comparison roary.xml @ 3:15ca041134a9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 9c9db9f5e815e6a9b55c4adf378c7aa6a76a58da"

2:f1ccc8a6eb05

<tool id="roary" name="Roary" version="3.10.2">
    <description>the pangenome pipeline - Quickly generate a core gene alignment from gff3 files</description>
    
    <requirements>
      <requirement type="package" version="3.10.2">roary</requirement>
    </requirements>
    
    <command detect_errors="exit_code"><![CDATA[
        
        #for $counter, $gff in enumerate($gff_input.gffs)
          cp $gff temp${counter}.gff &&
        #end for
                
        roary
          -f out 
          -p \${GALAXY_SLOTS:-1}
          -e
          -n
          -i '$percent_ident'
          -cd '$core_diff'
          -g '$advanced.maxclust'
          $advanced.split_para
          -t '$advanced.trans_tab'
          -iv '$advanced.mcl'
          
          temp*.gff
          
    ]]></command>
    
    <inputs>
      <conditional name="gff_input">
        <param name="gff_input_selector" type="select" label="Individual gff files or a dataset collection" help="Select between individual gff files or a collection of gff files">
          <option value="individual">Individual</option>
          <option value="collection">Collection</option>
        </param>
        <when value="individual">
          <param name="gffs" type="data" multiple="true" format="gff3" label="select gff inputs to Roary" help="Select the files you wish to send to Roary, must be in gff3 format with the sequence data at the end of the file." />
        </when>
        <when value='collection'>
          <param name="gffs" type="data_collection" collection_type="list" format="gff3" label="Dataset collection to submit to Roary" help="A dataset list collection of gff3 files to send to Roary for analysis." />
        </when>
      </conditional>
      <param name="percent_ident" type="integer" label="minimum percentage identity for blastp" help="Sets the minimum percentage identity for protein matches" value="95"/>
      <param name="core_diff" type="float" label="percentage of isolates a gene must be in to be core" help="The total percentage of the isolates that must have the gene for it to be considered a core gene." value="99.0"/>
      

For further info see: http://sanger-pathogens.github.io/Roary/
    
    ]]></help>
    
    <citations>
        <citation type="doi">http://doi.org/10.1093/bioinformatics/btv421</citation>
    </citations>
    
</tool>

3:15ca041134a9

<tool id="roary" name="Roary" version="3.12.0+galaxy0">
    <description>the pangenome pipeline - Quickly generate a core gene alignment from gff3 files</description>
    
    <requirements>
      <requirement type="package" version="3.12.0">roary</requirement>
    </requirements>
    
    <command detect_errors="exit_code"><![CDATA[
        
        #for $gff in $gff_input.gffs
          cp $gff '${gff.element_identifier}'.gff &&
        #end for

        roary
          -f out
          -p \${GALAXY_SLOTS:-1}
          -e
          -n
          -i '$percent_ident'
          -cd '$core_diff'
          -g '$advanced.maxclust'
          $advanced.split_para
          -t '$advanced.trans_tab'
          -iv '$advanced.mcl'

          *.gff
          
    ]]></command>
    
    <inputs>
      <conditional name="gff_input">
        <param name="gff_input_selector" type="select" label="Individual gff files or a dataset collection" help="Select between individual gff files or a collection of gff files">
          <option value="individual">Individual</option>
          <option value="collection">Collection</option>
        </param>
        <when value="individual">
          <param name="gffs" type="data" multiple="true" format="gff,gff3" label="select gff inputs to Roary" help="Select the files you wish to send to Roary, must be in gff3 format with the sequence data at the end of the file." />
        </when>
        <when value='collection'>
          <param name="gffs" type="data_collection" collection_type="list" format="gff,gff3" label="Dataset collection to submit to Roary" help="A dataset list collection of gff3 files to send to Roary for analysis." />
        </when>
      </conditional>
      <param name="percent_ident" type="integer" label="minimum percentage identity for blastp" help="Sets the minimum percentage identity for protein matches" value="95"/>
      <param name="core_diff" type="float" label="percentage of isolates a gene must be in to be core" help="The total percentage of the isolates that must have the gene for it to be considered a core gene." value="99.0"/>
      

For further info see: http://sanger-pathogens.github.io/Roary/
    
    ]]></help>
    
    <citations>
        <citation type="doi">10.1093/bioinformatics/btv421</citation>
    </citations>
    
</tool>