comparison phyml.xml @ 12:7f2fdaeaa723 draft

Uploaded

11:b0d5f7b87402

    <stdio>
        <regex match="*"
               source="stdrr"
               level="fatal"/>
    </stdio>

    <command><![CDATA[
          ##PhyML outputs are based on input path and we need to create outputs in working_dir.
          ln -sf $input '${input.name}';
         
          phyml --input '${input.name}'
                ${phylip_format}
                --datatype ${seq.type_of_seq}
                --multiple ${nb_data_set}
                

                --search ${move}
                -o ${optimisationTopology}
                
                #if ($usetree.inputTree == "true"):
                    --inputtree ${inputTree.userInputTree}
                #end if
                
                #if ($numStartSeed != "0"):
                    --r_seed ${numStartSeed}
                #end if
                
                --no_memory_check
                --quiet > ${output_stdout};
                grep 'failed' ${output_stdout} >&2;
            ]]>
    </command>
    <inputs>
        <param name="input" type="data" format="phylip, phy" label="Alignment file" help="phylip format"/>
        <param name="phylip_format" type="select"  label="Changes interleaved format" display="radio">
            <option value="">Interleaved</option>

12:7f2fdaeaa723

    <stdio>
        <regex match="*"
               source="stdrr"
               level="fatal"/>
    </stdio>
    <command>
        <![CDATA[
          ##PhyML outputs are based on input path and we need to create outputs in working_dir.
          ln -sf $input '${input.name}';
          #if ($usetree.inputTree == "true"):
          ln -sf ${$usetree.userInputTree} ${$usetree.userInputTree.name};
          #end if

          phyml --input '${input.name}'
                ${phylip_format}
                --datatype ${seq.type_of_seq}
                --multiple ${nb_data_set}
                

                --search ${move}
                -o ${optimisationTopology}
                
                #if ($usetree.inputTree == "true"):
                    --inputtree ${$usetree.userInputTree.name}
                #end if
                
                #if ($numStartSeed != "0"):
                    --r_seed ${numStartSeed}
                #end if
                
                --no_memory_check > ${output_stdout};
                grep 'failed' ${output_stdout} >&2;
        ]]>
    </command>
    <inputs>
        <param name="input" type="data" format="phylip, phy" label="Alignment file" help="phylip format"/>
        <param name="phylip_format" type="select"  label="Changes interleaved format" display="radio">
            <option value="">Interleaved</option>