Mercurial > repos > bvalot > pymlst

comparison clamlst_search.xml @ 0:a3cc35af3635 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
author bvalot
date Thu, 16 Jun 2022 12:32:28 +0000
parents
children 5b2c48fa0175
comparison
equal deleted inserted replaced
-1:000000000000 0:a3cc35af3635
1 <tool id="clamlst_search_wrapper" name="Search MLST database" version="2.1.3">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="2.1.3">pymlst</requirement>
5 <requirement type="package" version="4.8">sed</requirement>
6 </requirements>
7 <stdio>
8 <exit_code range="1:" level="fatal" />
9 </stdio>
10 <version_command>claMLST -v</version_command>
11 <command><![CDATA[
12 ln -s $database.file_name \$_GALAXY_JOB_TMP_DIR/ &&
13 claMLST
14 #if $data.input == "fasta"
15 search
16 #else
17 search2
18 #end if
19 #if str($coverage)
20 -c $coverage
21 #end if
22 #if str($identity)
23 -i $identity
24 #end if
25 #if $fasta
26 -f '${fastaout}'
27 #end if
28 #if $data.input == "fasta"
29 \$_GALAXY_JOB_TMP_DIR/`echo $database.file_name | sed -e '~s/.*\///'` '${data.fastain}'
30 | sed -e "~s/`echo $data.fastain.file_name | sed -e '~s/.*\///' |
31 sed -e '~s/.dat$//'`/$data.fastain.name/"
32 #end if
33 #if $data.input == "fastqsingle"
34 #if str($data.reads)
35 -r $data.reads
36 #end if
37 --single
38 \$_GALAXY_JOB_TMP_DIR/`echo $database.file_name | sed -e '~s/.*\///'` '${data.single}'
39 | sed -e "~s/`echo $data.single.file_name | sed -e '~s/.*\///'
40 | sed -e '~s/.dat$//'`/$data.single.name/"
41 #end if
42 #if $data.input == "fastqpaired"
43 #if str($data.reads)
44 -r $data.reads
45 #end if
46 --paired
47 \$_GALAXY_JOB_TMP_DIR/`echo $database.file_name | sed -e '~s/.*\///'` '${data.forward}' '${data.reverse}'
48 | sed -e "~s/`echo $data.forward.file_name | sed -e '~s/.*\///'
49 | sed -e '~s/.dat$//'`/$data.forward.name/"
50 #end if
51 #if $data.input == "fastqpaired2"
52 #if str($data.reads)
53 -r $data.reads
54 #end if
55 --paired
56 \$_GALAXY_JOB_TMP_DIR/`echo $database.file_name | sed -e '~s/.*\///'` '${data.pairedfile.forward}'
57 '${data.pairedfile.reverse}'
58 | sed -e "~s/`echo $data.pairedfile.forward.file_name | sed -e '~s/.*\///'
59 | sed -e '~s/.dat$//'`/$data.pairedfile.name/"
60 #end if
61 > '${mlst}'
62 #if $log
63 2> '${logfile}'
64 #end if
65 ]]>
66 </command>
67 <inputs>
68 <param name="database" type="data"
69 format="sqlite"
70 label="Classical MLST database"
71 help="Sqlite format from claMLST import" />
72 <conditional name="data">
73 <param name="input" type="select" label="Select type of data">
74 <option value="fasta" selected="true">Assembly (fasta)</option>
75 <option value="fastqsingle">Raw data (single)</option>
76 <option value="fastqpaired">Raw data (paired separated)</option>
77 <option value="fastqpaired2">Raw data (paired)</option>
78 </param>
79 <when value="fasta">
80 <param name="fastain" type="data" format="fasta"
81 label="Assembly Genome" help="Fasta format" />
82 </when>
83 <when value="fastqsingle">
84 <param name="single" type="data" format="fastq,fastq.gz"
85 label="Single read file" help="Fastq(gz) format" />
86 <param name="reads" type="integer" value="10" optional="true"
87 label="Minimum reads coverage to search gene" />
88 </when>
89 <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"
99 label="Paired of read files" help="Fastq(gz) format"
100 collection_type="paired" />
101 <param name="reads" type="integer" value="10" optional="true"
102 label="Minimum reads coverage to search gene" />
103 </when>
104 </conditional>
105 <param name="fasta" type="boolean" checked="false"
106 label="Write fasta file with MLST genes allele" />
107 <param name="identity" type="float" value="0.9" optional="false"
108 label="Identity"
109 help="Minimum identity to search gene" />
110 <param name="coverage" type="float" value="0.9" optional="false"
111 label="Coverage"
112 help="Minimum coverage to search gene" />
113 <param name="log" type="boolean" checked="false"
114 label="Write log file" />
115 </inputs>
116 <outputs>
117 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log">
118 <filter>log</filter>
119 </data>
120 <data name="mlst" format="txt" label="${tool.name} on ${on_string}: mlst" />
121 <data name="fastaout" format="fasta" label="${tool.name} on {on_string}: fasta">
122 <filter>fasta</filter>
123 </data>
124 </outputs>
125 <tests>
126 <test expect_num_outputs="1">
127 <param name="database" value="clamlst_ecoli.db" />
128 <conditional name="data">
129 <param name="input" value="fasta" />
130 <param name="fastain" ftype="fasta" value="EHSB-021.fasta" />
131 </conditional>
132 <param name="identity" value="0.8" />
133 <output name="mlst" ftype="txt">
134 <assert_contents>
135 <has_text_matching expression="155\t6\t4\t14\t16\t24\t8\t14" />
136 </assert_contents>
137 </output>
138 </test>
139 <!-- <test expect_num_outputs="3"> -->
140 <!-- <param name="database" value="clamlst_ecoli.db" /> -->
141 <!-- <conditional name="data"> -->
142 <!-- <param name="input" value="fastqpaired" /> -->
143 <!-- <param name="forward" ftype="fastq.gz" value="EHSB-021_R1.fastq.gz" /> -->
144 <!-- <param name="reverse" ftype="fastq.gz" value="EHSB-021_R2.fastq.gz" /> -->
145 <!-- <param name="reads" value="5" /> -->
146 <!-- </conditional> -->
147 <!-- <param name="fasta" value="true" /> -->
148 <!-- <param name="log" value="true" /> -->
149 <!-- <output name="fastaout" ftype="fasta"> -->
150 <!-- <assert_contents> -->
151 <!-- <has_n_lines n="14" /> -->
152 <!-- </assert_contents> -->
153 <!-- </output> -->
154 <!-- <output name="mlst" ftype="txt"> -->
155 <!-- <assert_contents> -->
156 <!-- <has_text_matching expression="4\t14\t16\t24\t8\t14" /> -->
157 <!-- </assert_contents> -->
158 <!-- </output> -->
159 <!-- </test> -->
160 </tests>
161 <help>
162 **What it does**
163
164 Search ST number from pubMLST database
165
166 You can use
167 - Genome assembly (blat search)
168 - Raw data (kma search)
169
170 **Options:**
171
172 -i, --identity FLOAT Minimum identity to search gene (default=0.9).
173 -c, --coverage FLOAT Minimum coverage to search gene (default=0.95).
174 -r, --reads INTEGER Minimum reads coverage to search gene (default=10).
175 -f, --fasta FILENAME Write fasta file with gene allele.
176
177 **License and citation**
178
179 This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
180 </help>
181 <citations>
182 </citations>
183 </tool>