Mercurial > repos > iuc > mirmachine

annotate mirmachine.xml @ 2:061b1cea3439 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine commit 4079726893896abcd8a0457563cd3c591f14638f
author iuc
date Fri, 21 Nov 2025 21:32:40 +0000
parents 0ad5db33c99e
children
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0
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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1 <tool id="mirmachine" name="MirMachine" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="22.05">
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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2 <description>A tool to detect miRNA homologs in genome sequences</description>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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3 <macros>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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4 <import>macros.xml</import>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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5 </macros>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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6 <expand macro="requirements"/>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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7 <command detect_errors="exit_code"><![CDATA[
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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8 ln -sf '$genome' ./genome.fasta &&
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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9 MirMachine.py
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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10 -n '$input_node'
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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11 -s '$input_species'
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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12 -m '$model'
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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13 $a
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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14 $o
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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15 --genome ./genome.fasta
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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16 -c \${GALAXY_SLOTS:-8}
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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17 &&
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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18 mv results/predictions/filtered_gff/*.PRE.gff species_filtered.PRE.gff &&
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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19 mv results/predictions/gff/*.PRE.gff species.PRE.gff &&
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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20 mv results/predictions/fasta/*.PRE.fasta species.PRE.fasta
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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21 ]]></command>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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22 <inputs>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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23 <param type="data" name="genome" format="fasta" label="Genome fasta file"/>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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24 <param name="input_node" type="select" label="Node name" help="e.g. Caenorhabditis">
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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25 <expand macro="node_options"/>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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26 </param>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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27 <param type="text" name="input_species" label="Scientific species name" help="Separated by underscore e.g. Caenorhabditis_elegans">
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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28 <sanitizer invalid_char="">
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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29 <valid initial="string.letters">
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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30 <add value="_"/>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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31 </valid>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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32 </sanitizer>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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33 <validator type="regex">[a-zA-Z_]+</validator>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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34 </param>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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35 <param type="select" name="model" label="Model" help="Model type: deutero, proto, combined">
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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36 <expand macro="model_options"/>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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37 </param>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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38 <param type="boolean" optional="true" truevalue="-a" falsevalue="" argument="-a" label="Add all nodes" help="Move on the tree both ways"/>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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39 <param type="boolean" optional="true" truevalue="-o" falsevalue="" argument="-o" label="Single node only" help="Run only on the given node for miRNA families"/>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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40 </inputs>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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41 <outputs>
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42 <data name="gff_file" format="gff" from_work_dir="species.PRE.gff" label="${tool.name} on ${on_string}: GFF file"/>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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43 <data name="filtered_gff_file" format="gff" from_work_dir="species_filtered.PRE.gff" label="${tool.name} on ${on_string}: filtered GFF file"/>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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44 <data name="fasta_file" format="fasta" from_work_dir="species.PRE.fasta" label="${tool.name} on ${on_string}: fasta sequence of annotation miRNAs"/>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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45 </outputs>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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46 <tests>
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47 <test expect_num_outputs="3">
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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48 <param name="genome" value="ref.fa"/>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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49 <param name="input_node" value="Caenorhabditis"/>
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50 <param name="input_species" value="Caenorhabditis_elegans"/>
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51 <output name="gff_file">
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52 <assert_contents>
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53 <has_n_lines n="24" delta="0"/>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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54 </assert_contents>
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55 </output>
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56 <output name="filtered_gff_file">
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57 <assert_contents>
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58 <has_n_lines n="15" delta="0"/>
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59 </assert_contents>
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60 </output>
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61 <output name="fasta_file">
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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62 <assert_contents>
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63 <has_n_lines n="24" delta="0"/>
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64 </assert_contents>
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65 </output>
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66 </test>
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67 <test expect_num_outputs="3">
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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68 <param name="genome" value="ref.fa"/>
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69 <param name="input_node" value="Caenorhabditis"/>
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70 <param name="input_species" value="Caenorhabditis_elegans"/>
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71 <param name="a" value="true"/>
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72 <output name="gff_file">
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73 <assert_contents>
2
061b1cea3439 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine commit 4079726893896abcd8a0457563cd3c591f14638f
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74 <has_n_lines n="24" delta="0"/>
0
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75 </assert_contents>
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76 </output>
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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77 <output name="filtered_gff_file">
6001cd3141a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit ff0a9b6e75c9e73b3011fa9f60a3fd4ff291c017
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78 <assert_contents>
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79 <has_n_lines n="15" delta="0"/>
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80 </assert_contents>
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81 </output>
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82 <output name="fasta_file">
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83 <assert_contents>
2
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84 <has_n_lines n="24" delta="0"/>
0
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85 </assert_contents>
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86 </output>
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87 </test>
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88 <test expect_num_outputs="3">
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89 <param name="genome" value="ref.fa"/>
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90 <param name="input_node" value="Caenorhabditis"/>
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91 <param name="input_species" value="Caenorhabditis_elegans"/>
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92 <param name="o" value="true"/>
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93 <output name="gff_file">
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94 <assert_contents>
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95 <has_n_lines n="20" delta="0"/>
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96 </assert_contents>
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97 </output>
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98 <output name="filtered_gff_file">
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99 <assert_contents>
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100 <has_n_lines n="12" delta="0"/>
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101 </assert_contents>
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102 </output>
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103 <output name="fasta_file">
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104 <assert_contents>
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105 <has_n_lines n="16" delta="0"/>
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106 </assert_contents>
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107 </output>
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108 </test>
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109 </tests>
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110 <help><![CDATA[
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111
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112 Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements. MirMachine facilitates automated genome annotation pipelines and deeper studies into the evolution of genome regulation, even in extinct organisms.
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113
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114 The MirMachine main executable will generate GFF annotations (filtered and unfiltered) and some other files
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115
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116 `gff` All predicted miRNA families
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117 `filtered_gff` High confidence miRNA family predictions after bitscore filtering. (This file is what you need in most cases)
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118 `fasta` Both high and low confidence predictions in FASTA format
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119
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120 miRNA prediction score is given in the header of the output filtered gff file
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121 ]]></help>
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122 <expand macro="citations"/>
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123 <expand macro="creator"/>
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124 </tool>