annotate wgmlst_export.xml @ 1:5b2c48fa0175 draft

planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b

<tool id="wgmlst_export_wrapper" name="Export result of cg/wgMLST database"
	  version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
  <description></description>
  <macros>
    <import>macro.xml</import>
  </macros>
  <expand macro="requirements" />
  <stdio>
    <exit_code range="1:" level="fatal" />
  </stdio>
  <version_command>wgMLST -v</version_command>
  <command>
    wgMLST 
	#if $export_result.export == "distance"
	  distance
	#end if
	#if $export_result.export == "mlst"
	  mlst
	  #if $export_result.mlsttype == "grapetree"
	  -f grapetree
	  #end if
	#end if
	#if $export_result.export == "strain"
	  strain
	  #if $export_result.count
	    -c
	  #end if
	#end if
	#if $export_result.export == "gene"
	  gene
	#end if
	#if str($mincover)
      -m $mincover
    #end if
    #if $keep
      -k
    #end if
    #if $inverse
      -V
    #end if
    #if $duplicate
      -d
    #end if
	'${database}'
	> '${$output}'
	#if $log
	  2> '${logfile}'
	#end if
  </command>
  <inputs>
	<param name="database" type="data"
           format="sqlite"
           label="cg/wgMLST database"
           help="Sqlite format from cg/wgMLST database" />
	<conditional name="export_result">
      <param name="export" type="select" label="Select the data export">
		<option value="distance" selected="true">Distance matrix between strains on the cg/wgMLST database</option>
		<option value="mlst">cg/wgMLST table for each strain on the cg/wgMLST database</option>
		<option value="strain">List of the strains on the cg/wgMLST database</option>
		<option value="gene">List of the genes on the cg/wgMLST database</option>
      </param>
      <when value="strain">
		<param name="count" type="boolean" checked="false"
               label="Report the number of gene found for each strain" />
      </when>
	  <when value="distance" />
	  <when value="mlst">
		<param name="mlsttype" type="select"
			   label="Select the format of export">
		  <option value="default" selected="true">Default format</option>
		  <option value="grapetree">Grapetree format</option>
		</param>
	  </when>
	  <when value="gene" />
	</conditional>
	<param name="mincover" type="integer" value="0"
           optional="true"
           label="Minimun number of strain found to keep a gene" />
	<param name="keep" type="boolean" checked="false"
           label="Keep only gene with different allele" help="Omit missing" />
	<param name="duplicate" type="boolean" checked="false"
           label="Conserve duplicate gene (default remove)" />
	<param name="inverse" type="boolean" checked="false"
           label="Keep only gene that not meet the filter of mincover or keep options" />
	<param name="log" type="boolean" checked="false"
           label="Write log file" />
  </inputs>
  <outputs>
	<data name="output" format="txt" label="Extract ${export_result.export} on ${database.name}">
      <change_format>
        <when input="export_result.export" value="mlst" format="tabular" />
        <when input="export_result.export" value="distance" format="txt" />
        <when input="export_result.export" value="strain" format="tabular" />
        <when input="export_result.export" value="gene" format="txt" />
      </change_format>
    </data>
    <data name="logfile" format="txt" label="${export_result.export} of ${database.name}: log">
	  <filter>log</filter>
	</data>
  </outputs>
  <tests>
	<test expect_num_outputs="1">
      <param name="database" value="wgmlst_ecoli.db" />
	  <conditional name="export_result">
		<param name="export" value="distance" />
	  </conditional>
	  <param name="mincover" value="4" />
      <output name="output" ftype="txt" file="wgmlst_ecoli.db.distance" />
    </test>
	<test expect_num_outputs="1">
      <param name="database" value="wgmlst_ecoli.db" />
	  <conditional name="export_result">
		<param name="export" value="mlst" />
	  </conditional>
	  <param name="keep" value="true" />
      <output name="output" ftype="tabular" file="wgmlst_ecoli.db.mlst" />
	</test>
	<test expect_num_outputs="2">
      <param name="database" value="wgmlst_ecoli.db" />
	  <conditional name="export_result">
		<param name="export" value="strain" />
		<param name="count" value="true" />
	  </conditional>
	  <param name="log" value="true" />
      <output name="output" ftype="tabular" file="wgmlst_ecoli.db.strain" />
	</test>
	<test expect_num_outputs="1">
      <param name="database" value="wgmlst_ecoli.db" />
	  <conditional name="export_result">
		<param name="export" value="gene" />
	  </conditional>
	  <param name="keep" value="true" />
	  <param name="inverse" value="true" />	  
      <output name="output" ftype="txt" file="wgmlst_ecoli.db.gene" />
    </test>
  </tests>
  <help>
**What it does**

Extract element from a cg/wgMLST DATABASE:
  - an distance matrix
  - an MLST table
  - a gene list
  - an strains list

Options:
  -m, --mincover INTEGER  Minimun number of strain found to keep a gene
                          (default:0)
  -k, --keep              Keep only gene with different allele (omit missing).
  -d, --duplicate         Conserve duplicate gene (default remove).
  -V, --inverse           Keep only gene that do not meet the filter of
                          mincover or keep options.

  -c, --count             Count the number of gene present in the database for
                          each strains.

**License and citation**

This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
  </help>
  <citations>
  </citations>
</tool>