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comparison wgmlst_export.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_export_wrapper" name="Export result of cg/wgMLST database" version="2.1.3"> 1 <tool id="wgmlst_export_wrapper" name="Export result of 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> 12 <command>
12 #if $export_result.export == "distance" 14 #if $export_result.export == "distance"
13 distance 15 distance
14 #end if 16 #end if
15 #if $export_result.export == "mlst" 17 #if $export_result.export == "mlst"
16 mlst 18 mlst
19 #if $export_result.mlsttype == "grapetree"
20 -f grapetree
21 #end if
17 #end if 22 #end if
18 #if $export_result.export == "strain" 23 #if $export_result.export == "strain"
19 strain 24 strain
20 #if $export_result.count 25 #if $export_result.count
21 -c 26 -c
47 format="sqlite" 52 format="sqlite"
48 label="cg/wgMLST database" 53 label="cg/wgMLST database"
49 help="Sqlite format from cg/wgMLST database" /> 54 help="Sqlite format from cg/wgMLST database" />
50 <conditional name="export_result"> 55 <conditional name="export_result">
51 <param name="export" type="select" label="Select the data export"> 56 <param name="export" type="select" label="Select the data export">
52 <option value="distance">Distance matrix between strains on the cg/wgMLST database</option> 57 <option value="distance" selected="true">Distance matrix between strains on the cg/wgMLST database</option>
53 <option value="mlst">cg/wgMLST table for each strain on the cg/wgMLST database</option> 58 <option value="mlst">cg/wgMLST table for each strain on the cg/wgMLST database</option>
54 <option value="strain">List of the strains on the cg/wgMLST database</option> 59 <option value="strain">List of the strains on the cg/wgMLST database</option>
55 <option value="gene">List of the genes on the cg/wgMLST database</option> 60 <option value="gene">List of the genes on the cg/wgMLST database</option>
56 </param> 61 </param>
57 <when value="strain"> 62 <when value="strain">
58 <param name="count" type="boolean" checked="false" 63 <param name="count" type="boolean" checked="false"
59 label="Report the number of gene found for each strain" /> 64 label="Report the number of gene found for each strain" />
60 </when> 65 </when>
61 <when value="distance" /> 66 <when value="distance" />
62 <when value="mlst" /> 67 <when value="mlst">
68 <param name="mlsttype" type="select"
69 label="Select the format of export">
70 <option value="default" selected="true">Default format</option>
71 <option value="grapetree">Grapetree format</option>
72 </param>
73 </when>
63 <when value="gene" /> 74 <when value="gene" />
64 </conditional> 75 </conditional>
65 <param name="mincover" type="integer" value="0" 76 <param name="mincover" type="integer" value="0"
66 optional="true" 77 optional="true"
67 label="Minimun number of strain found to keep a gene" /> 78 label="Minimun number of strain found to keep a gene" />