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comparison cryptogenotyper.xml @ 1:d4a96287909e draft default tip

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"planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit 232da91ef9014d518a1c14dac403961bfb9223cf"
author nml
date Fri, 16 Oct 2020 22:32:56 +0000
parents 06afaa20dd23
children
comparison
equal deleted inserted replaced
0:06afaa20dd23 1:d4a96287909e
1 <tool id="CryptoGenotyper" name = "CryptoGenotyper" version="@VERSION@"> 1 <tool id="CryptoGenotyper" name = "CryptoGenotyper" version="@VERSION@+galaxy0">
2 <description> 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. 3 classifies Cryptosporidium species subtypes based on SSU rRNA and gp60 gene markers from Sanger sequencing data.
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <token name="@VERSION@">1.0</token> 6 <token name="@VERSION@">1.0</token>
7 </macros> 7 </macros>
8 <requirements> 8 <requirements>
12 <command detect_errors="exit_code"> 12 <command detect_errors="exit_code">
13 <![CDATA[ 13 <![CDATA[
14 14
15 #set $ref_file='' 15 #set $ref_file=''
16 16
17 #if $reference.ref == "no" 17 #if $db
18 ln -s "${reference.db}" "${reference.db.name}" && 18 ln -s '${db}' '${db.name}' &&
19 #set $ref_file = $reference.db.name 19 #set $ref_file = $db.name
20 #end if 20 #end if
21 21
22 #if $primers["seqtype"] == "contig" 22 #if $primers['seqtype'] == 'contig'
23 ln -s "${$primers.abi_input["forward"]}" "${primers.abi_input.name}_forward.ab1" && 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" && 24 ln -s '${$primers.abi_input['reverse']}' '${primers.abi_input.name}_reverse.ab1' &&
25 cryptogenotyper -i "." -m "$marker" -t "$primers.seqtype" -f "forward" -r "reverse" 25 cryptogenotyper -i '.' -m '$marker' -t '$primers.seqtype' -f 'forward' -r 'reverse'
26 #if $reference.ref == "no" 26 #if $db
27 --databasefile $ref_file 27 --databasefile $ref_file
28 #end if 28 #end if
29 #else 29 #else
30 ln -s "${primers.abi_input}" "${primers.abi_input.element_identifier}" && 30 ln -s '${primers.abi_input}' '${primers.abi_input.element_identifier}' &&
31 cryptogenotyper -i "./${primers.abi_input.element_identifier}" -m "$marker" -t "$primers.seqtype" -f "" -r "" 31 cryptogenotyper -i './${primers.abi_input.element_identifier}' -m '$marker' -t '$primers.seqtype'
32 #if $reference.ref == "no" 32 #if $db
33 --databasefile $ref_file 33 --databasefile $ref_file
34 #end if 34 #end if
35 #end if 35 #end if
36 #if $outputheader == "no" 36 $outputheader
37 --noheaderline 37 -o 'result'
38 #end if
39 -o "result";
40 ]]> 38 ]]>
41 </command> 39 </command>
42 <inputs> 40 <inputs>
43 <param name="marker" type="select" label="Marker"> 41 <param name="marker" type="select" label="Marker">
44 <option value="18S">SSU rRNA</option> 42 <option value="18S">SSU rRNA</option>
45 <option value="gp60">gp60</option> 43 <option value="gp60">gp60</option>
46 </param> 44 </param>
47 <conditional name="reference"> 45 <param name="db" type="data" optional="true" format="fasta" label="Reference Database File (optional):"/>
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"> 46 <conditional name="primers">
59 <param name="seqtype" type="select" label="Type of Sequences"> 47 <param name="seqtype" type="select" label="Type of Sequences">
60 <option value="forward">Forward Only</option> 48 <option value="forward">Forward Only</option>
61 <option value="reverse">Reverse Only</option> 49 <option value="reverse">Reverse Only</option>
62 <option selected="true" value="contig">Contig</option> 50 <option selected="true" value="contig">Contig</option>
63 </param> 51 </param>
64 <when value="contig"> 52 <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"/> 53 <param name="abi_input" type="data_collection" collection_type="paired" format="ab1" label="Paired Sequencing File(s)"/>
66 </when> 54 </when>
67 <when value="forward"> 55 <when value="forward">
68 <param name="abi_input" type="data" format="ab1" label="Forward Sequencing File(s)" help=".ab1 file type"/> 56 <param name="abi_input" type="data" format="ab1" label="Forward Sequencing File(s)"/>
69 </when> 57 </when>
70 <when value="reverse"> 58 <when value="reverse">
71 <param name="abi_input" type="data" format="ab1" label="Reverse Sequencing File(s)" help=".ab1 file type"/> 59 <param name="abi_input" type="data" format="ab1" label="Reverse Sequencing File(s)"/>
72 </when> 60 </when>
73 </conditional> 61 </conditional>
74 <param name="outputheader" type="select" value="yes" label="Output header line in the report?"> 62 <param name="outputheader" type="boolean" truevalue="" falsevalue="--noheaderline" checked="true" label="Output header line in the report?">
75 <option value="yes">Yes</option>
76 <option value="no">No</option>
77 </param> 63 </param>
78 64
79 65
80 </inputs> 66 </inputs>
81 <outputs> 67 <outputs>
82 <data name="outfile" format="fasta" from_work_dir="result_cryptogenotyper_report.fa" label="${tool.name}:${on_string}:fastas"/> 68 <data name="outfile" format="fasta" from_work_dir="result_cryptogenotyper_report.fa" label="${tool.name}:${on_string}:fastas"/>
83 <data name="outfile_report" format="tabular" from_work_dir="result_cryptogenotyper_report.txt" label="${tool.name}:${on_string}:reports"/> 69 <data name="outfile_report" format="tabular" from_work_dir="result_cryptogenotyper_report.txt" label="${tool.name}:${on_string}:reports"/>
84 </outputs> 70 </outputs>
85 71
86 <tests> 72 <tests>
87 <test> 73 <test expect_num_outputs="2">
88 <param name="marker" value="18S"/> 74 <param name="marker" value="18S"/>
89 <param name="seqtype" value="forward"/> 75 <param name="seqtype" value="forward"/>
90 <param name="abi_input" value="P17705_Crypto16-2F-20170927_SSUF_G12_084.ab1"/> 76 <param name="abi_input" value="P17705_Crypto16-2F-20170927_SSUF_G12_084.ab1"/>
91 <output name="outfile_report" ftype="tabular"> 77 <output name="outfile_report" ftype="tabular">
92 <assert_contents> 78 <assert_contents>
93 <has_text_matching expression="C.parvum"/> 79 <has_text_matching expression="C.parvum"/>
94 </assert_contents> 80 </assert_contents>
95 </output> 81 </output>
96 </test> 82 </test>
97 <test> 83 <test expect_num_outputs="2">
98 <param name="marker" value="gp60"/> 84 <param name="marker" value="gp60"/>
99 <param name="seqtype" value="forward"/> 85 <param name="seqtype" value="forward"/>
100 <param name="abi_input" value="P17705_gp60-Crypt14-1F-20170927_gp60F_G07_051.ab1"/> 86 <param name="abi_input" value="P17705_gp60-Crypt14-1F-20170927_gp60F_G07_051.ab1"/>
101 <output name="outfile_report" ftype="tabular" > 87 <output name="outfile_report" ftype="tabular" >
102 <assert_contents> 88 <assert_contents>