comparison samtools_mpileup.xml @ 7:bfc4517aa037 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_mpileup commit a1517c9d22029095120643bbe2c8fa53754dd2b7

6:820754ab8901

<tool id="samtools_mpileup" name="MPileup" version="2.1">
    <description>call variants</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

    #if $reference_source.reference_source_selector != "history":
        -f "${reference_source.ref_file.fields.path}"
    #else:
        -f "${reference_source.ref_file}"
    #end if
    #for $i, $input_bam in enumerate( $reference_source.input_bams ):
        "${input_bam.input_bam}"
    #end for
    #if str( $advanced_options.advanced_options_selector ) == "advanced":
        #if str( $advanced_options.filter_by_flags.filter_flags ) == "filter":
            #if $advanced_options.filter_by_flags.require_flags:
                --rf ${sum([int(flag) for flag in str($advanced_options.filter_by_flags.require_flags).split(',')])}

        -q "${advanced_options.minimum_mapping_quality}"
        -Q "${advanced_options.minimum_base_quality}"
        #if str( $advanced_options.region_string ):
            -r "${advanced_options.region_string}"
        #end if
        
    #end if
    #if str( $genotype_likelihood_computation_type.genotype_likelihood_computation_type_selector ) == 'perform_genotype_likelihood_computation':
        ##

        ${genotype_likelihood_computation_type.output_format}
        ${genotype_likelihood_computation_type.compressed}
        
        #if str( $genotype_likelihood_computation_type.output_tags ) != "None":
            --output-tags "${genotype_likelihood_computation_type.output_tags}"
        #end if

        #if str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'perform_indel_calling':

                -P "${ ",".join( [ str( platform.platform_entry ) for platform in $genotype_likelihood_computation_type.perform_indel_calling.platform_list_repeat ] ) }"
            #end if
        #elif str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'do_not_perform_indel_calling':
            -I
        #end if
        
         
    #else:
        ${genotype_likelihood_computation_type.base_position_on_reads}
        ${genotype_likelihood_computation_type.output_mapping_quality}
    #end if
    --output "$output_mpileup" 2> "$output_log"

            <param label="Choose the source for the reference genome" name="reference_source_selector" type="select">
                <option value="cached">Use a built-in genome</option>
                <option value="history">Use a genome from the history</option>
            </param>
            <when value="cached">
                <repeat min="1" name="input_bams" title="BAM file">
                    <param format="bam" label="BAM file" name="input_bam" type="data">
                        <validator type="unspecified_build" />
                        <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="fasta_indexes" type="dataset_metadata_in_data_table" />
                    </param>
                </repeat>
                <param label="Using reference genome" name="ref_file" type="select">
                    <options from_data_table="fasta_indexes" />
                </param>
            </when>
            <when value="history">
                <repeat min="1" name="input_bams" title="BAM file">
                    <param format="bam" label="BAM file" name="input_bam" type="data">
                        <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
                    </param>
                </repeat>
                <param format="fasta" label="Using reference genome" name="ref_file" type="data" />
            </when>
        </conditional>
        <conditional name="genotype_likelihood_computation_type">
            <param label="Genotype Likelihood Computation" name="genotype_likelihood_computation_type_selector" type="select">

                            <param label="Platform to use for INDEL candidates" name="platform_entry" type="text" value="" help="It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA"/>
                        </repeat>
                    </when>
                    <when value="do_not_perform_indel_calling" />
                </conditional>
                
            </when>
            <when value="do_not_perform_genotype_likelihood_computation">
                <param checked="False" falsevalue="" label="Output base positions on reads" name="base_position_on_reads" truevalue="-O" type="boolean" help="--output-BP"/>
                <param checked="False" falsevalue="" label="Output mapping quality" name="output_mapping_quality" truevalue="-s" type="boolean" help="--output-MQ"/>
            </when>

    </tests>
    <help>
<![CDATA[
**What it does**

Report variants for one or multiple BAM files. Alignment records are grouped by sample identifiers in @RG header lines. If sample identifiers are absent, each input file is regarded as one sample. 

------

**Input options**::

7:bfc4517aa037

<tool id="samtools_mpileup" name="MPileup" version="2.1.1">
    <description>call variants</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

    #if $reference_source.reference_source_selector != "history":
        -f "${reference_source.ref_file.fields.path}"
    #else:
        -f "${reference_source.ref_file}"
    #end if
    #for $bam in $reference_source.input_bam:
        "${bam}"
    #end for
    #if str( $advanced_options.advanced_options_selector ) == "advanced":
        #if str( $advanced_options.filter_by_flags.filter_flags ) == "filter":
            #if $advanced_options.filter_by_flags.require_flags:
                --rf ${sum([int(flag) for flag in str($advanced_options.filter_by_flags.require_flags).split(',')])}

        -q "${advanced_options.minimum_mapping_quality}"
        -Q "${advanced_options.minimum_base_quality}"
        #if str( $advanced_options.region_string ):
            -r "${advanced_options.region_string}"
        #end if

    #end if
    #if str( $genotype_likelihood_computation_type.genotype_likelihood_computation_type_selector ) == 'perform_genotype_likelihood_computation':
        ##

        ${genotype_likelihood_computation_type.output_format}
        ${genotype_likelihood_computation_type.compressed}

        #if str( $genotype_likelihood_computation_type.output_tags ) != "None":
            --output-tags "${genotype_likelihood_computation_type.output_tags}"
        #end if

        #if str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'perform_indel_calling':

                -P "${ ",".join( [ str( platform.platform_entry ) for platform in $genotype_likelihood_computation_type.perform_indel_calling.platform_list_repeat ] ) }"
            #end if
        #elif str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'do_not_perform_indel_calling':
            -I
        #end if


    #else:
        ${genotype_likelihood_computation_type.base_position_on_reads}
        ${genotype_likelihood_computation_type.output_mapping_quality}
    #end if
    --output "$output_mpileup" 2> "$output_log"

            <param label="Choose the source for the reference genome" name="reference_source_selector" type="select">
                <option value="cached">Use a built-in genome</option>
                <option value="history">Use a genome from the history</option>
            </param>
            <when value="cached">
                <param format="bam" label="BAM file(s)" name="input_bam" type="data" min="1" multiple="True">
                    <validator type="unspecified_build" />
                    <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="fasta_indexes" type="dataset_metadata_in_data_table" />
                </param>
                <param label="Using reference genome" name="ref_file" type="select">
                    <options from_data_table="fasta_indexes" />
                </param>
            </when>
            <when value="history">
                <param format="bam" label="BAM file(s)" name="input_bam" type="data" min="1" multiple="True">
                    <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
                </param>
                <param format="fasta" label="Using reference genome" name="ref_file" type="data" />
            </when>
        </conditional>
        <conditional name="genotype_likelihood_computation_type">
            <param label="Genotype Likelihood Computation" name="genotype_likelihood_computation_type_selector" type="select">

                            <param label="Platform to use for INDEL candidates" name="platform_entry" type="text" value="" help="It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA"/>
                        </repeat>
                    </when>
                    <when value="do_not_perform_indel_calling" />
                </conditional>

            </when>
            <when value="do_not_perform_genotype_likelihood_computation">
                <param checked="False" falsevalue="" label="Output base positions on reads" name="base_position_on_reads" truevalue="-O" type="boolean" help="--output-BP"/>
                <param checked="False" falsevalue="" label="Output mapping quality" name="output_mapping_quality" truevalue="-s" type="boolean" help="--output-MQ"/>
            </when>

    </tests>
    <help>
<![CDATA[
**What it does**

Report variants for one or multiple BAM files. Alignment records are grouped by sample identifiers in @RG header lines. If sample identifiers are absent, each input file is regarded as one sample.

------

**Input options**::