comparison samtools_mpileup.xml @ 13:9da0311ab1dd draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 1354b1358df89a922c3243f7e27ce789094b8644"

12:329deb17a9f7

<tool id="samtools_mpileup" name="Samtools mpileup" version="2.1.5" profile="@PROFILE@">
    <description>multi-way pileup of variants</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

                -l '$advanced_options.limit_by_region.bed_regions'
            #end if
        #end if

        #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste":
            -G '$excluded_read_groups'
        #elif str( $advanced_options.exclude_read_group.exclude_read_groups ) == "history"
            -G '$advanced_options.exclude_read_group.read_groups'
        #end if
        ${advanced_options.ignore_overlaps}
        ${advanced_options.skip_anomalous_read_pairs}

            <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>
        <expand macro="mandatory_reference" argument="-f"/>
        <conditional name="advanced_options">
            <param name="advanced_options_selector" type="select" label="Set advanced options">
                <option selected="True" value="default">Basic</option>
                <option value="advanced">Advanced</option>
            </param>
            <when value="default" />
            <when value="advanced">
                <conditional name="filter_by_flags">
                    <param name="filter_flags" type="select" label="Set filter by flags">
                        <option selected="True" value="nofilter">Do not filter</option>
                        <option value="filter">Filter by flags to exclude or require</option>
                    </param>
                    <when value="filter">
                        <param name="require_flags" argument="--rf/--incl-flags" type="select" multiple="True" display="checkboxes" label="Require">
                            <expand  macro="flag_options" />
                        </param>
                        <param name="exclude_flags" argument="--ff/--excl-flags" type="select" multiple="True" display="checkboxes" label="Exclude">
                            <expand  macro="flag_options" s4="true" s256="true" s512="true" s1024="true"/>
                        </param>
                    </when>
                    <when value="nofilter" />
                </conditional>
                <conditional name="limit_by_region">
                    <param name="limit_by_regions" type="select" label="Select regions to call">
                        <option selected="True" value="no_limit">Do not limit</option>
                        <option value="limit">Specify regions</option>
                    </param>
                    <when value="limit">
                        <param name="bed_regions" argument="-l/--positions" type="data" format="bed" optional="true" label="skip unlisted positions (chr pos) or regions">
                            <validator type="dataset_ok_validator" />

                </conditional>


                <conditional name="exclude_read_group">
                    <param name="exclude_read_groups" argument="-R/--exclude-RG" type="select" label="Select read groups to exclude">
                        <option selected="True" value="no_limit">Do not exclude</option>
                        <option value="history">From a text file</option>
                        <option value="paste">Paste a list of read groups</option>
                    </param>
                    <when value="history">
                        <param name="read_groups" type="data" format="txt" label="Text file">

                <param name="qualities_illumina_onethree" argument="-6/--illumina1.3+" type="boolean" truevalue="-6" falsevalue="" checked="False" label="quality is in the Illumina-1.3+ encoding"/>
            </when>
        </conditional>
        <conditional name="output_options_cond">
            <param name="output_options_selector" type="select" label="Output options">
                <option selected="True" value="default">Default</option>
                <option value="advanced">Advanced</option>
            </param>
            <when value="default"/>
            <when value="advanced">
                <param name="base_position_on_reads" argument="-O/--output-BP" type="boolean" truevalue="-O" falsevalue="" checked="False" label="Output base positions on reads" />
                <param name="output_mapping_quality" argument="-s/--output-MQ" type="boolean" truevalue="-s" falsevalue="" checked="False" label="Output mapping quality" />
                <param name="output_read_names" argument="--output-QNAME" type="boolean" truevalue="--output-QNAME" falsevalue="" checked="False" label="Output an extra column containing comma-separated read names. (--output-QNAME)" />
                <param name="output_all_pos" argument="-a" type="select" label="Output absolutely all positions" help="Output all positions, including those with zero depth. (-a) Output absolutely all positions, including unused reference sequences (-aa). Note that when used in conjunction with a BED file the -a option may sometimes operate as if -aa was specified if the reference sequence has coverage outside of the region specified in the BED file.">
                    <option selected="True" value="">No</option>
                    <option value="-a">all (including those with zero depth)</option>
                    <option value="-aa">absolutely all (including unused reference sequences)</option>
                </param>
                <param name="output_tags" type="text" argument="--output-extra" label="Add tags to output" help="Output extra read fields and read tag values, e.g., NM and XS (must be comma seperated, e.g., NM,XS)" />
            </when>

13:9da0311ab1dd

<tool id="samtools_mpileup" name="Samtools mpileup" version="2.1.6" profile="@PROFILE@">
    <description>multi-way pileup of variants</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

                -l '$advanced_options.limit_by_region.bed_regions'
            #end if
        #end if

        #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste":
            -G '$$advanced_options.exclude_read_group.group_paste'
        #elif str( $advanced_options.exclude_read_group.exclude_read_groups ) == "history"
            -G '$advanced_options.exclude_read_group.read_groups'
        #end if
        ${advanced_options.ignore_overlaps}
        ${advanced_options.skip_anomalous_read_pairs}

            <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>
        <expand macro="mandatory_reference" argument="-f"/>
        <conditional name="advanced_options">
            <param name="advanced_options_selector" type="select" label="Set advanced options">
                <option selected="true" value="default">Basic</option>
                <option value="advanced">Advanced</option>
            </param>
            <when value="default" />
            <when value="advanced">
                <conditional name="filter_by_flags">
                    <param name="filter_flags" type="select" label="Set filter by flags">
                        <option selected="true" value="nofilter">Do not filter</option>
                        <option value="filter">Filter by flags to exclude or require</option>
                    </param>
                    <when value="filter">
                        <param name="require_flags" argument="--rf/--incl-flags" type="select" multiple="true" display="checkboxes" label="Require">
                            <expand  macro="flag_options" />
                        </param>
                        <param name="exclude_flags" argument="--ff/--excl-flags" type="select" multiple="true" display="checkboxes" label="Exclude">
                            <expand  macro="flag_options" s4="true" s256="true" s512="true" s1024="true"/>
                        </param>
                    </when>
                    <when value="nofilter" />
                </conditional>
                <conditional name="limit_by_region">
                    <param name="limit_by_regions" type="select" label="Select regions to call">
                        <option selected="true" value="no_limit">Do not limit</option>
                        <option value="limit">Specify regions</option>
                    </param>
                    <when value="limit">
                        <param name="bed_regions" argument="-l/--positions" type="data" format="bed" optional="true" label="skip unlisted positions (chr pos) or regions">
                            <validator type="dataset_ok_validator" />

                </conditional>


                <conditional name="exclude_read_group">
                    <param name="exclude_read_groups" argument="-R/--exclude-RG" type="select" label="Select read groups to exclude">
                        <option selected="true" value="no_limit">Do not exclude</option>
                        <option value="history">From a text file</option>
                        <option value="paste">Paste a list of read groups</option>
                    </param>
                    <when value="history">
                        <param name="read_groups" type="data" format="txt" label="Text file">

                <param name="qualities_illumina_onethree" argument="-6/--illumina1.3+" type="boolean" truevalue="-6" falsevalue="" checked="False" label="quality is in the Illumina-1.3+ encoding"/>
            </when>
        </conditional>
        <conditional name="output_options_cond">
            <param name="output_options_selector" type="select" label="Output options">
                <option selected="true" value="default">Default</option>
                <option value="advanced">Advanced</option>
            </param>
            <when value="default"/>
            <when value="advanced">
                <param name="base_position_on_reads" argument="-O/--output-BP" type="boolean" truevalue="-O" falsevalue="" checked="False" label="Output base positions on reads" />
                <param name="output_mapping_quality" argument="-s/--output-MQ" type="boolean" truevalue="-s" falsevalue="" checked="False" label="Output mapping quality" />
                <param name="output_read_names" argument="--output-QNAME" type="boolean" truevalue="--output-QNAME" falsevalue="" checked="False" label="Output an extra column containing comma-separated read names. (--output-QNAME)" />
                <param name="output_all_pos" argument="-a" type="select" label="Output absolutely all positions" help="Output all positions, including those with zero depth. (-a) Output absolutely all positions, including unused reference sequences (-aa). Note that when used in conjunction with a BED file the -a option may sometimes operate as if -aa was specified if the reference sequence has coverage outside of the region specified in the BED file.">
                    <option selected="true" value="">No</option>
                    <option value="-a">all (including those with zero depth)</option>
                    <option value="-aa">absolutely all (including unused reference sequences)</option>
                </param>
                <param name="output_tags" type="text" argument="--output-extra" label="Add tags to output" help="Output extra read fields and read tag values, e.g., NM and XS (must be comma seperated, e.g., NM,XS)" />
            </when>