comparison ob_filter.xml @ 12:340f8d63c1f4 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"

11:da0059ee548a

    <command detect_errors="aggressive">
<![CDATA[
    python '$__tool_directory__/ob_filter.py'
      -i '${infile}'
      -o '${outfile}'
      -iformat '${infile.ext}'
      -oformat '${infile.ext}'
      #if $filter_methods.filter_methods_opts == "__filter_by_name__":
          --list_of_names '$name_file'
          --filters '__filter_by_name__'
      #else
          --filters '{
            #if $filter_methods.filter_methods_opts == "ruleof5":
              "hbd" : [0, 5],
              "hba" : [0, 10],
              "molwt" : [0, 500],
              "logp" : [-5, 5],
            #elif $filter_methods.filter_methods_opts == "LeadLike":
              "rotbonds" : [0, 7],
              "molwt" : [0, 350],
              "logp" : [-5, 3.5],
            #elif $filter_methods.filter_methods_opts == "DrugLike":
              "hba" : [0, 10],
              "rotbonds" : [0, 8],
              "molwt" : [150, 500],
              "logp" : [-5, 5],
              "psa" : [0, 150],
            #elif $filter_methods.filter_methods_opts == "FragmentLike":
              "rotbonds" : [0, 5],
              "molwt" : [0, 250],
              "logp" : [-5, 2.5],
            #else:
              #for $filter in $filter_methods.filter_set:
                #set $filter_selected = $filter.filter_sel.filter_sel_opts
                #set $filter_min = $filter_selected + "_min"
                #set $filter_max = $filter_selected + "_max"
                "$filter_selected" : [$filter.filter_sel[$filter_min], $filter.filter_sel[$filter_max] ],
              #end for
            #end if
          }'
        #end if
]]>
  </command>
  <inputs>

              <option value="rotbonds">Number of rotatable bonds</option>
              <option value="molwt">Molecular weight</option>
              <option value="logp">Predicted value of logP</option>
              <option value="mr">Predicted value for the molecular refractivity</option>
              <option value="atoms">Number of atoms</option>
              <!-- Add later, we need to add a new smarts pattern to plugindefines.txt
              <option value="hatoms">Number of heavy atoms</option>-->
              <!-- We skip that options, for further information please read: http://www.dalkescientific.com/writings/diary/archive/2011/06/04/dealing_with_sssr.html -->
              <!--<option value="rings">Number of rings</option>-->
            </param>

              <param name="mr_max" type="float" value="" label="Maximum threshold value for the molecular refractivity"/>
            </when>
            <when value="atoms">
              <param name="atoms_min" type="integer" value="" label="Minimum number of atoms"/>
              <param name="atoms_max" type="integer" value="" label="Maximum number of atoms"/>
            </when>
            <!--<when value="rings">
              <param name="rings_min" type="integer" value="" label="Minimum number of rings"/>
              <param name="rings_max" type="integer" value="" label="Maximum number of rings"/>
            </when>-->

    <test>
        <param name="infile" ftype="smi" value="CID_2244.smi"/>
        <param name="filter_methods_opts" value="ruleof5" />
        <output name="outfile" ftype="smi" file="ob_filter_on_CID2244.smi" />
    </test>
    <!--
    Limitation of the test framework:
    https://trello.com/card/disambiguated-conditional-parameters-not-supported-in-unit-tests/506338ce32ae458f6d15e4b3/820
    <test>
        <param name="infile" ftype="smi" value="CID_2244.smi"/>

12:340f8d63c1f4

    <command detect_errors="aggressive">
<![CDATA[
    python '$__tool_directory__/ob_filter.py'
      -i '${infile}'
      -o '${outfile}'
      -iformat "${infile.ext}"
      -oformat "${infile.ext}"
      #if $filter_methods.filter_methods_opts == "__filter_by_name__":
          --list_of_names '$name_file'
          --filters '__filter_by_name__'
      #else
        --filters '{
          #if $filter_methods.filter_methods_opts == "ruleof5":
            "hbd" : [0, 5],
            "hba" : [0, 10],
            "molwt" : [0, 500],
            "logp" : [-5, 5],
          #elif $filter_methods.filter_methods_opts == "LeadLike":
            "rotbonds" : [0, 7],
            "molwt" : [0, 350],
            "logp" : [-5, 3.5],
          #elif $filter_methods.filter_methods_opts == "DrugLike":
            "hba" : [0, 10],
            "rotbonds" : [0, 8],
            "molwt" : [150, 500],
            "logp" : [-5, 5],
            "psa" : [0, 150],
          #elif $filter_methods.filter_methods_opts == "FragmentLike":
            "rotbonds" : [0, 5],
            "molwt" : [0, 250],
            "logp" : [-5, 2.5],
          #else:
            #for $filter in $filter_methods.filter_set:
              #if $filter.filter_sel.filter_sel_opts == "field":
                #set $filter_selected = $filter.filter_sel['field_name']
                "$filter_selected": [$filter.filter_sel['field_min'], $filter.filter_sel['field_max'] ],
              #else:
                #set $filter_selected = $filter.filter_sel.filter_sel_opts
                #set $filter_min = $filter_selected + "_min"
                #set $filter_max = $filter_selected + "_max"
                "$filter_selected" : [$filter.filter_sel[$filter_min], $filter.filter_sel[$filter_max] ],
              #end if
            #end for
          #end if
          }'
        #end if
]]>
  </command>
  <inputs>

              <option value="rotbonds">Number of rotatable bonds</option>
              <option value="molwt">Molecular weight</option>
              <option value="logp">Predicted value of logP</option>
              <option value="mr">Predicted value for the molecular refractivity</option>
              <option value="atoms">Number of atoms</option>
              <option value="field">Filter by a user-defined SDF property</option>
              <!-- Add later, we need to add a new smarts pattern to plugindefines.txt
              <option value="hatoms">Number of heavy atoms</option>-->
              <!-- We skip that options, for further information please read: http://www.dalkescientific.com/writings/diary/archive/2011/06/04/dealing_with_sssr.html -->
              <!--<option value="rings">Number of rings</option>-->
            </param>

              <param name="mr_max" type="float" value="" label="Maximum threshold value for the molecular refractivity"/>
            </when>
            <when value="atoms">
              <param name="atoms_min" type="integer" value="" label="Minimum number of atoms"/>
              <param name="atoms_max" type="integer" value="" label="Maximum number of atoms"/>
            </when>
            <when value="field">
              <param name="field_name" type="text" value="" label="Name of the SDF property to filter by">
                <sanitizer invalid_char="">
                  <valid initial="string.ascii_letters,string.digits">
                    <add value="_" />
                    <add value="." />
                    <add value=" " />
                  </valid>
                </sanitizer>
              </param>
              <param name="field_min" type="integer" value="" label="Minimum value"/>
              <param name="field_max" type="integer" value="" label="Maximum value"/>
            </when>
            <!--<when value="rings">
              <param name="rings_min" type="integer" value="" label="Minimum number of rings"/>
              <param name="rings_max" type="integer" value="" label="Maximum number of rings"/>
            </when>-->

    <test>
        <param name="infile" ftype="smi" value="CID_2244.smi"/>
        <param name="filter_methods_opts" value="ruleof5" />
        <output name="outfile" ftype="smi" file="ob_filter_on_CID2244.smi" />
    </test>
    <test>
        <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
        <param name="filter_methods_opts" value="user" />
        <param name="filter_sel_opts" value="field" />
        <param name="field_name" value="PUBCHEM_EXACT_MASS"/>
        <param name="field_min" value="100"/>
        <param name="field_max" value="200"/>
        <output name="outfile" ftype="sdf" file="ob_filter_on_CID2244.sdf" lines_diff="2"/>
    </test>
    <!--
    Limitation of the test framework:
    https://trello.com/card/disambiguated-conditional-parameters-not-supported-in-unit-tests/506338ce32ae458f6d15e4b3/820
    <test>
        <param name="infile" ftype="smi" value="CID_2244.smi"/>