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comparison mob_typer.xml @ 2:2c7f721a4905 draft

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planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
author nml
date Fri, 17 Aug 2018 11:12:08 -0400
parents 2c419df5cdaa
children 09424ec94e80
comparison
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1:2c419df5cdaa 2:2c7f721a4905
1 <tool id="mob_typer" name="MOB-Typer" version="1.4.5"> 1 <tool id="mob_typer" name="MOB-Typer" version="1.4.8">
2 <description>Get the plasmid type and mobility given its sequence</description> 2 <description>Get the plasmid type and mobility given its sequence</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.4.5">mob_suite</requirement> 4 <requirement type="package" version="1.4.8">mob_suite</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"> 6 <command detect_errors="exit_code">
7 <![CDATA[ 7 <![CDATA[
8 ln -s "${input}" "${input.name}"; 8 ln -s "${input}" "${input.name}";
9 mob_typer --num_threads \${GALAXY_SLOTS:-4} --infile "${input.name}" 9 mob_typer --num_threads \${GALAXY_SLOTS:-4} --infile "${input.name}"
10 #if str($adv_param.min_rep_evalue_condition.min_rep_evalue_param) == "True": 10 --min_rep_evalue '$adv_param.min_rep_evalue_value'
11 --min_rep_evalue $adv_param.min_rep_evalue_condition.min_rep_evalue_value 11 --min_mob_evalue '$adv_param.min_mob_evalue_value'
12 #end if 12 --min_con_evalue '$adv_param.min_con_evalue_value'
13 #if str($adv_param.min_mob_evalue_condition.min_mob_evalue_param) == "True": 13 --min_ori_evalue '$adv_param.min_ori_evalue_value'
14 --min_mob_evalue $adv_param.min_mob_evalue_condition.min_mob_evalue_value 14 --min_mpf_evalue '$adv_param.min_mpf_evalue'
15 #end if 15 --min_rep_ident '$adv_param.min_rep_ident'
16 #if str($adv_param.min_con_evalue_condition.min_con_evalue_param) == "True": 16 --min_mob_ident '$adv_param.min_mob_ident'
17 --min_con_evalue $adv_param.min_con_evalue_condition.min_con_evalue_value 17 --min_ori_ident '$adv_param.min_ori_ident'
18 #end if 18 --min_mpf_ident '$adv_param.min_mpf_ident'
19 #if str($adv_param.min_ori_evalue_condition.min_ori_evalue_param) == "True":
20 --min_ori_evalue $adv_param.min_ori_evalue_condition.min_ori_evalue_value
21 #end if
22 --outdir '.'; 19 --outdir '.';
23 ]]> 20 ]]>
24 </command> 21 </command>
25 <inputs> 22 <inputs>
26 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/> 23 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
27 <section name="adv_param" title="Advanced parameters" expanded="False"> 24 <section name="adv_param" title="Advanced parameters" expanded="False">
28 <conditional name="min_rep_evalue_condition"> 25 <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn"/>
29 <param name="min_rep_evalue_param" label="Minimum evalue threshold for replicon blastn" type="select" value="False"> 26 <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn"/>
30 <option value="False">No</option> 27 <param name="min_con_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for contig blastn"/>
31 <option value="True">Yes</option> 28 <param name="min_ori_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for oriT elements blastn"/>
32 </param> 29 <param name="min_mpf_evalue" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for mpf elements blastn"/>
33 <when value="True"> 30 <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer" min="0" max="100" value="80"/>
34 <param name="min_rep_evalue_value" type="float" value="0.00001" min="0" max="1" label="e-value (default: 0.00001)"/> 31 <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer" min="0" max="100" value="80"/>
35 </when> 32 <param name="min_ori_ident" label="Minimum sequence identity for oriT elements" type="integer" min="0" max="100" value="90"/>
36 <when value="False"/> 33 <param name="min_mpf_ident" label="Minimum sequence identity for mpf elements" type="integer" min="0" max="100" value="80"/>
37 </conditional>
38 <conditional name="min_mob_evalue_condition">
39 <param name="min_mob_evalue_param" label="Minimum evalue threshold for relaxase tblastn" type="select" value="False">
40 <option value="False">No</option>
41 <option value="True">Yes</option>
42 </param>
43 <when value="True">
44 <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="e-value (default: 0.00001)"/>
45 </when>
46 <when value="False"/>
47 </conditional>
48 <conditional name="min_con_evalue_condition">
49 <param name="min_con_evalue_param" label="Minimum evalue threshold for contig blastn" type="select" value="False">
50 <option value="False">No</option>
51 <option value="True">Yes</option>
52 </param>
53 <when value="True">
54 <param name="min_con_evalue_value" type="float" value="0.00001" min="0" max="1" label="e-value (default: 0.00001)"/>
55 </when>
56 <when value="False"/>
57 </conditional>
58 <conditional name="min_ori_evalue_condition">
59 <param name="min_ori_evalue_param" label="Minimum evalue threshold for oriT elements blastn" type="select" value="False">
60 <option value="False">No</option>
61 <option value="True">Yes</option>
62 </param>
63 <when value="True">
64 <param name="min_ori_evalue_value" type="float" value="0.00001" min="0" max="1" label="e-value (default: 0.00001)"/>
65 </when>
66 <when value="False"/>
67 </conditional>
68 </section> 34 </section>
69 </inputs> 35 </inputs>
70 <outputs> 36 <outputs>
71 <data name="outfile1" label="${tool.name}: Plasmid report on ${input.name}" format="tabular"> 37 <data name="outfile1" label="${tool.name}: Plasmid report on ${input.name}" format="tabular">
72 <discover_datasets pattern=".+_report\.txt" visible="true" format="tabular" assign_primary_output="true"/> 38 <discover_datasets pattern=".+_report\.txt" visible="true" format="tabular" assign_primary_output="true"/>