Mercurial > repos > nml > mob_suite
comparison mob_recon.xml @ 6:9424de64bfa8 draft
"planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a"
author | nml |
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date | Wed, 11 Dec 2019 19:17:11 -0500 |
parents | 09424ec94e80 |
children | 822575bf359f |
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5:09424ec94e80 | 6:9424de64bfa8 |
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1 <tool id="mob_recon" name="MOB-Recon" version="1.4.9.1+galaxy0"> | 1 <tool id="mob_recon" name="MOB-Recon" version="2.0.5+galaxy0"> |
2 <description>Type contigs and extract plasmid sequences</description> | 2 <description>Type contigs and extract plasmid sequences</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="1.4.9.1">mob_suite</requirement> | 4 <requirement type="package" version="2.0.5">mob_suite</requirement> |
5 </requirements> | 5 </requirements> |
6 <version_command>mob_recon --version</version_command> | |
6 <command detect_errors="exit_code"> | 7 <command detect_errors="exit_code"> |
7 <![CDATA[ | 8 <![CDATA[ |
8 #import re | 9 #import re |
9 #import os.path | 10 #import os.path |
10 | 11 |
11 #set $named_input = re.sub(r'(\s|\(|\)|:|!)', '_', str($input.element_identifier)+".fasta") | 12 #set $named_input = re.sub(r'(\s|\(|\)|:|!)', '_', str($input.element_identifier)+'.fasta') |
12 ln -s "$input" $named_input && | 13 ln -s '$input' '$named_input' && |
13 | 14 |
14 mob_recon --num_threads \${GALAXY_SLOTS:-4} --infile "${named_input}" | 15 mob_recon --num_threads \${GALAXY_SLOTS:-4} --infile '${named_input}' |
15 #if str($adv_param.unicycler_contigs) == "True": | 16 #if str($adv_param.unicycler_contigs) == "True": |
16 --unicycler_contigs | 17 --unicycler_contigs |
17 #end if | 18 #end if |
18 #if str($adv_param.run_circlator) == "True": | 19 #if str($adv_param.run_circlator) == "True": |
19 --run_circlator | 20 --run_circlator |
20 #end if | 21 #end if |
21 #if str($adv_param.min_length_condition.min_length_param) == "True": | 22 #if str($adv_param.min_length_condition.min_length_param) == "True": |
22 --min_length ${adv_param.min_length_condition.min_length_value} | 23 --min_length '${adv_param.min_length_condition.min_length_value}' |
23 #end if | 24 #end if |
24 --run_typer --min_rep_evalue '${adv_param.min_rep_evalue}' | 25 --run_typer --min_rep_evalue '${adv_param.min_rep_evalue}' |
25 --min_rep_evalue '${adv_param.min_rep_evalue}' | 26 --min_rep_evalue '${adv_param.min_rep_evalue}' |
26 --min_mob_evalue '${adv_param.min_mob_evalue}' | 27 --min_mob_evalue '${adv_param.min_mob_evalue}' |
27 --min_con_evalue '${adv_param.min_con_evalue}' | 28 --min_con_evalue '${adv_param.min_con_evalue}' |
28 --min_rep_ident '${adv_param.min_rep_ident}' | 29 --min_rep_ident '${adv_param.min_rep_ident}' |
29 --min_mob_ident '${adv_param.min_mob_ident}' | 30 --min_mob_ident '${adv_param.min_mob_ident}' |
30 --min_con_ident '${adv_param.min_con_ident}' | 31 --min_con_ident '${adv_param.min_con_ident}' |
31 --min_rpp_ident '${adv_param.min_rpp_ident}' | 32 --min_rpp_ident '${adv_param.min_rpp_ident}' |
32 --outdir '.' && | 33 --outdir 'outdir' && |
33 mkdir ./sequences && (cp plasmid*.fasta chromosome.fasta ./sequences 2> /dev/null || true) | 34 mkdir ./outdir/plasmids && (mv outdir/plasmid*.fasta ./outdir/plasmids 2> /dev/null || true) |
34 ]]> | 35 ]]> |
35 </command> | 36 </command> |
36 <inputs> | 37 <inputs> |
37 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/> | 38 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/> |
38 <section name="adv_param" title="Advanced parameters" expanded="False"> | 39 <section name="adv_param" title="Advanced parameters" expanded="False"> |
63 <param name="min_con_ident" label="Minimum sequence identity for contigs" type="integer" min="0" max="100" value="80"/> | 64 <param name="min_con_ident" label="Minimum sequence identity for contigs" type="integer" min="0" max="100" value="80"/> |
64 <param name="min_rpp_ident" label="Minimum sequence identity for repetitive elements" type="integer" min="0" max="100" value="80"/> | 65 <param name="min_rpp_ident" label="Minimum sequence identity for repetitive elements" type="integer" min="0" max="100" value="80"/> |
65 </section> | 66 </section> |
66 </inputs> | 67 </inputs> |
67 <outputs> | 68 <outputs> |
68 <data name="outfile1" format="tabular" from_work_dir="contig_report.txt" label="${tool.name} on ${on_string}: Overall contig MOB-recon report"/> | 69 <data name="contig_report" format="tabular" from_work_dir="outdir/contig_report.txt" label="${tool.name} on ${input.element_identifier}: Overall contig MOB-recon report"/> |
69 <data name="outfile2" format="tabular" from_work_dir="repetitive_blast_report.txt" label="${tool.name} on ${on_string}: Repetitive elements BLAST report"/> | 70 <data name="repetitive_blast_report" format="tabular" from_work_dir="outdir/repetitive_blast_report.txt" label="${tool.name} on ${input.element_identifier}: Repetitive elements BLAST report"/> |
70 <data name="outfile3" format="tabular" from_work_dir="mobtyper_aggregate_report.txt" label="${tool.name} on ${on_string}: Aggregate MOB-typer report for all contigs"/> | 71 <data name="mobtyper_aggregate_report" format="tabular" from_work_dir="outdir/mobtyper_aggregate_report.txt" label="${tool.name} on ${input.element_identifier}: Aggregate MOB-typer report for all contigs"/> |
71 <collection name="seqhits" type="list" label="${tool.name} on ${on_string}: Extracted sequences (plasmids,chromosome(s))"> | 72 <data name="chromosome" format="fasta" from_work_dir="outdir/chromosome.fasta" label="${tool.name} on ${input.element_identifier}: Chromosomal sequences"/> |
72 <discover_datasets pattern="__name_and_ext__" directory="sequences" /> | 73 <collection name="plasmids" type="list" label="${tool.name} on ${input.element_identifier}: Plasmids"> |
74 <discover_datasets pattern="__name_and_ext__" directory="outdir/plasmids" /> | |
73 </collection> | 75 </collection> |
74 </outputs> | 76 </outputs> |
75 <tests> | 77 <tests> |
76 <test> | 78 <test> |
77 <param name="input" value="plasmid_476.fasta" ftype="fasta"/> | 79 <param name="input" value="plasmid_476.fasta" ftype="fasta"/> |
78 <section name="adv_param"> | 80 <section name="adv_param"> |
79 <param name="unicycler_contigs" value="True"/> | 81 <param name="unicycler_contigs" value="True"/> |
80 <param name="run_circlator" value="True"/> | 82 <param name="run_circlator" value="True"/> |
81 </section> | 83 </section> |
82 <output name="outfile1"> | 84 <output name="contig_report"> |
83 <assert_contents> | 85 <assert_contents> |
84 <has_text text="NC_019097"/> | 86 <has_text text="NC_019097"/> |
85 </assert_contents> | 87 </assert_contents> |
86 </output> | 88 </output> |
87 </test> | 89 </test> |
88 </tests> | 90 </tests> |
89 <help> | 91 <help> |
90 | 92 |
91 **Syntax** | 93 **Syntax** |