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comparison cryptogenotyper.xml @ 0:06afaa20dd23 draft

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"planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit 2754239279293498574292d06f8f77b4a326b177"
author nml
date Fri, 16 Oct 2020 02:23:24 +0000
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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>