Mercurial > repos > iuc > ppanggolin_msa

annotate ppanggolin_msa.xml @ 0:6e3a117b43d5 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 10:34:12 +0000
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6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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1 <tool id="ppanggolin_msa" name="PPanGGOLiN MSA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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2 <description>computes MSA of pangenome's gene families</description>
6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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3 <macros>
6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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4 <import>macros.xml</import>
6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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5 </macros>
6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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6 <expand macro="xrefs"/>
6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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7 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
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11 mkdir -p "./tmp_ppanggolin/msa" &&
6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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12 mkdir -p "./tmp_ppanggolin/tmpdir_msa" &&
6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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14 ppanggolin msa
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15 --pangenome '$pangenome_h5'
6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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16 --output ./tmp_ppanggolin/msa
6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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17 --tmpdir ./tmp_ppanggolin/tmpdir_msa
6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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18 --force
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19 --cpu "\${GALAXY_SLOTS:-4}"
6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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20 --disable_prog_bar
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21 --partition $choice_partition
6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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22 #if str($input_choose_partition.choice_partition) == "softcore"
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23 --soft_core $choice_soft_core
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24 #end if
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25
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26 --source $choice_source
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27 $do_phylo
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28 $do_single_copy
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29 --translation_table $translation_table
6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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31 #set base_msa_source = "msa_" + str($input_choose_partition.choice_partition) + "_" + str($choice_source)
6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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32 #set base_genome_alignment = str($input_choose_partition.choice_partition) + "_genome_alignment.aln"
6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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33 #if str($input_choose_partition.choice_partition) == "softcore"
6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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34 #set base_genome_alignment = str($input_choose_partition.choice_partition) + "_" + str($choice_soft_core) + "_genome_alignment.aln"
6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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35 #end if
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37 && tar -cvf ./tmp_ppanggolin/msa/archive_${base_msa_source}.tar ./tmp_ppanggolin/msa/${base_msa_source}
6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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38 && gzip ./tmp_ppanggolin/msa/archive_${base_msa_source}.tar
6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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39 && mv ./tmp_ppanggolin/msa/archive_${base_msa_source}.tar.gz '${archive_msa_partition_source}'
6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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41 #if str($do_phylo) == "--phylo"
6e3a117b43d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
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42 && mv ./tmp_ppanggolin/msa/${base_genome_alignment} '${partition_genome_alignment}'
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43 #end if
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44
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45 ]]></command>
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46
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47 <inputs>
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48
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49 <param argument="--pangenome" name="pangenome_h5" type="data" format="h5" label="Input pangenome h5 file"/>
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50
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51 <conditional name="input_choose_partition">
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52 <param argument="--partition" name="choice_partition" type="select" label="Partition">
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53 <option value="core" selected="true">Core</option>
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54 <option value="persistent">Persistent</option>
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55 <option value="shell">Shell</option>
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56 <option value="cloud">Cloud</option>
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57 <option value="softcore">Softcore</option>
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58 <option value="accessory">Accessory</option>
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59 <option value="all">All</option>
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60 </param>
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61 <when value="core"/>
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62 <when value="persistent"/>
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63 <when value="shell"/>
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64 <when value="cloud"/>
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65 <when value="softcore">
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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"/>
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67 </when>
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68 <when value="accessory"/>
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69 <when value="all"/>
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70 </conditional>
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71
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72 <param argument="--source" name="choice_source" type="select" label="Source">
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73 <option value="protein" selected="true">Protein</option>
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74 <option value="dna">DNA</option>
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75 </param>
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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=""/>
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78
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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=""/>
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80
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81 <param argument="--translation_table" type="select" label="Translation table">
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82 <option value="1" selected="true">1 - Standard Code</option>
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83 <option value="2">2 - Vertebrate Mitochondrial</option>
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84 <option value="3">3 - Yeast Mitochondrial</option>
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85 <option value="4">4 - Mold, Protozoan, and Coelenterate Mitochondrial</option>
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86 <option value="5">5 - Invertebrate Mitochondrial</option>
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87 <option value="6">6 - Ciliate Nuclear</option>
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88 <option value="9">9 - Echinoderm Mitochondrial</option>
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89 <option value="10">10 - Euplotid Nuclear</option>
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90 <option value="11">11 - Bacterial and Plant Plastid</option>
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91 <option value="12">12 - Alternative Yeast Nuclear</option>
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92 <option value="13">13 - Ascidian Mitochondrial</option>
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93 <option value="14">14 - Flatworm Mitochondrial</option>
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94 <option value="15">15 - Blepharisma Nuclear</option>
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95 <option value="16">16 - Chlorophycean Mitochondrial</option>
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96 <option value="21">21 - Trematode Mitochondrial</option>
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97 <option value="22">22 - Scenedesmus obliquus Mitochondrial</option>
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98 <option value="23">23 - Thraustochytrium Mitochondrial</option>
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99 <option value="24">24 - Pterobranchia Mitochondrial</option>
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100 <option value="25">25 - Candidate Division SR1 and Gracilibacteria</option>
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101 <option value="26">26 - Pachysolen tannophilus Nuclear</option>
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102 <option value="27">27 - Karyorelict Nuclear</option>
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103 <option value="28">28 - Condylostoma Nuclear</option>
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104 <option value="29">29 - Mesodinium Nuclear</option>
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105 <option value="30">30 - Peritrich Nuclear</option>
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106 <option value="31">31 - Blastocrithidia Nuclear</option>
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107 <option value="32">32 - Balanophoraceae Plastid</option>
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108 <option value="33">33 - Cephalodiscidae Mitochondrial</option>
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109 </param>
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110
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111 </inputs>
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112
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113 <outputs>
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114 <data name="archive_msa_partition_source" format="tar.gz" label="PPanGGOLiN msa on ${on_string}: archive msa ${choice_partition} ${choice_source}" />
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115 <data name="partition_genome_alignment" format="aln" label="PPanGGOLiN msa on ${on_string}: ${choice_partition} genome alignment" >
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116 <filter>do_phylo is True</filter>
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117 </data>
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118 </outputs>
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119
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120 <tests>
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121 <test expect_num_outputs="2">
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122 <param name="choice_partition" value="core"/>
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123 <param name="choice_source" value="protein"/>
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124 <param name="do_phylo" value="true"/>
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125 <param name="do_single_copy" value="false"/>
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126 <param name="pangenome_h5" value="h5/test_data.h5" ftype="h5"/>
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127 <param name="translation_table" value="1"/>
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128
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129 <output name="partition_genome_alignment" >
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130 <assert_contents>
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131 <has_text text=">" />
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132 </assert_contents>
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133 </output>
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134
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135 </test>
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136 </tests>
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137
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138 <help><![CDATA[
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139
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140 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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141 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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142 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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143 of gene families where each node is a gene family, and each edge is a relation of genetic contiguity.
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144
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145 The `ppanggolin msa` command computes multiple sequence alignment of any partition of the pangenome. The command uses mafft with default options to perform the alignment. Please see the documentation_ on how parameters can be tuned for this command.
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146
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147 .. _PPanGGOLiN: https://github.com/labgem/PPanGGOLiN
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148 .. _documentation: https://ppanggolin.readthedocs.io/en/latest/user/MSA.html
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149
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150 ]]></help>
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151
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152 <expand macro="citation"/>
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153
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154 </tool>
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155