annotate cdhit_macros.xml @ 0:54d811ad2b52 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty

<macros>
  <xml name="requirements">
      <requirements>
        <requirement type="package" version="4.6.4">cd-hit</requirement>
      </requirements>
    </xml>

  <template name="common_cdhit_options">
    #if $advanced.settings == 'yes':

      #if str($advanced.band_width) != 'None':
        -b $advanced.band_width
      #end if

      #if str($advanced.throw_away_len) != 'None':
        -l $advanced.throw_away_len
      #end if

      #if str($advanced.description_len) != 'None':
        -d $advanced.description_len
      #end if

      #if str($advanced.cutoff_diff_len) != 'None':
        -s $advanced.cutoff_diff_len
      #end if

      #if str($advanced.aa_cutoff_diff_len) != 'None':
        -S $advanced.aa_cutoff_diff_len
      #end if

      #if $advanced.align.style == 'local':
        -G 0
        #if str($advance.align.align_coverage_long) != 'None':
          -aL $advance.align.align_coverage_long
        #end if

        #if str($advance.align.align_coverage_long_control) != 'None':
          -AL $advance.align.align_coverage_long_control
        #end if

        #if str($advance.aling.align_coverage_short) != 'None':
          -aS $advance.align.align_coverage_short
        #end if

        #if str($advance.aling.align_coverage_short_control) != 'None':
          -AS $advance.align.align_coverage_short_control
        #end if

        #if str($advance.align.align_coverage_min) != 'None':
          -A $advance.align.aling_coverage_min
        #end if
      #end if
    #end if 

    #if $print_alignment:
      $print_alignment
    #end if

    #if $cluster_type:
      $cluster_type
    #end if

    \$CDHIT_SITE_OPTIONS

    -T \${GALAXY_SLOTS:-1}
  </template>

  <macro name="common_cdhit_options">
    <conditional name="advanced">
      <param name="settings" type="select" label="Use advanced settings?">
        <option value="no" selected="true">No</option>
        <option value="yes">Yes</option>
      </param>

      <when value="no"/>

      <when value="yes">
        <param name="band_width" type="integer" value="20" optional="true" label="Alignment band width" min="1" help="(-b)"/>

        <param name="throw_away_len" type="integer" value="10" optional="true" label="Length of throw away sequences" min="1" help="(-l)"/>

        <param name="description_len" type="integer" value="20" optional="true" label="Length of the description" min="0" help="If set to 0, it takes the fasta defline and stops at first space (-d)"/>

        <param name="cutoff_diff_len" type="float" value="0.0" optional="true" label="Length difference cutoff" min="0.0" max="1.0" help="If set to 0.9, the shorter sequences need to be at least 90% length of the representative of the cluster (-s)"/>

        <param name="aa_cutoff_diff_len" type="integer" value="999999" optional="true" label="Length difference cutoff in amino acid" min="0" help="If set to 60, the length difference between the shorter sequences and the representative of the cluster can not be bigger than 60 (-S)"/>

        <conditional name="align">
          <param name="style" type="select" label="global or local alignments" help="Local sequence identity, calculated as : number of identical amino acids in alignment divided by the length of the alignment. You must set alignment coverage by length or fraction.">
            <option value="global" selected="true">Global</option>
            <option value="local" >Local</option>
          </param>

          <when value="global"/>

          <when value="local">
	             <param name="align_coverage_long" type="float" value="0.0" optional="true" label="Alignment coverage for the longer sequence" min="0.0" max="1.0" help="If set to 0.9, the alignment must covers 90% of the sequence (-aL)"/>
	
	             <param name="align_coverage_long_control" type="integer" value="99999999" optional="true" label="Alignment coverage control for the longer sequence " min="0" help="If set to 60, and the sequence's length 400,then the alignment must be at least 340 (400-60) residues (-AL)"/>
	    
	             <param name="align_coverage_short" type="float" value="0.0" optional="true" label="Alignment coverage for the shorter sequence" min="0.0" max="1.0" help="As for the longer (-aS)"/>
	    
	             <param name="align_coverage_short_control" type="integer" value="99999999" optional="true" label="Alignment coverage control for the shorter sequence" min="0" help="As for the longer (-AS)"/>
	    
	             <param name="align_coverage_min" type="integer" value="0" optional="true" label="Minimal alignment coverage control for the both sequences" min="0" help="Alignment must cover at least this value for both sequences (-A)"/>
          </when>
        </conditional>
      </when>
    </conditional>

    <param name="print_alignment" type="boolean" truevalue="-p 1" falsevalue="" checked="false" label="Print alignment overlap in .clstr file"/>

    <param name="cluster_type" type="boolean" truevalue="-g 1" falsevalue="" checked="false" label="Slow Cluster" help="In cd-hit's default algorithm, a sequence is clustered to the first cluster that meet the threshold (fast cluster). If set to slow, the program will cluster it into the most similar cluster that meet the threshold (accurate but slow mode). This won't change the representatives of final clusters (-g)"/>
  </macro>

</macros>