Mercurial > repos > bvalot > pymlst
comparison wgmlst_export.xml @ 1:5b2c48fa0175 draft
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" /> |