Mercurial > repos > iuc > plasmidfinder

annotate plasmidfinder.xml @ 3:7075b7a5441b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder commit 464661a59ed12a642d365f485a222764b55048a5
author iuc
date Thu, 02 Mar 2023 14:58:17 +0000
parents eccc7495c3d9
children
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2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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1 <tool id="plasmidfinder" name="PlasmidFinder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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2 <description>
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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3 Plasmid identification in bacteria.
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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4 </description>
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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5 <macros>
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6 <import>macro.xml</import>
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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7 </macros>
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8 <expand macro='xrefs'/>
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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9 <expand macro="requirements" />
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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10 <command detect_errors="aggressive"><![CDATA[
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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11 mkdir output_dir &&
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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12 mkdir temp_dir &&
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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13 plasmidfinder.py
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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14 -i '$input.input_file'
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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15 -p '$input.database_name.fields.path'
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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16 -l '$options.min_cov'
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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17 -t '$options.threshold'
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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18 #if $input.input_file.ext == 'fasta' or $input.input_file.ext == 'fasta.gz'
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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19 -mp blastn
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20 #elif $input.input_file.ext == 'fastqsanger' or $input.input_file.ext == 'fastqsanger.gz'
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21 -mp kma
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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22 #end if
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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23 -x
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24 -o output_dir
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25 -tmp temp_dir
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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26 #*======================================
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27 LOG file
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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28 ======================================*#
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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29 | tee '$log_file'
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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30 ]]>
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31 </command>
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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32 <inputs>
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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33 <section name="input" title="Input parameters" expanded="true">
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34 <param name="input_file" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Choose a fasta or fastq file" help="File to be analyzed"/>
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35 <param name="database_name" type="select" label="PlasmidFinder database">
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7075b7a5441b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder commit 464661a59ed12a642d365f485a222764b55048a5
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36 <options from_data_table="plasmidfinder_database">
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37 <validator message="No PlasmidFinder database is available" type="no_options"/>
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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38 </options>
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39 </param>
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40 </section>
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41 <section name="options" title="Options">
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42 <param name="min_cov" type="float" min="0" max="1" value="0.6" label="Minimal coverage" help=" Fraction of matching sequence on the total target sequence(default: 0.6)"/>
eccc7495c3d9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 69aab27f0210af0f0986d63575f9bfdb3f9d1f6a
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43 <param name="threshold" type="float" min="0" max="1" value="0.95" label="Minimal identity" help=" Fraction of shared nucleotide on the match (default: 0.95)"/>
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44 </section>
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45 <section name="output_files" title="Output file selection">
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46 <param name="output_selection" type="select" display="checkboxes" multiple="true" label="Output files selection">
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47 <option value="data_json">JSON file result</option>
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48 <option value="hit_fasta" selected="true">Matching sequences in the genome for plasmid</option>
eccc7495c3d9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 69aab27f0210af0f0986d63575f9bfdb3f9d1f6a
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49 <option value="plasmid_fasta" selected="true">Plasmid sequences discovered in the genome</option>
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50 <option value="result_tsv" selected="true">Plasmid match list</option>
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51 <option value="result_txt" selected="true">Plasmid match list in raw format</option>
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52 <option value="logfile">Log file</option>
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53 </param>
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54 </section>
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55 </inputs>
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56 <outputs>
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57 <data name="json_file" format="json" from_work_dir="output_dir/data.json" label="${tool.name} on ${on_string}: data.json">
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58 <filter> "data_json" in output_files['output_selection'] </filter>
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59 </data>
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60 <data name="hit_file" format="fasta" from_work_dir="output_dir/Hit_in_genome_seq.fsa" label="${tool.name} on ${on_string}: hit_in_genome.fasta">
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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61 <filter> "hit_fasta" in output_files['output_selection'] </filter>
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62 </data>
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63 <data name="plasmid_file" format="fasta" from_work_dir="output_dir/Plasmid_seqs.fsa" label="${tool.name} on ${on_string}: plasmid.fasta">
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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64 <filter> "plasmid_fasta" in output_files['output_selection'] </filter>
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65 </data>
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66 <data name="result_file" format="tabular" from_work_dir="output_dir/results_tab.tsv" label="${tool.name} on ${on_string}: results.tsv">
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67 <filter> "result_tsv" in output_files['output_selection'] </filter>
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68 </data>
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69 <data name="raw_file" format="txt" from_work_dir="output_dir/results.txt" label="${tool.name} on ${on_string}: raw_result.txt">
2b6e795b22a9 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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70 <filter> "result_txt" in output_files['output_selection'] </filter>
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71 </data>
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72 <data name="log_file" format="txt" from_work_dir="output_dir" label="${tool.name} on ${on_string}: log file">
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73 <filter> "logfile" in output_files['output_selection'] </filter>
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74 </data>
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75 </outputs>
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76 <tests>
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77 <!--test_1 with default value and all output files for contigs -->
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78 <test expect_num_outputs="6">
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79 <section name="input">
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80 <param name="input_file" value="contigs.fasta"/>
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81 <param name="input_type" value="genome"/>
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82 <param name="database_name" value="plasmidfinder_9002e7282dd0_2022-12-20"/>
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83 </section>
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84 <section name="output_files">
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85 <param name="output_selection" value="data_json,hit_fasta,plasmid_fasta,result_tsv,result_txt,logfile"/>
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86 </section>
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87 <output name="json_file" value="test_1/data_test1.json" ftype="json" compare="sim_size"/>
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88 <output name="hit_file" value="test_1/Hit_in_genome_seq_test1.fsa" ftype="fasta"/>
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89 <output name="plasmid_file" value="test_1/Plasmid_seqs_test1.fsa" ftype="fasta"/>
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90 <output name="result_file" value="test_1/results_tab_test1.tsv"/>
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91 <output name="raw_file" value="test_1/results_test1.txt" lines_diff="2"/>
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92 <output name="log_file" value="test_1/logfile_test1.log" lines_diff="7"/>
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93 </test>
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94 <!--test_2 with default value and for fastq file -->
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95 <test expect_num_outputs="4">
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96 <section name="input">
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97 <param name="input_file" value="data.fastq.gz"/>
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98 <param name="input_type" value="raw"/>
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99 <param name="database_name" value="plasmidfinder_9002e7282dd0_2022-12-20"/>
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100 </section>
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101 <section name="output_files">
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102 <param name="output_selection" value="data_json,result_tsv,result_txt,logfile"/>
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103 </section>
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104 <output name="json_file" value="test_2/data_test2.json" ftype="json" compare="sim_size"/>
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105 <output name="result_file" value="test_2/results_tab_test2.tsv"/>
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106 <output name="raw_file" value="test_2/results_test2.txt" lines_diff="2"/>
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107 <output name="log_file" value="test_2/logfile_test2.log" lines_diff="7"/>
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108 </test>
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109 <!--test_3 with default value and for fastq file -->
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110 <test expect_num_outputs="3">
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111 <section name="input">
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112 <param name="input_file" value="contigs.fasta"/>
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113 <param name="input_type" value="genome"/>
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114 <param name="database_name" value="plasmidfinder_9002e7282dd0_2022-12-20"/>
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115 </section>
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116 <section name="options">
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117 <param name="min_cov" value="0.2" />
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118 <param name="threshold" value="0.6"/>
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119 </section>
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120 <section name="output_files">
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121 <param name="output_selection" value="hit_fasta,plasmid_fasta,result_tsv"/>
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122 </section>
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123 <output name="hit_file" value="test_3/Hit_in_genome_seq_test3.fsa" ftype="fasta"/>
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124 <output name="plasmid_file" value="test_3/Plasmid_seqs_test3.fsa" ftype="fasta"/>
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125 <output name="result_file" value="test_3/results_tab_test3.tsv"/>
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126 </test>
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127 </tests>
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128 <help><![CDATA[
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129 **What it does**
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130 PlasmidFinder characterize plasmid sequences into whole genome sequencing.
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131 It is based on the [plasmidfinder database](https://bitbucket.org/genomicepidemiology/plasmidfinder_db/) with hundreds sequences.
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132 **Input**
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133 PlasmidFinder takes raw data (with a k-mer analysisi) as reads or genome assembly (blastn analysis) to search plasmids.
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134 **Output**
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135 Some output files are availables
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136 - A fasta file with all available sequences detected in the genome
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137 - A fasta file with all plasmid sequences from the database
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138 - A summary of the analysis in tabular format
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139 - A Raw result file in text format
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140 - A JSON file could be use for other boinformatic analysis
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141 - A log file with analysis parameters
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142
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143 ]]></help>
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144 <expand macro="citations"/>
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145 </tool>