comparison mafft.xml @ 16:8e649f27aa0d draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 3d98df472498e1273369d23822d10db14f337443

15:bf28a8cff401

    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements" />
    <stdio>
        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
        <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
    </stdio>
    <version_command><![CDATA[mafft --version]]></version_command>
    <command><![CDATA[
  ## Concatenate all input datasets no matter how they were provided
  bash inputs.sh &&

  ## Count total number of sequences across input datasets
  ## Can't do this on the concatenated input data prepared above because it's

                    <param name="inputs" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format. Add Dataset for concatenation of every additional dataset with each file of the first upload panel"/>
                </repeat>
            </when>
            <when value="merge">
                <repeat name="batches" title="Input batch" default="1" min="1">
                    <param name="inputs" multiple="true" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/>
                </repeat>
            </when>
        </conditional>
        <conditional name="datatype_selection">
            <param name="datatype" type="select" label="Type of sequences" help="The tool can try to detect the type of the input sequences, but you likely want to declare it explicitly. Doing so will also give you control over the scoring matrix used for the alignment, while autodetection will result in the Kimura PAM200 and the BLOSUM62 matrix being used for nucleic acids and protein alignments, respectively.">

                <conditional name="scoring_matrix">
                    <param name="type" type="select" label="Type of scoring matrix" help="See the tool help below for details about the available options.">
                        <option value="--kimura">Kimura</option>
                    </param>
                    <when value="--kimura">
                        <param argument="--kimura" name="coefficient" type="integer" value="200" min="1" label="PAM value of the matrix" />
                    </when>
                </conditional>
                <expand macro="misc_scoring_scheme" />
            </when>
            <when value="--amino">

                        <option value="--jtt">JTT</option>
                        <option value="--tm">transmembrane protein-optimized JTT</option>
                        <option value="custom">custom matrix</option>
                    </param>
                    <when value="--bl">
                        <param argument="--bl" name="coefficient" type="select" display="radio" label="Coefficient of the BLOSUM matrix">
                            <option value="30">30</option>
                            <option value="45">45</option>
                            <option value="62" selected="true">62</option>
                            <option value="80">80</option>
                        </param>
                    </when>
                    <when value="--jtt">
                        <param argument="--jtt" name="coefficient" type="integer" value="200" min="1" label="PAM value of the matrix" />
                    </when>
                    <when value="--tm">
                        <param argument="--tm" name="coefficient" type="integer" value="200" min="1" label="PAM value of the matrix"/>
                    </when>
                    <when value="custom">
                        <param argument="--aamatrix" type="data" format="txt" label="User-defined AA scoring matrix" help="The expected format of the matrix is the same as that used by BLAST."/>
                    </when>
                </conditional>

                                <option value="--localpair">Local alignment (Smith-Waterman) (--localpair)</option>
                                <option value="--genafpair">Local, affine gap cost (--genafpair)</option>
                                <option value="--fastapair">All pairwise alignments are computed with FASTA (--fastapair)</option>
                            </param>
                            <when value="--6merpair">
                                <param argument="--retree" type="integer" value="2" min="1" max="3" label="Guide tree is build this number of times in the progressive stage."/>
                            </when>
                            <when value="--globalpair">
                                <expand macro="global_align_options"/>
                                <expand macro="weighti_param" />
                            </when>

                            </when>
                        </conditional>
                    </when>
                </conditional>
                <section name="progressive_alignment_calculation" title="Progressive alignment calculation" expanded="true">
                    <param argument="--maxiterate" type="integer" value="0" min="0" max="1000" label="Maximum number of iterations" help="1000 for maximum quality" />
                    <param argument="--fft" type="boolean" truevalue="--fft" falsevalue="--nofft" checked="True" label="Use FFT approximation in group-to-group alignment?" />
                    <param argument="--noscore" type="boolean" truevalue="" falsevalue="--noscore" checked="True" label="Check alignment score in the iterative refinement stage?" />
                </section>
            </when>
        </conditional>

            </conditional>
            <conditional name="flavour">
                <param name="type" value="mafft-fftns"/>
            </conditional>
            <param name="outputFormat" value="--clustalout"/>
            <output name="outputAlignment" ftype="clustal" file="mafft_explicit_amino_blosum80.clustal.aln" />
        </test>
        <test expect_num_outputs="1" >
            <conditional name="input">
                <param name="mapping" value="implicit"/>
                <repeat name="batches">

                <section name="progressive_alignment_calculation">
                    <param name="maxiterate" value="1000"/>
                </section>
            </conditional>
            <param name="outputFormat" value="--clustalout"/>
            <output name="outputAlignment" ftype="clustal" file="mafft_custom_original.clustal.aln">
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="input">
                <param name="mapping" value="implicit"/>

16:8e649f27aa0d

    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements" />
    <version_command>mafft --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
  ## Concatenate all input datasets no matter how they were provided
  bash inputs.sh &&

  ## Count total number of sequences across input datasets
  ## Can't do this on the concatenated input data prepared above because it's

                    <param name="inputs" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format. Add Dataset for concatenation of every additional dataset with each file of the first upload panel"/>
                </repeat>
            </when>
            <when value="merge">
                <repeat name="batches" title="Input batch" default="1" min="1">
                    <param name="inputs" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format." multiple="true"/>
                </repeat>
            </when>
        </conditional>
        <conditional name="datatype_selection">
            <param name="datatype" type="select" label="Type of sequences" help="The tool can try to detect the type of the input sequences, but you likely want to declare it explicitly. Doing so will also give you control over the scoring matrix used for the alignment, while autodetection will result in the Kimura PAM200 and the BLOSUM62 matrix being used for nucleic acids and protein alignments, respectively.">

                <conditional name="scoring_matrix">
                    <param name="type" type="select" label="Type of scoring matrix" help="See the tool help below for details about the available options.">
                        <option value="--kimura">Kimura</option>
                    </param>
                    <when value="--kimura">
                        <param name="coefficient" argument="--kimura" type="integer" min="1" value="200" label="PAM value of the matrix" />
                    </when>
                </conditional>
                <expand macro="misc_scoring_scheme" />
            </when>
            <when value="--amino">

                        <option value="--jtt">JTT</option>
                        <option value="--tm">transmembrane protein-optimized JTT</option>
                        <option value="custom">custom matrix</option>
                    </param>
                    <when value="--bl">
                        <param name="coefficient" argument="--bl" type="select" label="Coefficient of the BLOSUM matrix" display="radio">
                            <option value="30">30</option>
                            <option value="45">45</option>
                            <option value="62" selected="true">62</option>
                            <option value="80">80</option>
                        </param>
                    </when>
                    <when value="--jtt">
                        <param name="coefficient" argument="--jtt" type="integer" min="1" value="200" label="PAM value of the matrix" />
                    </when>
                    <when value="--tm">
                        <param name="coefficient" argument="--tm" type="integer" min="1" value="200" label="PAM value of the matrix"/>
                    </when>
                    <when value="custom">
                        <param argument="--aamatrix" type="data" format="txt" label="User-defined AA scoring matrix" help="The expected format of the matrix is the same as that used by BLAST."/>
                    </when>
                </conditional>

                                <option value="--localpair">Local alignment (Smith-Waterman) (--localpair)</option>
                                <option value="--genafpair">Local, affine gap cost (--genafpair)</option>
                                <option value="--fastapair">All pairwise alignments are computed with FASTA (--fastapair)</option>
                            </param>
                            <when value="--6merpair">
                                <param argument="--retree" type="integer" min="1" max="3" value="2" label="Guide tree is build this number of times in the progressive stage."/>
                            </when>
                            <when value="--globalpair">
                                <expand macro="global_align_options"/>
                                <expand macro="weighti_param" />
                            </when>

                            </when>
                        </conditional>
                    </when>
                </conditional>
                <section name="progressive_alignment_calculation" title="Progressive alignment calculation" expanded="true">
                    <param argument="--maxiterate" type="integer" min="0" max="1000" value="0" label="Maximum number of iterations" help="1000 for maximum quality" />
                    <param argument="--fft" type="boolean" truevalue="--fft" falsevalue="--nofft" checked="True" label="Use FFT approximation in group-to-group alignment?" />
                    <param argument="--noscore" type="boolean" truevalue="" falsevalue="--noscore" checked="True" label="Check alignment score in the iterative refinement stage?" />
                </section>
            </when>
        </conditional>

            </conditional>
            <conditional name="flavour">
                <param name="type" value="mafft-fftns"/>
            </conditional>
            <param name="outputFormat" value="--clustalout"/>
            <output name="outputAlignment" ftype="clustal" file="mafft_explicit_amino_blosum80.clustal.aln" lines_diff="2" />
        </test>
        <test expect_num_outputs="1" >
            <conditional name="input">
                <param name="mapping" value="implicit"/>
                <repeat name="batches">

                <section name="progressive_alignment_calculation">
                    <param name="maxiterate" value="1000"/>
                </section>
            </conditional>
            <param name="outputFormat" value="--clustalout"/>
            <output name="outputAlignment" ftype="clustal" file="mafft_custom_original.clustal.aln" lines_diff="2">
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="input">
                <param name="mapping" value="implicit"/>