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comparison mob_hostrange.xml @ 44:e2b09f608636 draft

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"planemo upload for repository https://github.com/phac-nml/mob-suite commit 1904171337e41b9f714838b6f7068aefb089d11d-dirty"
author dfornika
date Thu, 14 Nov 2019 01:33:40 +0000
parents 21ccebc96bd9
children 4c5276f87370
comparison
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43:21ccebc96bd9 44:e2b09f608636
1 <tool id="mob_hostrange" name="MOB-Hostrange" version="2.0.2+galaxy0"> 1 <tool id="mob_hostrange" name="MOB-Hostrange" version="2.0.2+galaxy0">
2 <description> 2 <description>
3 Provides information on plasmid reproductive host range and transfer rate using both sequencing 3 Provides information on plasmid reproductive host range and transfer rate using both sequencing
4 and experimental data from public databases (NCBI) and publications (PubMED). 4 and experimental data from public databases (NCBI) and publications (PubMED).
5 </description> 5 </description>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="2.0.2">mob_suite</requirement> 7 <requirement type="package" version="2.0.2">mob_suite</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"> 9 <command detect_errors="exit_code">
10 <![CDATA[ 10 <![CDATA[
11 mob_hostrange 11 mob_hostrange
12 ${exact_match} 12 ${exact_match}
13 ${loose_match} 13 ${loose_match}
14 ${host_range_detailed} 14 ${host_range_detailed}
15 #if str(${replicon_name}) != "": 15 #if str(${replicon_name}) != '':
16 --replicon_name '${replicon_name}' 16 --replicon_name '${replicon_name}'
17 #end if 17 #end if
18 #if str(${relaxase_name}) != "": 18 #if str(${relaxase_name}) != '':
19 --relaxase_name '${relaxase_name}' 19 --relaxase_name '${relaxase_name}'
20 #end if 20 #end if
21 #if str(${relaxase_accession}) != "": 21 #if str(${relaxase_accession}) != '':
22 --relaxase_accession '${relaxase_accession}' 22 --relaxase_accession '${relaxase_accession}'
23 #end if 23 #end if
24 #if str(${cluster_id}) != "": 24 #if str(${cluster_id}) != '':
25 --cluster_id '${cluster_id}' 25 --cluster_id '${cluster_id}'
26 #end if 26 #end if
27 --inputseq "${inputseq}" 27 --inputseq '${inputseq}'
28 --outdir '.' 28 --outdir '.'
29 ]]> 29 ]]>
30 </command> 30 </command>
31 <inputs> 31 <inputs>
32 <param name="inputseq" type="data" format="fasta" label="Input" help="plasmid FASTA file"/> 32 <param name="inputseq" type="data" format="fasta" label="Input" help="plasmid FASTA file"/>
33 <param name="exact_match" type="boolean" truevalue="--exact_match" falsevalue="" checked="false"/> 33 <param name="exact_match" type="boolean" truevalue="--exact_match" falsevalue="" checked="false"/>
34 <param name="loose_match" type="boolean" truevalue="--loose_match" falsevalue="" checked="false"/> 34 <param name="loose_match" type="boolean" truevalue="--loose_match" falsevalue="" checked="false"/>
35 <param name="host_range_detailed" type="boolean" truevalue="--host_range_detailed" falsevalue="" checked="false"/> 35 <param name="host_range_detailed" type="boolean" truevalue="--host_range_detailed" falsevalue="" checked="false"/>
36 <param name="replicon_name" type="text" /> 36 <param name="replicon_name" type="text" />
37 <param name="relaxase_name" type="text" /> 37 <param name="relaxase_name" type="text" />
38 <param name="relaxase_accession" type="text" /> 38 <param name="relaxase_accession" type="text" />
39 <param name="cluster_id" type="text" /> 39 <param name="cluster_id" type="text" />
40 </inputs> 40 </inputs>
41 <outputs> 41 <outputs>
42 <data name="hostrange_phylostats" label="${tool.name}: Phylostats report on ${input.name}" format="tabular"> 42 <data name="hostrange_phylostats" label="${tool.name}: Phylostats report on ${input.name}" format="tabular">
43 <discover_datasets pattern=".+hostrange_phylostats\.txt" visible="true" format="tabular" /> 43 <discover_datasets pattern=".+hostrange_phylostats\.txt" visible="true" format="tabular" />
44 </data> 44 </data>
45 <data name="hostrange_report" label="${tool.name}: Hostrange report on ${input.name}" format="tabular"> 45 <data name="hostrange_report" label="${tool.name}: Hostrange report on ${input.name}" format="tabular">
46 <discover_datasets pattern=".+hostrange_report\.txt" visible="true" format="tabular" /> 46 <discover_datasets pattern=".+hostrange_report\.txt" visible="true" format="tabular" />
47 </data> 47 </data>
48 </outputs> 48 </outputs>
49 <tests> 49 <tests>
50 <test> 50 <test>
51 <param name="inputseq" value="plasmid_476.fasta" ftype="fasta"/> 51 <param name="inputseq" value="plasmid_476.fasta" ftype="fasta"/>
52 <assert_stderr> 52 <assert_stderr>
53 <has_text text="RefSeq Plasmid database found no hits"/> 53 <has_text text="RefSeq Plasmid database found no hits"/>
54 </assert_stderr> 54 </assert_stderr>
55 </test> 55 </test>
56 </tests> 56 </tests>
57 <help> 57 <help>
58 58
59 **Syntax** 59 **Syntax**
60 60
61 This tool provides information on plasmid reproductive host range and transfer rate using both sequencing and experimental data from public databases (NCBI) and publications (PubMED). The predicted host range represents a range of putative hosts where a given plasmid can stably replicate and be maintained by the host. The host range module makes no source attribution predictions of a plasmid. 61 This tool provides information on plasmid reproductive host range and transfer rate using both sequencing and experimental data from public databases (NCBI) and publications (PubMED). The predicted host range represents a range of putative hosts where a given plasmid can stably replicate and be maintained by the host. The host range module makes no source attribution predictions of a plasmid.
62 62
63 For more information please visit https://github.com/phac-nml/mob-suite/. 63 For more information please visit https://github.com/phac-nml/mob-suite/.
64 64
65 ----- 65 -----
66 66
67 **Input:** 67 **Input:**
68 68
69 A FASTA file with a single or multiple contigs (e.g. plasmid.fasta): 69 A FASTA file with a single or multiple contigs (e.g. plasmid.fasta):
70 70
71 71
72 **Output:** 72 **Output:**
73 73
74 Tab-delimited reports listing predicted hostrange information. Refer to https://github.com/phac-nml/mob-suite#mob-hostrange-report-file-format for the description of each column. 74 Tab-delimited reports listing predicted hostrange information. Refer to https://github.com/phac-nml/mob-suite#mob-hostrange-report-file-format for the description of each column.
75 75
76 76
77 </help> 77 </help>
78 <citations> 78 <citations>
79 <citation type="bibtex"> 79 <citation type="bibtex">
80 @misc{githubmob-suite, 80 @misc{githubmob-suite,
81 author = {Robertson J, Nash J}, 81 author = {Robertson J, Nash J},
82 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.}, 82 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
83 publisher = {GitHub}, 83 publisher = {GitHub},
84 journal = {GitHub repository}, 84 journal = {GitHub repository},
85 doi = {10.1099/mgen.0.000206}, 85 doi = {10.1099/mgen.0.000206},
86 url = {https://github.com/phac-nml/mob-suite} 86 url = {https://github.com/phac-nml/mob-suite}
87 }</citation> 87 }</citation>
88 </citations> 88 </citations>
89 </tool> 89 </tool>