comparison bowtie2_macros.xml @ 33:f76cbb84d67f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a

32:d5ceb9f3c25b

<macros>
    <token name="@TOOL_VERSION@">2.5.3</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <!-- Import this at the top of your command block and then
         define rg_auto_name. -->
    <token name="@define_read_group_helpers@">
#def identifier_or_name($input1)
    #if hasattr($input1, 'element_identifier')

    -->
    <token name="@set_read_group_vars@">
#if $use_rg
    #if $rg_param('read_group_id_conditional') is None
        #set $rg_id = $rg_auto_name
    #elif $rg_param('read_group_id_conditional').do_auto_name
        #set $rg_id = $rg_auto_name
    #else
        #set $rg_id = str($rg_param('read_group_id_conditional').ID)
    #end if

    #if $rg_param('read_group_sm_conditional') is None
        #set $rg_sm = ''
    #elif $rg_param('read_group_sm_conditional').do_auto_name
        #set $rg_sm = $rg_auto_name
    #else
        #set $rg_sm = str($rg_param('read_group_sm_conditional').SM)
    #end if

        #set $rg_pl = ''
    #end if

    #if $rg_param('read_group_lb_conditional') is None
        #set $rg_lb = ''
    #elif $rg_param('read_group_lb_conditional').do_auto_name
        #set $rg_lb = $rg_auto_name
    #else
        #set $rg_lb = str($rg_param('read_group_lb_conditional').LB)
    #end if

    </token>
    <token name="@set_use_rg_var@">
#set $use_rg = str($rg.rg_selector) != "do_not_set"
    </token>
    <xml name="read_group_auto_name_conditional">
        <param name="do_auto_name" type="boolean" label="Auto-assign" help="Use dataset name or collection information to automatically assign this value" checked="false" />
        <when value="true">
        </when>
        <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">

    </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">

    </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>
    <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" />

                <expand macro="read_group_inputs_picard" />
            </when>
            <when value="set">
                <expand macro="read_group_inputs_spec" />
            </when>
            <when value="set_id_auto">
            </when>
            <when value="do_not_set">
            </when>
        </conditional>
    </xml>
    <xml name="paired_end_options">
        <conditional name="paired_options">
            <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information">

33:f76cbb84d67f

<macros>
    <token name="@TOOL_VERSION@">2.5.4</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">23.0</token>
    <!-- Import this at the top of your command block and then
         define rg_auto_name. -->
    <token name="@define_read_group_helpers@">
#def identifier_or_name($input1)
    #if hasattr($input1, 'element_identifier')

    -->
    <token name="@set_read_group_vars@">
#if $use_rg
    #if $rg_param('read_group_id_conditional') is None
        #set $rg_id = $rg_auto_name
    #elif $rg_param('read_group_id_conditional').do_auto_name == "yes"
        #set $rg_id = $rg_auto_name
    #else
        #set $rg_id = str($rg_param('read_group_id_conditional').ID)
    #end if

    #if $rg_param('read_group_sm_conditional') is None
        #set $rg_sm = ''
    #elif $rg_param('read_group_sm_conditional').do_auto_name == "yes"
        #set $rg_sm = $rg_auto_name
    #else
        #set $rg_sm = str($rg_param('read_group_sm_conditional').SM)
    #end if

        #set $rg_pl = ''
    #end if

    #if $rg_param('read_group_lb_conditional') is None
        #set $rg_lb = ''
    #elif $rg_param('read_group_lb_conditional').do_auto_name == "yes"
        #set $rg_lb = $rg_auto_name
    #else
        #set $rg_lb = str($rg_param('read_group_lb_conditional').LB)
    #end if

    </token>
    <token name="@set_use_rg_var@">
#set $use_rg = str($rg.rg_selector) != "do_not_set"
    </token>
    <xml name="read_group_auto_name_conditional">
        <param name="do_auto_name" type="select" optional="false" label="Auto-assign" help="Use dataset name or collection information to automatically assign this value">
            <option value="yes">Yes</option>
            <option value="no" selected="true">No</option>
        </param>
        <when value="yes"/>
        <when value="no">
            <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">
            <validator type="empty_field" />
        </param>
    </xml>
    <xml name="read_group_id_conditional">
        <conditional name="read_group_id_conditional">

    </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)" 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)"/>
    </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)">
            <validator type="empty_field" />
        </param>
    </xml>
    <xml name="read_group_lb_required_conditional">
        <conditional name="read_group_lb_conditional">

    </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" 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>
    <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)" />
    </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)" />
    </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" />

                <expand macro="read_group_inputs_picard" />
            </when>
            <when value="set">
                <expand macro="read_group_inputs_spec" />
            </when>
            <when value="set_id_auto"/>
            <when value="do_not_set"/>
        </conditional>
    </xml>
    <xml name="paired_end_options">
        <conditional name="paired_options">
            <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information">