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comparison clamlst_search.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
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0:a3cc35af3635 1:5b2c48fa0175
1 <tool id="clamlst_search_wrapper" name="Search MLST database" version="2.1.3"> 1 <tool id="clamlst_search_wrapper" name="Search MLST 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>
6 </macros>
7 <expand macro="requirements">
5 <requirement type="package" version="4.8">sed</requirement> 8 <requirement type="package" version="4.8">sed</requirement>
6 </requirements> 9 </expand>
7 <stdio> 10 <stdio>
8 <exit_code range="1:" level="fatal" /> 11 <exit_code range="1:" level="fatal" />
9 </stdio> 12 </stdio>
10 <version_command>claMLST -v</version_command> 13 <version_command>claMLST -v</version_command>
11 <command><![CDATA[ 14 <command><![CDATA[
15 #set $databaselink = $database.file_name.split("/")[-1]
12 ln -s $database.file_name \$_GALAXY_JOB_TMP_DIR/ && 16 ln -s $database.file_name \$_GALAXY_JOB_TMP_DIR/ &&
13 claMLST 17 claMLST
14 #if $data.input == "fasta" 18 #if $data.input == "fasta"
15 search 19 search
16 #else 20 #else
24 #end if 28 #end if
25 #if $fasta 29 #if $fasta
26 -f '${fastaout}' 30 -f '${fastaout}'
27 #end if 31 #end if
28 #if $data.input == "fasta" 32 #if $data.input == "fasta"
29 \$_GALAXY_JOB_TMP_DIR/`echo $database.file_name | sed -e '~s/.*\///'` '${data.fastain}' 33 \$_GALAXY_JOB_TMP_DIR/'${databaselink}'
30 | sed -e "~s/`echo $data.fastain.file_name | sed -e '~s/.*\///' | 34 #for $datain in $data.fastain:
31 sed -e '~s/.dat$//'`/$data.fastain.name/" 35 '${datain}'
36 #end for
37 #for $datain in $data.fastain:
38 #set $name = $datain.file_name.split("/")[-1].rstrip(".dat")
39 | sed -e "~s/$name/$datain.name/"
40 #end for
32 #end if 41 #end if
33 #if $data.input == "fastqsingle" 42 #if $data.input == "fastqsingle"
34 #if str($data.reads) 43 #if str($data.reads)
35 -r $data.reads 44 -r $data.reads
36 #end if 45 #end if
37 --single 46 --single
38 \$_GALAXY_JOB_TMP_DIR/`echo $database.file_name | sed -e '~s/.*\///'` '${data.single}' 47 \$_GALAXY_JOB_TMP_DIR/'${databaselink}'
39 | sed -e "~s/`echo $data.single.file_name | sed -e '~s/.*\///' 48 #for $datain in $data.single:
40 | sed -e '~s/.dat$//'`/$data.single.name/" 49 '${datain}'
50 #end for
51 #for $datain in $data.single:
52 #set $name = $datain.file_name.split("/")[-1].rstrip(".dat")
53 | sed -e "~s/$name/$datain.name/"
54 #end for
41 #end if 55 #end if
42 #if $data.input == "fastqpaired" 56 #if $data.input == "fastqpaired"
43 #if str($data.reads) 57 #if str($data.reads)
44 -r $data.reads 58 -r $data.reads
45 #end if 59 #end if
46 --paired 60 --paired
47 \$_GALAXY_JOB_TMP_DIR/`echo $database.file_name | sed -e '~s/.*\///'` '${data.forward}' '${data.reverse}' 61 \$_GALAXY_JOB_TMP_DIR/'${databaselink}'
48 | sed -e "~s/`echo $data.forward.file_name | sed -e '~s/.*\///' 62 '${data.pairedfile.forward}' '${data.pairedfile.reverse}'
49 | sed -e '~s/.dat$//'`/$data.forward.name/" 63 #set $name = $data.pairedfile.forward.file_name.split("/")[-1].rstrip(".dat")
64 | sed -e "~s/$name/$data.pairedfile.name/"
50 #end if 65 #end if
51 #if $data.input == "fastqpaired2" 66 #if $data.input == "fastqpaired2"
52 #if str($data.reads) 67 #if str($data.reads)
53 -r $data.reads 68 -r $data.reads
54 #end if 69 #end if
55 --paired 70 --paired
56 \$_GALAXY_JOB_TMP_DIR/`echo $database.file_name | sed -e '~s/.*\///'` '${data.pairedfile.forward}' 71 \$_GALAXY_JOB_TMP_DIR/'${databaselink}'
57 '${data.pairedfile.reverse}' 72 #for $datain in $data.pairedfilelist:
58 | sed -e "~s/`echo $data.pairedfile.forward.file_name | sed -e '~s/.*\///' 73 '${datain.forward}' '${datain.reverse}'
59 | sed -e '~s/.dat$//'`/$data.pairedfile.name/" 74 #end for
75 #for $datain in $data.pairedfilelist:
76 #set $name = $datain.forward.file_name.split("/")[-1].rstrip(".dat")
77 | sed -e "~s/$name/$datain.name/"
78 #end for
60 #end if 79 #end if
61 > '${mlst}' 80 > '${mlst}'
62 #if $log 81 #if $log
63 2> '${logfile}' 82 2> '${logfile}'
64 #end if 83 #end if
71 help="Sqlite format from claMLST import" /> 90 help="Sqlite format from claMLST import" />
72 <conditional name="data"> 91 <conditional name="data">
73 <param name="input" type="select" label="Select type of data"> 92 <param name="input" type="select" label="Select type of data">
74 <option value="fasta" selected="true">Assembly (fasta)</option> 93 <option value="fasta" selected="true">Assembly (fasta)</option>
75 <option value="fastqsingle">Raw data (single)</option> 94 <option value="fastqsingle">Raw data (single)</option>
76 <option value="fastqpaired">Raw data (paired separated)</option> 95 <option value="fastqpaired">Raw data (paired)</option>
77 <option value="fastqpaired2">Raw data (paired)</option> 96 <option value="fastqpaired2">Raw data (List of paired)</option>
78 </param> 97 </param>
79 <when value="fasta"> 98 <when value="fasta">
80 <param name="fastain" type="data" format="fasta" 99 <param name="fastain" type="data" format="fasta"
81 label="Assembly Genome" help="Fasta format" /> 100 label="Assembly Genome" help="Fasta format"
101 multiple="true" />
82 </when> 102 </when>
83 <when value="fastqsingle"> 103 <when value="fastqsingle">
84 <param name="single" type="data" format="fastq,fastq.gz" 104 <param name="single" type="data" format="fastq,fastq.gz"
85 label="Single read file" help="Fastq(gz) format" /> 105 label="Single read file" help="Fastq(gz) format"
106 multiple="true" />
86 <param name="reads" type="integer" value="10" optional="true" 107 <param name="reads" type="integer" value="10" optional="true"
87 label="Minimum reads coverage to search gene" /> 108 label="Minimum reads coverage to search gene" />
88 </when> 109 </when>
89 <when value="fastqpaired"> 110 <when value="fastqpaired">
90 <param name="forward" type="data" format="fastq,fastq.gz"
91 label="Forward read file" help="Fastq(gz) format" />
92 <param name="reverse" type="data" format="fastq,fastq.gz"
93 label="Reverse read file" help="Fastq(gz) format" />
94 <param name="reads" type="integer" value="10" optional="true"
95 label="Minimum reads coverage to search gene" />
96 </when>
97 <when value="fastqpaired2">
98 <param name="pairedfile" type="data_collection" format="fastq,fastq.gz" 111 <param name="pairedfile" type="data_collection" format="fastq,fastq.gz"
99 label="Paired of read files" help="Fastq(gz) format" 112 label="Paired of read files" help="Fastq(gz) format"
100 collection_type="paired" /> 113 collection_type="paired" />
114 <param name="reads" type="integer" value="10" optional="true"
115 label="Minimum reads coverage to search gene" />
116 </when>
117 <when value="fastqpaired2">
118 <param name="pairedfilelist" type="data_collection" format="fastq,fastq.gz"
119 label="Paired of read files" help="Fastq(gz) format"
120 collection_type="list:paired" />
101 <param name="reads" type="integer" value="10" optional="true" 121 <param name="reads" type="integer" value="10" optional="true"
102 label="Minimum reads coverage to search gene" /> 122 label="Minimum reads coverage to search gene" />
103 </when> 123 </when>
104 </conditional> 124 </conditional>
105 <param name="fasta" type="boolean" checked="false" 125 <param name="fasta" type="boolean" checked="false"
125 <tests> 145 <tests>
126 <test expect_num_outputs="1"> 146 <test expect_num_outputs="1">
127 <param name="database" value="clamlst_ecoli.db" /> 147 <param name="database" value="clamlst_ecoli.db" />
128 <conditional name="data"> 148 <conditional name="data">
129 <param name="input" value="fasta" /> 149 <param name="input" value="fasta" />
130 <param name="fastain" ftype="fasta" value="EHSB-021.fasta" /> 150 <param name="fastain" ftype="fasta" value="EHSB-021.fasta,EHSB-092.fasta" />
131 </conditional> 151 </conditional>
132 <param name="identity" value="0.8" /> 152 <param name="identity" value="0.8" />
133 <output name="mlst" ftype="txt"> 153 <output name="mlst" ftype="txt">
134 <assert_contents> 154 <assert_contents>
135 <has_text_matching expression="155\t6\t4\t14\t16\t24\t8\t14" /> 155 <has_text_matching expression="155\t6\t4\t14\t16\t24\t8\t14" />
136 </assert_contents> 156 <has_text_matching expression="3018\t12\t58\t54\t344\t1\t2\t47" />
137 </output> 157 </assert_contents>
138 </test> 158 </output>
139 <!-- <test expect_num_outputs="3"> --> 159 </test>
140 <!-- <param name="database" value="clamlst_ecoli.db" /> --> 160 <test expect_num_outputs="1">
141 <!-- <conditional name="data"> --> 161 <param name="database" value="clamlst_ecoli.db" />
142 <!-- <param name="input" value="fastqpaired" /> --> 162 <conditional name="data">
143 <!-- <param name="forward" ftype="fastq.gz" value="EHSB-021_R1.fastq.gz" /> --> 163 <param name="input" value="fastqsingle" />
144 <!-- <param name="reverse" ftype="fastq.gz" value="EHSB-021_R2.fastq.gz" /> --> 164 <param name="single" ftype="fastqsanger" value="EHSB-021_R1.fastq.gz,EHSB-021_R2.fastq.gz" />
145 <!-- <param name="reads" value="5" /> --> 165 </conditional>
146 <!-- </conditional> --> 166 <param name="identity" value="0.8" />
147 <!-- <param name="fasta" value="true" /> --> 167 <param name="reads" value="5" />
148 <!-- <param name="log" value="true" /> --> 168 <output name="mlst" ftype="txt">
149 <!-- <output name="fastaout" ftype="fasta"> --> 169 <assert_contents>
150 <!-- <assert_contents> --> 170 <has_text_matching expression="14\t16\t24\t8" />
151 <!-- <has_n_lines n="14" /> --> 171 </assert_contents>
152 <!-- </assert_contents> --> 172 </output>
153 <!-- </output> --> 173 </test>
154 <!-- <output name="mlst" ftype="txt"> --> 174 <test expect_num_outputs="1">
155 <!-- <assert_contents> --> 175 <param name="database" value="clamlst_ecoli.db" />
156 <!-- <has_text_matching expression="4\t14\t16\t24\t8\t14" /> --> 176 <conditional name="data">
157 <!-- </assert_contents> --> 177 <param name="input" value="fastqpaired" />
158 <!-- </output> --> 178 <param name="pairedfile">
159 <!-- </test> --> 179 <collection type="paired">
180 <element name="forward" value="EHSB-021_R1.fastq.gz" />
181 <element name="reverse" value="EHSB-021_R2.fastq.gz" />
182 </collection>
183 </param>
184 <param name="reads" value="5" />
185 </conditional>
186 <output name="mlst" ftype="txt">
187 <assert_contents>
188 <has_text_matching expression="4\t14\t16\t24\t8\t14" />
189 </assert_contents>
190 </output>
191 </test>
192 <test expect_num_outputs="3">
193 <param name="database" value="clamlst_ecoli.db" />
194 <conditional name="data">
195 <param name="input" value="fastqpaired2" />
196 <param name="pairedfilelist">
197 <collection type="list:paired">
198 <element name="EHSB-021">
199 <collection type="paired">
200 <element name="forward" value="EHSB-021_R1.fastq.gz" />
201 <element name="reverse" value="EHSB-021_R2.fastq.gz" />
202 </collection>
203 </element>
204 </collection>
205 </param>
206 <param name="reads" value="5" />
207 </conditional>
208 <param name="fasta" value="true" />
209 <param name="log" value="true" />
210 <output name="fastaout" ftype="fasta">
211 <assert_contents>
212 <has_n_lines n="14" />
213 </assert_contents>
214 </output>
215 <output name="mlst" ftype="txt">
216 <assert_contents>
217 <has_text_matching expression="4\t14\t16\t24\t8\t14" />
218 </assert_contents>
219 </output>
220 </test>
160 </tests> 221 </tests>
161 <help> 222 <help>
162 **What it does** 223 **What it does**
163 224
164 Search ST number from pubMLST database 225 Search ST number from pubMLST database