Mercurial > repos > bvalot > pymlst

annotate wgmlst_add.xml @ 1:5b2c48fa0175 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 fe04f6232a5f7ea78b666cb8036872902e79998b
author bvalot
date Wed, 07 Dec 2022 15:25:06 +0000
parents a3cc35af3635
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
1 <tool id="wgmlst_add_wrapper" name="Add strain to cg/wgMLST database"
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
2 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
0
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
3 <description></description>
1
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
4 <macros>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
5 <import>macro.xml</import>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
6 </macros>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
7 <expand macro="requirements" />
0
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
8 <stdio>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
9 <exit_code range="1:" level="fatal" />
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
10 </stdio>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
11 <version_command>wgMLST -v</version_command>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
12 <command><![CDATA[
1
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
13 cp '${database}' '${databaseout}'
0
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
14 #if $data.input == "fasta"
1
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
15 #for $datain in $data.fastain:
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
16 && wgMLST add
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
17 -s '$datain.name.replace(" ", "_").replace("-", "_")'
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
18 #if str($coverage)
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
19 -c $coverage
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
20 #end if
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
21 #if str($identity)
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
22 -i $identity
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
23 #end if
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
24 '${databaseout}' '${datain}'
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
25 #if $log
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
26 2>> '${logfile}'
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
27 #end if
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
28 #end for
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
29 #else if $data.input == "fastqsingle"
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
30 #for $datain in $data.single:
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
31 && wgMLST add2
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
32 -s '$datain.name.replace(" ", "_").replace("-", "_")'
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
33 #if str($data.reads)
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
34 -r $data.reads
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
35 #end if
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
36 #if str($coverage)
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
37 -c $coverage
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
38 #end if
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
39 #if str($identity)
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
40 -i $identity
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
41 #end if
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
42 '${databaseout}' '${datain}'
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
43 #if $log
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
44 2>> '${logfile}'
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
45 #end if
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
46 #end for
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
47 #else if $data.input == "fastqpaired"
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
48 && wgMLST add2
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
49 -s '$data.pairedfile.name.replace(" ", "_").replace("-", "_")'
0
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
50 #if str($data.reads)
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
51 -r $data.reads
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
52 #end if
1
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
53 #if str($coverage)
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
54 -c $coverage
0
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
55 #end if
1
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
56 #if str($identity)
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
57 -i $identity
0
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
58 #end if
1
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
59 '${databaseout}' '${data.pairedfile.forward}' '${data.pairedfile.reverse}'
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
60 #if $log
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
61 2>> '${logfile}'
0
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
62 #end if
1
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
63 #else
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
64 #for $datain in $data.pairedfilelist:
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
65 && wgMLST add2
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
66 -s '$datain.name.replace(" ", "_").replace("-", "_")'
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
67 #if str($data.reads)
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
68 -r $data.reads
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
69 #end if
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
70 #if str($coverage)
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
71 -c $coverage
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
72 #end if
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
73 #if str($identity)
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
74 -i $identity
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
75 #end if
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
76 '${databaseout}' '${datain.forward}' '${datain.reverse}'
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
77 #if $log
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
78 2>> '${logfile}'
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
79 #end if
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
80 #end for
0
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
81 #end if
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
82 ]]>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
83 </command>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
84 <inputs>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
85 <param name="database" type="data"
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
86 format="sqlite"
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
87 label="cg/wgMLST database"
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
88 help="Sqlite format from cg/wgMLST database" />
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
89 <conditional name="data">
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
90 <param name="input" type="select" label="Select type of data">
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
91 <option value="fasta" selected="true">Assembly (fasta)</option>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
92 <option value="fastqsingle">Raw data (single)</option>
1
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
93 <option value="fastqpaired">Raw data (paired)</option>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
94 <option value="fastqpaired2">Raw data (List of paired)</option>
0
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
95 </param>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
96 <when value="fasta">
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
97 <param name="fastain" type="data" format="fasta"
1
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
98 label="Assembly Genome" help="Fasta format"
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
99 multiple="true" />
0
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
100 </when>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
101 <when value="fastqsingle">
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
102 <param name="single" type="data" format="fastq,fastq.gz"
1
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
103 label="Single read file" help="Fastq(gz) format"
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
104 multiple="true" />
0
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
105 <param name="reads" type="integer" value="10" optional="true"
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
106 label="Minimum reads coverage to search gene" />
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
107 </when>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
108 <when value="fastqpaired">
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
109 <param name="pairedfile" type="data_collection" format="fastq,fastq.gz"
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
110 label="Paired of read files" help="Fastq(gz) format"
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
111 collection_type="paired" />
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
112 <param name="reads" type="integer" value="10" optional="true"
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
113 label="Minimum reads coverage to search gene" />
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
114 </when>
1
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
115 <when value="fastqpaired2">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
116 <param name="pairedfilelist" type="data_collection" format="fastq,fastq.gz"
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
117 label="Paired of read files" help="Fastq(gz) format"
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
118 collection_type="list:paired" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
119 <param name="reads" type="integer" value="10" optional="true"
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
120 label="Minimum reads coverage to search gene" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
121 </when>
0
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
122 </conditional>
1
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
123 <!-- <param name="strain" type="text" value="" size="50" -->
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
124 <!-- optional="false" -->
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
125 <!-- label="Strain" -->
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
126 <!-- help="Name of the strain"> -->
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
127 <!-- <sanitizer invalid_char="_" > -->
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
128 <!-- <valid initial="string.ascii_letters,string.digits"> -->
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
129 <!-- <add value="_" /> -->
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
130 <!-- <add value="." /> -->
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
131 <!-- </valid> -->
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
132 <!-- </sanitizer> -->
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
133 <!-- </param> -->
0
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
134 <param name="identity" type="float" value="0.9" optional="false"
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
135 label="Identity"
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
136 help="Minimum identity to search gene" />
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
137 <param name="coverage" type="float" value="0.9" optional="false"
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
138 label="Coverage"
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
139 help="Minimum coverage to search gene" />
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
140 <param name="log" type="boolean" checked="true"
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
141 label="Write log file" />
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
142 </inputs>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
143 <outputs>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
144 <data name="databaseout" format="sqlite" label="${database.name}">
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
145 </data>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
146 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log">
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
147 <filter>log</filter>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
148 </data>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
149 </outputs>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
150 <tests>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
151 <test expect_num_outputs="2">
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
152 <param name="database" value="wgmlst_ecoli.db" />
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
153 <conditional name="data">
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
154 <param name="input" value="fasta" />
1
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
155 <param name="fastain" ftype="fasta" value="EHSB-021.fasta,EHSB-092.fasta" />
0
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
156 </conditional>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
157 <param name="identity" value="0.8" />
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
158 <output name="logfile" ftype="txt">
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
159 <assert_contents>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
160 <has_text text="Added 2497 new MLST genes to the database" />
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
161 <has_text text="Found 32 partial genes, filled 30" />
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
162 <has_text text="Removed 4 genes" />
1
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
163 <has_text text="Added 2496 new MLST genes to the database" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
164 <has_text text="Found 44 partial genes, filled 40" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
165 <has_text text="Removed 5 genes" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
166 </assert_contents>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
167 </output>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
168 </test>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
169 <test expect_num_outputs="2">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
170 <param name="database" value="wgmlst_ecoli.db" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
171 <conditional name="data">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
172 <param name="input" value="fastqsingle" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
173 <param name="single"
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
174 value="EHSB-021_R1.fastq.gz,EHSB-021_R2.fastq.gz" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
175 <param name="reads" value="5" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
176 </conditional>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
177 <output name="logfile" ftype="txt">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
178 <assert_contents>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
179 <has_text_matching expression="Add 14\d\d new MLST genes to database" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
180 <has_text_matching expression="Remove \d genes with uncertain bases" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
181 <has_text_matching expression="Remove \d\d\d genes with bad CDS" />
0
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
182 </assert_contents>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
183 </output>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
184 </test>
1
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
185 <test expect_num_outputs="2">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
186 <param name="database" value="wgmlst_ecoli.db" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
187 <conditional name="data">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
188 <param name="input" value="fastqpaired" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
189 <param name="pairedfile">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
190 <collection type="paired">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
191 <element name="forward" value="EHSB-021_R1.fastq.gz" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
192 <element name="reverse" value="EHSB-021_R2.fastq.gz" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
193 </collection>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
194 </param>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
195 <param name="reads" value="5" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
196 </conditional>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
197 <output name="logfile" ftype="txt">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
198 <assert_contents>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
199 <has_text_matching expression="Add 24\d\d new MLST genes to database" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
200 <has_text_matching expression="Remove \d genes with uncertain bases" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
201 <has_text_matching expression="Remove \d\d genes with bad CDS" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
202 </assert_contents>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
203 </output>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
204 </test>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
205 <test expect_num_outputs="2">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
206 <param name="database" value="wgmlst_ecoli.db" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
207 <conditional name="data">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
208 <param name="input" value="fastqpaired2" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
209 <param name="pairedfilelist">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
210 <collection type="list:paired">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
211 <element name="EHSB-021">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
212 <collection type="paired">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
213 <element name="forward" value="EHSB-021_R1.fastq.gz" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
214 <element name="reverse" value="EHSB-021_R2.fastq.gz" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
215 </collection>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
216 </element>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
217 <element name="EHSB-021bis">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
218 <collection type="paired">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
219 <element name="forward" value="EHSB-021_R1.fastq.gz" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
220 <element name="reverse" value="EHSB-021_R2.fastq.gz" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
221 </collection>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
222 </element>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
223 </collection>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
224 </param>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
225 <param name="reads" value="5" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
226 </conditional>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
227 <output name="logfile" ftype="txt">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
228 <assert_contents>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
229 <has_text_matching expression="Add 24\d\d new MLST genes to database" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
230 <has_text_matching expression="Remove \d genes with uncertain bases" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
231 <has_text_matching expression="Remove \d\d genes with bad CDS" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
232 </assert_contents>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
233 </output>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
bvalot
parents: 0
diff changeset
234 </test>
0
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
235 </tests>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
236 <help>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
237 **What it does**
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
238
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
239 Add a Strain to the cg/wgMLST database
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
240
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
241 You can use
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
242 - Genome assembly (blat search)
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
243 - Raw data (kma search)
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
244
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
245 **Options:**
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
246 -s, --strain TEXT Name of the strain (default:genome name).
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
247 -i, --identity FLOAT Minimum identity to search gene (default=0.9).
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
248 -c, --coverage FLOAT Minimum coverage to search gene (default=0.95).
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
249 -r, --reads INTEGER Minimum reads coverage to search gene (default=10).
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
250 -f, --fasta FILENAME Write fasta file with gene allele.
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
251
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
252 **License and citation**
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
253
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
254 This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
255 </help>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
256 <citations>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
257 </citations>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
bvalot
parents:
diff changeset
258 </tool>