Mercurial > repos > nml > cryptogenotyper
comparison cryptogenotyper.xml @ 0:06afaa20dd23 draft
"planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit 2754239279293498574292d06f8f77b4a326b177"
author | nml |
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date | Fri, 16 Oct 2020 02:23:24 +0000 |
parents | |
children | d4a96287909e |
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1 <tool id="CryptoGenotyper" name = "CryptoGenotyper" version="@VERSION@"> | |
2 <description> | |
3 CryptoGenotyper is a standalone tool to analyze Cryptosporidium Sanger sequencing data and classify the species and subtype based on SSU rRNA and gp60 gene markers, respectively. | |
4 </description> | |
5 <macros> | |
6 <token name="@VERSION@">1.0</token> | |
7 </macros> | |
8 <requirements> | |
9 <requirement type="package" version ="@VERSION@">cryptogenotyper</requirement> | |
10 </requirements> | |
11 <version_command>cryptogenotyper --version</version_command> | |
12 <command detect_errors="exit_code"> | |
13 <![CDATA[ | |
14 | |
15 #set $ref_file='' | |
16 | |
17 #if $reference.ref == "no" | |
18 ln -s "${reference.db}" "${reference.db.name}" && | |
19 #set $ref_file = $reference.db.name | |
20 #end if | |
21 | |
22 #if $primers["seqtype"] == "contig" | |
23 ln -s "${$primers.abi_input["forward"]}" "${primers.abi_input.name}_forward.ab1" && | |
24 ln -s "${$primers.abi_input["reverse"]}" "${primers.abi_input.name}_reverse.ab1" && | |
25 cryptogenotyper -i "." -m "$marker" -t "$primers.seqtype" -f "forward" -r "reverse" | |
26 #if $reference.ref == "no" | |
27 --databasefile $ref_file | |
28 #end if | |
29 #else | |
30 ln -s "${primers.abi_input}" "${primers.abi_input.element_identifier}" && | |
31 cryptogenotyper -i "./${primers.abi_input.element_identifier}" -m "$marker" -t "$primers.seqtype" -f "" -r "" | |
32 #if $reference.ref == "no" | |
33 --databasefile $ref_file | |
34 #end if | |
35 #end if | |
36 #if $outputheader == "no" | |
37 --noheaderline | |
38 #end if | |
39 -o "result"; | |
40 ]]> | |
41 </command> | |
42 <inputs> | |
43 <param name="marker" type="select" label="Marker"> | |
44 <option value="18S">SSU rRNA</option> | |
45 <option value="gp60">gp60</option> | |
46 </param> | |
47 <conditional name="reference"> | |
48 <param name="ref" type="select" label="Use default reference file?"> | |
49 <option value="yes">Yes</option> | |
50 <option value="no">No</option> | |
51 </param> | |
52 <when value="yes"> | |
53 </when> | |
54 <when value="no"> | |
55 <param name="db" type="data" format="fasta" label="Reference Database File:" help=".fa fasta file type"/> | |
56 </when> | |
57 </conditional> | |
58 <conditional name="primers"> | |
59 <param name="seqtype" type="select" label="Type of Sequences"> | |
60 <option value="forward">Forward Only</option> | |
61 <option value="reverse">Reverse Only</option> | |
62 <option selected="true" value="contig">Contig</option> | |
63 </param> | |
64 <when value="contig"> | |
65 <param name="abi_input" type="data_collection" collection_type="paired" format="ab1" label="Paired Sequencing File(s)" help=".ab1 file type"/> | |
66 </when> | |
67 <when value="forward"> | |
68 <param name="abi_input" type="data" format="ab1" label="Forward Sequencing File(s)" help=".ab1 file type"/> | |
69 </when> | |
70 <when value="reverse"> | |
71 <param name="abi_input" type="data" format="ab1" label="Reverse Sequencing File(s)" help=".ab1 file type"/> | |
72 </when> | |
73 </conditional> | |
74 <param name="outputheader" type="select" value="yes" label="Output header line in the report?"> | |
75 <option value="yes">Yes</option> | |
76 <option value="no">No</option> | |
77 </param> | |
78 | |
79 | |
80 </inputs> | |
81 <outputs> | |
82 <data name="outfile" format="fasta" from_work_dir="result_cryptogenotyper_report.fa" label="${tool.name}:${on_string}:fastas"/> | |
83 <data name="outfile_report" format="tabular" from_work_dir="result_cryptogenotyper_report.txt" label="${tool.name}:${on_string}:reports"/> | |
84 </outputs> | |
85 | |
86 <tests> | |
87 <test> | |
88 <param name="marker" value="18S"/> | |
89 <param name="seqtype" value="forward"/> | |
90 <param name="abi_input" value="P17705_Crypto16-2F-20170927_SSUF_G12_084.ab1"/> | |
91 <output name="outfile_report" ftype="tabular"> | |
92 <assert_contents> | |
93 <has_text_matching expression="C.parvum"/> | |
94 </assert_contents> | |
95 </output> | |
96 </test> | |
97 <test> | |
98 <param name="marker" value="gp60"/> | |
99 <param name="seqtype" value="forward"/> | |
100 <param name="abi_input" value="P17705_gp60-Crypt14-1F-20170927_gp60F_G07_051.ab1"/> | |
101 <output name="outfile_report" ftype="tabular" > | |
102 <assert_contents> | |
103 <has_text_matching expression="C.parvum"/> | |
104 </assert_contents> | |
105 </output> | |
106 </test> | |
107 </tests> | |
108 | |
109 | |
110 <help> | |
111 | |
112 | |
113 **Syntax** | |
114 | |
115 CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. | |
116 For more information please visit https://github.com/phac-nml/CryptoGenotyper. | |
117 | |
118 ----- | |
119 | |
120 **Input:** | |
121 | |
122 AB1 file(s) representing *Cryptosporidium's* SSU rRNA or gp60 locus (forward, reverse, or contig (forward and reverse paired-end reads)). | |
123 Optional: A custom reference database in .fa file format, to be used during the homology search for *Cryptosporidium* classification. | |
124 | |
125 | |
126 **Output:** | |
127 | |
128 FASTA file containing the identification of the *Cryptosporidium* species/subtype and its corresponding sequence for each sample. | |
129 </help> | |
130 <citations> | |
131 <citation type="bibtex"> | |
132 @misc{githubCryptoGenotyper, | |
133 author = {Yanta C, Bessonov K, Robinson G, Troell K, Guy R}, | |
134 title = {CryptoGenotyper: a new bioinformatics tool to enhance Cryptosporidium identification}, | |
135 publisher = {GitHub}, | |
136 journal = {GitHub repository}, | |
137 url = {https://github.com/phac-nml/CryptoGenotyper} | |
138 }</citation> | |
139 </citations> | |
140 | |
141 </tool> |