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comparison mob_recon.xml @ 6:9424de64bfa8 draft

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"planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a"
author nml
date Wed, 11 Dec 2019 19:17:11 -0500
parents 09424ec94e80
children 822575bf359f
comparison
equal deleted inserted replaced
5:09424ec94e80 6:9424de64bfa8
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**