 <option value="9">9 - Echinoderm Mitochondrial</option>
89 <option value="10">10 - Euplotid Nuclear</option>
90 <option value="11">11 - Bacterial and Plant Plastid</option>
91 <option value="12">12 - Alternative Yeast Nuclear</option>
92 <option value="13">13 - Ascidian Mitochondrial</option>
93 <option value="14">14 - Flatworm Mitochondrial</option>
94 <option value="15">15 - Blepharisma Nuclear</option>
95 <option value="16">16 - Chlorophycean Mitochondrial</option>
96 <option value="21">21 - Trematode Mitochondrial</option>
97 <option value="22">22 - Scenedesmus obliquus Mitochondrial</option>
98 <option value="23">23 - Thraustochytrium Mitochondrial</option>
99 <option value="24">24 - Pterobranchia Mitochondrial</option>
100 <option value="25">25 - Candidate Division SR1 and Gracilibacteria</option>
101 <option value="26">26 - Pachysolen tannophilus Nuclear</option>
102 <option value="27">27 - Karyorelict Nuclear</option>
103 <option value="28">28 - Condylostoma Nuclear</option>
104 <option value="29">29 - Mesodinium Nuclear</option>
105 <option value="30">30 - Peritrich Nuclear</option>
106 <option value="31">31 - Blastocrithidia Nuclear</option>
107 <option value="32">32 - Balanophoraceae Plastid</option>
108 <option value="33">33 - Cephalodiscidae Mitochondrial</option>
109 </param>
110 82
111 </inputs> 83 </inputs>
112 84
113 <outputs> 85 <outputs>
114 <data name="archive_msa_partition_source" format="tar.gz" label="PPanGGOLiN msa on ${on_string}: archive msa ${choice_partition} ${choice_source}" /> 86 <data name="archive_msa_partition_source" format="tar.gz" label="PPanGGOLiN msa on ${on_string}: archive msa ${choice_partition} ${choice_source}" />
115 <data name="partition_genome_alignment" format="aln" label="PPanGGOLiN msa on ${on_string}: ${choice_partition} genome alignment" > 87 <data name="partition_genome_alignment" format="maf" label="PPanGGOLiN msa on ${on_string}: ${choice_partition} genome alignment" >
116 <filter>do_phylo is True</filter> 88 <filter>do_phylo is True</filter>
117 </data> 89 </data>
118 </outputs> 90 </outputs>
119 91
120 <tests> 92 <tests>