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comparison wgmlst_add.xml @ 1:5b2c48fa0175 draft

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planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
author bvalot
date Wed, 07 Dec 2022 15:25:06 +0000
parents a3cc35af3635
children
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0:a3cc35af3635 1:5b2c48fa0175
1 <tool id="wgmlst_add_wrapper" name="Add strain to cg/wgMLST database" version="2.1.3"> 1 <tool id="wgmlst_add_wrapper" name="Add strain to cg/wgMLST database"
2 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description></description> 3 <description></description>
3 <requirements> 4 <macros>
4 <requirement type="package" version="2.1.3">pymlst</requirement> 5 <import>macro.xml</import>
5 </requirements> 6 </macros>
7 <expand macro="requirements" />
6 <stdio> 8 <stdio>
7 <exit_code range="1:" level="fatal" /> 9 <exit_code range="1:" level="fatal" />
8 </stdio> 10 </stdio>
9 <version_command>wgMLST -v</version_command> 11 <version_command>wgMLST -v</version_command>
10 <command><![CDATA[ 12 <command><![CDATA[
11 cp '${database}' '${databaseout}' && 13 cp '${database}' '${databaseout}'
12 wgMLST
13 #if $data.input == "fasta" 14 #if $data.input == "fasta"
14 add 15 #for $datain in $data.fastain:
15 #else 16 && wgMLST add
16 add2 17 -s '$datain.name.replace(" ", "_").replace("-", "_")'
17 #end if 18 #if str($coverage)
18 #if str($coverage) 19 -c $coverage
19 -c $coverage 20 #end if
20 #end if 21 #if str($identity)
21 #if str($identity) 22 -i $identity
22 -i $identity 23 #end if
23 #end if 24 '${databaseout}' '${datain}'
24 #if $data.input == "fasta" 25 #if $log
25 #if $strain 26 2>> '${logfile}'
26 -s '$strain' 27 #end if
27 #else 28 #end for
28 -s '$data.fastain.name.replace(" ", "_").replace("-", "_")' 29 #else if $data.input == "fastqsingle"
29 #end if 30 #for $datain in $data.single:
30 '${databaseout}' '${data.fastain}' 31 && wgMLST add2
31 #end if 32 -s '$datain.name.replace(" ", "_").replace("-", "_")'
32 #if $data.input == "fastqsingle" 33 #if str($data.reads)
34 -r $data.reads
35 #end if
36 #if str($coverage)
37 -c $coverage
38 #end if
39 #if str($identity)
40 -i $identity
41 #end if
42 '${databaseout}' '${datain}'
43 #if $log
44 2>> '${logfile}'
45 #end if
46 #end for
47 #else if $data.input == "fastqpaired"
48 && wgMLST add2
49 -s '$data.pairedfile.name.replace(" ", "_").replace("-", "_")'
33 #if str($data.reads) 50 #if str($data.reads)
34 -r $data.reads 51 -r $data.reads
35 #end if 52 #end if
36 #if $strain 53 #if str($coverage)
37 -s '$strain' 54 -c $coverage
38 #else 55 #end if
39 -s '$data.single.name.replace(" ", "_").replace("-", "_")' 56 #if str($identity)
40 #end if 57 -i $identity
41 '${databaseout}' '${data.single}' 58 #end if
42 #end if 59 '${databaseout}' '${data.pairedfile.forward}' '${data.pairedfile.reverse}'
43 #if $data.input == "fastqpaired" 60 #if $log
44 #if str($data.reads) 61 2>> '${logfile}'
45 -r $data.reads 62 #end if
46 #end if 63 #else
47 #if $strain 64 #for $datain in $data.pairedfilelist:
48 -s '$strain' 65 && wgMLST add2
49 #else 66 -s '$datain.name.replace(" ", "_").replace("-", "_")'
50 -s '$data.forward.name.replace(" ", "_").replace("-", "_")' 67 #if str($data.reads)
51 #end if 68 -r $data.reads
52 '${databaseout}' '${data.forward}' '${data.reverse}' 69 #end if
53 #end if 70 #if str($coverage)
54 #if $data.input == "fastqpaired2" 71 -c $coverage
55 #if str($data.reads) 72 #end if
56 -r $data.reads 73 #if str($identity)
57 #end if 74 -i $identity
58 #if $strain 75 #end if
59 -s '$strain' 76 '${databaseout}' '${datain.forward}' '${datain.reverse}'
60 #else 77 #if $log
61 -s '$data.pairedfile.name.replace(" ", "_").replace("-", "_")' 78 2>> '${logfile}'
62 #end if 79 #end if
63 '${databaseout}' '${data.pairedfile.forward}' 80 #end for
64 '${data.pairedfile.reverse}'
65 #end if
66 #if $log
67 2> '${logfile}'
68 #end if 81 #end if
69 ]]> 82 ]]>
70 </command> 83 </command>
71 <inputs> 84 <inputs>
72 <param name="database" type="data" 85 <param name="database" type="data"
75 help="Sqlite format from cg/wgMLST database" /> 88 help="Sqlite format from cg/wgMLST database" />
76 <conditional name="data"> 89 <conditional name="data">
77 <param name="input" type="select" label="Select type of data"> 90 <param name="input" type="select" label="Select type of data">
78 <option value="fasta" selected="true">Assembly (fasta)</option> 91 <option value="fasta" selected="true">Assembly (fasta)</option>
79 <option value="fastqsingle">Raw data (single)</option> 92 <option value="fastqsingle">Raw data (single)</option>
80 <option value="fastqpaired">Raw data (paired separated)</option> 93 <option value="fastqpaired">Raw data (paired)</option>
81 <option value="fastqpaired2">Raw data (paired)</option> 94 <option value="fastqpaired2">Raw data (List of paired)</option>
82 </param> 95 </param>
83 <when value="fasta"> 96 <when value="fasta">
84 <param name="fastain" type="data" format="fasta" 97 <param name="fastain" type="data" format="fasta"
85 label="Assembly Genome" help="Fasta format" /> 98 label="Assembly Genome" help="Fasta format"
99 multiple="true" />
86 </when> 100 </when>
87 <when value="fastqsingle"> 101 <when value="fastqsingle">
88 <param name="single" type="data" format="fastq,fastq.gz" 102 <param name="single" type="data" format="fastq,fastq.gz"
89 label="Single read file" help="Fastq(gz) format" /> 103 label="Single read file" help="Fastq(gz) format"
104 multiple="true" />
90 <param name="reads" type="integer" value="10" optional="true" 105 <param name="reads" type="integer" value="10" optional="true"
91 label="Minimum reads coverage to search gene" /> 106 label="Minimum reads coverage to search gene" />
92 </when> 107 </when>
93 <when value="fastqpaired"> 108 <when value="fastqpaired">
94 <param name="forward" type="data" format="fastq,fastq.gz"
95 label="Forward read file" help="Fastq(gz) format" />
96 <param name="reverse" type="data" format="fastq,fastq.gz"
97 label="Reverse read file" help="Fastq(gz) format" />
98 <param name="reads" type="integer" value="10" optional="true"
99 label="Minimum reads coverage to search gene" />
100 </when>
101 <when value="fastqpaired2">
102 <param name="pairedfile" type="data_collection" format="fastq,fastq.gz" 109 <param name="pairedfile" type="data_collection" format="fastq,fastq.gz"
103 label="Paired of read files" help="Fastq(gz) format" 110 label="Paired of read files" help="Fastq(gz) format"
104 collection_type="paired" /> 111 collection_type="paired" />
105 <param name="reads" type="integer" value="10" optional="true" 112 <param name="reads" type="integer" value="10" optional="true"
106 label="Minimum reads coverage to search gene" /> 113 label="Minimum reads coverage to search gene" />
107 </when> 114 </when>
115 <when value="fastqpaired2">
116 <param name="pairedfilelist" type="data_collection" format="fastq,fastq.gz"
117 label="Paired of read files" help="Fastq(gz) format"
118 collection_type="list:paired" />
119 <param name="reads" type="integer" value="10" optional="true"
120 label="Minimum reads coverage to search gene" />
121 </when>
108 </conditional> 122 </conditional>
109 <param name="strain" type="text" value="" size="50" 123 <!-- <param name="strain" type="text" value="" size="50" -->
110 optional="false" 124 <!-- optional="false" -->
111 label="Strain" 125 <!-- label="Strain" -->
112 help="Name of the strain"> 126 <!-- help="Name of the strain"> -->
113 <sanitizer invalid_char="_" > 127 <!-- <sanitizer invalid_char="_" > -->
114 <valid initial="string.ascii_letters,string.digits"> 128 <!-- <valid initial="string.ascii_letters,string.digits"> -->
115 <add value="_" /> 129 <!-- <add value="_" /> -->
116 <add value="." /> 130 <!-- <add value="." /> -->
117 </valid> 131 <!-- </valid> -->
118 </sanitizer> 132 <!-- </sanitizer> -->
119 </param> 133 <!-- </param> -->
120 <param name="identity" type="float" value="0.9" optional="false" 134 <param name="identity" type="float" value="0.9" optional="false"
121 label="Identity" 135 label="Identity"
122 help="Minimum identity to search gene" /> 136 help="Minimum identity to search gene" />
123 <param name="coverage" type="float" value="0.9" optional="false" 137 <param name="coverage" type="float" value="0.9" optional="false"
124 label="Coverage" 138 label="Coverage"
136 <tests> 150 <tests>
137 <test expect_num_outputs="2"> 151 <test expect_num_outputs="2">
138 <param name="database" value="wgmlst_ecoli.db" /> 152 <param name="database" value="wgmlst_ecoli.db" />
139 <conditional name="data"> 153 <conditional name="data">
140 <param name="input" value="fasta" /> 154 <param name="input" value="fasta" />
141 <param name="fastain" ftype="fasta" value="EHSB-021.fasta" /> 155 <param name="fastain" ftype="fasta" value="EHSB-021.fasta,EHSB-092.fasta" />
142 </conditional> 156 </conditional>
143 <param name="identity" value="0.8" /> 157 <param name="identity" value="0.8" />
144 <output name="logfile" ftype="txt"> 158 <output name="logfile" ftype="txt">
145 <assert_contents> 159 <assert_contents>
146 <has_text text="Added 2497 new MLST genes to the database" /> 160 <has_text text="Added 2497 new MLST genes to the database" />
147 <has_text text="Found 32 partial genes, filled 30" /> 161 <has_text text="Found 32 partial genes, filled 30" />
148 <has_text text="Removed 4 genes" /> 162 <has_text text="Removed 4 genes" />
149 </assert_contents> 163 <has_text text="Added 2496 new MLST genes to the database" />
150 </output> 164 <has_text text="Found 44 partial genes, filled 40" />
151 </test> 165 <has_text text="Removed 5 genes" />
152 <!-- <test expect_num_outputs="2"> --> 166 </assert_contents>
153 <!-- <param name="database" value="wgmlst_ecoli.db" /> --> 167 </output>
154 <!-- <param name="strain" value="EHSB-021" /> --> 168 </test>
155 <!-- <conditional name="data"> --> 169 <test expect_num_outputs="2">
156 <!-- <param name="input" value="fastqpaired" /> --> 170 <param name="database" value="wgmlst_ecoli.db" />
157 <!-- <param name="forward" ftype="fastq.gz" value="EHSB-021_R1.fastq.gz" /> --> 171 <conditional name="data">
158 <!-- <param name="reverse" ftype="fastq.gz" value="EHSB-021_R2.fastq.gz" /> --> 172 <param name="input" value="fastqsingle" />
159 <!-- <param name="reads" value="5" /> --> 173 <param name="single"
160 <!-- </conditional> --> 174 value="EHSB-021_R1.fastq.gz,EHSB-021_R2.fastq.gz" />
161 <!-- <output name="logfile" ftype="txt"> --> 175 <param name="reads" value="5" />
162 <!-- <assert_contents> --> 176 </conditional>
163 <!-- <has_text_matching expression="Add 24\d\d new MLST genes to database" /> --> 177 <output name="logfile" ftype="txt">
164 <!-- <has_text_matching expression="Remove \d genes with uncertain bases" /> --> 178 <assert_contents>
165 <!-- <has_text_matching expression="Remove \d\d genes with bad CDS" /> --> 179 <has_text_matching expression="Add 14\d\d new MLST genes to database" />
166 <!-- </assert_contents> --> 180 <has_text_matching expression="Remove \d genes with uncertain bases" />
167 <!-- </output> --> 181 <has_text_matching expression="Remove \d\d\d genes with bad CDS" />
168 <!-- </test> --> 182 </assert_contents>
183 </output>
184 </test>
185 <test expect_num_outputs="2">
186 <param name="database" value="wgmlst_ecoli.db" />
187 <conditional name="data">
188 <param name="input" value="fastqpaired" />
189 <param name="pairedfile">
190 <collection type="paired">
191 <element name="forward" value="EHSB-021_R1.fastq.gz" />
192 <element name="reverse" value="EHSB-021_R2.fastq.gz" />
193 </collection>
194 </param>
195 <param name="reads" value="5" />
196 </conditional>
197 <output name="logfile" ftype="txt">
198 <assert_contents>
199 <has_text_matching expression="Add 24\d\d new MLST genes to database" />
200 <has_text_matching expression="Remove \d genes with uncertain bases" />
201 <has_text_matching expression="Remove \d\d genes with bad CDS" />
202 </assert_contents>
203 </output>
204 </test>
205 <test expect_num_outputs="2">
206 <param name="database" value="wgmlst_ecoli.db" />
207 <conditional name="data">
208 <param name="input" value="fastqpaired2" />
209 <param name="pairedfilelist">
210 <collection type="list:paired">
211 <element name="EHSB-021">
212 <collection type="paired">
213 <element name="forward" value="EHSB-021_R1.fastq.gz" />
214 <element name="reverse" value="EHSB-021_R2.fastq.gz" />
215 </collection>
216 </element>
217 <element name="EHSB-021bis">
218 <collection type="paired">
219 <element name="forward" value="EHSB-021_R1.fastq.gz" />
220 <element name="reverse" value="EHSB-021_R2.fastq.gz" />
221 </collection>
222 </element>
223 </collection>
224 </param>
225 <param name="reads" value="5" />
226 </conditional>
227 <output name="logfile" ftype="txt">
228 <assert_contents>
229 <has_text_matching expression="Add 24\d\d new MLST genes to database" />
230 <has_text_matching expression="Remove \d genes with uncertain bases" />
231 <has_text_matching expression="Remove \d\d genes with bad CDS" />
232 </assert_contents>
233 </output>
234 </test>
169 </tests> 235 </tests>
170 <help> 236 <help>
171 **What it does** 237 **What it does**
172 238
173 Add a Strain to the cg/wgMLST database 239 Add a Strain to the cg/wgMLST database