comparison read_group_macros.xml @ 4:2589e6207cb4 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

3:52fdfc45590a

        <when value="false">
            <yield />
        </when>
    </xml>
    <xml name="read_group_id_param">
        <param name="ID" type="text" value="" size="20" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment" optional="false">
            <validator type="empty_field" />
        </param>
    </xml>
    <xml name="read_group_id_conditional">
        <conditional name="read_group_id_conditional">

                <expand macro="read_group_id_param" />
            </expand>
        </conditional>
    </xml>
    <xml name="read_group_sm_param">
        <param name="SM" type="text" value="" size="20" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced" />
    </xml>
    <xml name="read_group_sm_conditional">
        <conditional name="read_group_sm_conditional">
            <expand macro="read_group_auto_name_conditional">
                <expand macro="read_group_sm_param" />

    </xml>
    <!-- Above SM param is optional (for SAM/BAM spec, this is required
         as per Picard.
    -->
    <xml name="read_group_sm_param_required">
        <param name="SM" type="text" value="" size="20" label="Read group sample name (SM)" optional="false" help="This value should be descriptive. Use pool name where a pool is being sequenced">
            <validator type="empty_field" />
        </param>
    </xml>
    <xml name="read_group_sm_required_conditional">
        <conditional name="read_group_sm_conditional">

            <option value="IONTORRENT">IONTORRENT</option>
            <option value="PACBIO">PACBIO</option>
        </param>
    </xml>
    <xml name="read_group_lb_param">
        <param name="LB" type="text" size="25" label="Library name (LB)" optional="true" />
    </xml>
    <xml name="read_group_lb_conditional">
        <conditional name="read_group_lb_conditional">
            <expand macro="read_group_auto_name_conditional">
                <expand macro="read_group_lb_param" />
            </expand>
        </conditional>
    </xml>
    <xml name="read_group_lb_required_param">
        <param name="LB" type="text" size="25" label="Library name (LB)" optional="false">
            <validator type="empty_field" />
        </param>
    </xml>
    <xml name="read_group_lb_required_conditional">
        <conditional name="read_group_lb_conditional">

                <expand macro="read_group_lb_required_param" />
            </expand>
        </conditional>
    </xml>
    <xml name="read_group_cn_param">
        <param name="CN" type="text" size="25" label="Sequencing center that produced the read (CN)" />
    </xml>
    <xml name="read_group_ds_param">
        <param name="DS" type="text" size="25" label="Description (DS)" />
    </xml>
    <xml name="read_group_dt_param">
        <param name="DT" type="text" size="25" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" />
    </xml>
    <xml name="read_group_fo_param">
        <param name="FO" type="text" size="25" optional="true" label="Flow order (FO)" help="The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\*|[ACMGRSVTWYHKDBN]+/">
          <validator type="regex" message="Invalid flow order">\*|[ACMGRSVTWYHKDBN]+$</validator>
        </param>
    </xml>
    <xml name="read_group_ks_param">
        <param name="KS" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" />
    </xml>
    <xml name="read_group_pg_param">
        <param name="PG" type="text" size="25" label="Programs used for processing the read group (PG)" />
    </xml>
    <xml name="read_group_pi_param">
        <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" />
    </xml>
    <xml name="read_group_pu_param">
        <param name="PU" type="text" size="25" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" />
    </xml>
    <xml name="read_group_pu_required_param">
        <param name="PU" type="text" size="25" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" />
    </xml>
    <!-- Only ID is required - all groups available -->
    <xml name="read_group_inputs_spec">
        <expand macro="read_group_id_conditional" />
        <expand macro="read_group_sm_conditional" />

4:2589e6207cb4

        <when value="false">
            <yield />
        </when>
    </xml>
    <xml name="read_group_id_param">
        <param name="ID" type="text" value="" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment" optional="false">
            <validator type="empty_field" />
        </param>
    </xml>
    <xml name="read_group_id_conditional">
        <conditional name="read_group_id_conditional">

                <expand macro="read_group_id_param" />
            </expand>
        </conditional>
    </xml>
    <xml name="read_group_sm_param">
        <param name="SM" type="text" value="" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced" />
    </xml>
    <xml name="read_group_sm_conditional">
        <conditional name="read_group_sm_conditional">
            <expand macro="read_group_auto_name_conditional">
                <expand macro="read_group_sm_param" />

    </xml>
    <!-- Above SM param is optional (for SAM/BAM spec, this is required
         as per Picard.
    -->
    <xml name="read_group_sm_param_required">
        <param name="SM" type="text" value="" label="Read group sample name (SM)" optional="false" help="This value should be descriptive. Use pool name where a pool is being sequenced">
            <validator type="empty_field" />
        </param>
    </xml>
    <xml name="read_group_sm_required_conditional">
        <conditional name="read_group_sm_conditional">

            <option value="IONTORRENT">IONTORRENT</option>
            <option value="PACBIO">PACBIO</option>
        </param>
    </xml>
    <xml name="read_group_lb_param">
        <param name="LB" type="text" label="Library name (LB)" optional="true" />
    </xml>
    <xml name="read_group_lb_conditional">
        <conditional name="read_group_lb_conditional">
            <expand macro="read_group_auto_name_conditional">
                <expand macro="read_group_lb_param" />
            </expand>
        </conditional>
    </xml>
    <xml name="read_group_lb_required_param">
        <param name="LB" type="text" label="Library name (LB)" optional="false">
            <validator type="empty_field" />
        </param>
    </xml>
    <xml name="read_group_lb_required_conditional">
        <conditional name="read_group_lb_conditional">

                <expand macro="read_group_lb_required_param" />
            </expand>
        </conditional>
    </xml>
    <xml name="read_group_cn_param">
        <param name="CN" type="text" label="Sequencing center that produced the read (CN)" />
    </xml>
    <xml name="read_group_ds_param">
        <param name="DS" type="text" label="Description (DS)" />
    </xml>
    <xml name="read_group_dt_param">
        <param name="DT" type="text" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" />
    </xml>
    <xml name="read_group_fo_param">
        <param name="FO" type="text" optional="true" label="Flow order (FO)" help="The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\*|[ACMGRSVTWYHKDBN]+/">
          <validator type="regex" message="Invalid flow order">\*|[ACMGRSVTWYHKDBN]+$</validator>
        </param>
    </xml>
    <xml name="read_group_ks_param">
        <param name="KS" type="text" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" />
    </xml>
    <xml name="read_group_pg_param">
        <param name="PG" type="text" label="Programs used for processing the read group (PG)" />
    </xml>
    <xml name="read_group_pi_param">
        <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" />
    </xml>
    <xml name="read_group_pu_param">
        <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" />
    </xml>
    <xml name="read_group_pu_required_param">
        <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" />
    </xml>
    <!-- Only ID is required - all groups available -->
    <xml name="read_group_inputs_spec">
        <expand macro="read_group_id_conditional" />
        <expand macro="read_group_sm_conditional" />