comparison multigps.xml @ 18:5f6b4c0fb473 draft

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17:3ea58bab5819

    <requirements>
        <requirement type="package" version="0.74">multigps</requirement>
    </requirements>
    <command detect_errors="aggressive">
        <![CDATA[
            #set design_file = '$build_design_file'
            #set output_dir = $output_html.files_path
            mkdir -p $output_dir &&
            multigps
            ## General options
            --design '$design_file'
            ## Append .txt extensions to events hrefs
            ## in output dataset so files will render
            ## in the browser.
            --eventsaretxt
            ## Do not run the parallel version of meme.

        ]]>
    </command>
    <configfiles>
        <configfile name="build_design_file">
<![CDATA[
#for $cond_i, $condition_items in enumerate($condition_repeat):
    #for $signal_items in $condition_items['signal_repeat']:
        #set signal = $signal_items['signal']
        #set replicate_name = $signal_items['replicate_name']
        #set experiment_type = $signal['experiment_type']
        #set line = str($signal) + '\t' + 'Signal' + '\t' + str($signal.ext.upper()) + '\t' + str($cond_i) + '\t' + str($replicate_name) + '\t' + str($experiment_type)
        #set fixedreadcount_cond = $signal_items['fixedreadcount_cond']
        #set fixedreadcount_select = $fixedreadcount_cond['fixedreadcount_select']
        #if str($fixedreadcount_select) == 'yes':
            #set line = $line + '\t' + str($fixedreadcount_cond['fixedreadcount'])
        #end if
        $line
    #end for
    #for $control_items in condition_items['control_repeat']:
        #set control = $control_items['control']
        #set experiment_type = $control_items['experiment_type']
        #set line = str($control_items) + '\t' + 'Control' + '\t' + str($control.ext.upper()) + '\t' + str($cond_i)
        #set specify_replicate_name_cond = $control_items['specify_replicate_name_cond']
        #set specify_replicate_name = $specify_replicate_name_cond['specify_replicate_name']
        #if str($specify_replicate_name) == 'yes':
            #set line = $line + '\t' + str($specify_replicate_name_cond['replicate_name'])
        #end if
        #set line = $line + '\t' + str($experiment_type)
        #set fixedreadcount_cond = $control_items['fixedreadcount_cond']
        #set fixedreadcount_select = $fixedreadcount_cond['fixedreadcount_select']
        #if str($fixedreadcount_select) == 'yes':
            #set line = $line + '\t' + str($fixedreadcount_cond['fixedreadcount'])
        #end if
        $line
    #end for
#end for
]]>
        </configfile>
    </configfiles>
    <inputs>
        <repeat name="condition_repeat" title="Condition" min="1">

18:5f6b4c0fb473

    <requirements>
        <requirement type="package" version="0.74">multigps</requirement>
    </requirements>
    <command detect_errors="aggressive">
        <![CDATA[
            #set output_dir = $output_html.files_path
            mkdir -p $output_dir &&
            python '$build_design_file' '$inputs' &&
            multigps
            ## General options
            --design 'design.tabular'
            ## Append .txt extensions to events hrefs
            ## in output dataset so files will render
            ## in the browser.
            --eventsaretxt
            ## Do not run the parallel version of meme.

        ]]>
    </command>
    <configfiles>
        <configfile name="build_design_file">
<![CDATA[
import json

inputs = sys.argv[1]
params = json.load(open(inputs, 'r'))
condition_repeat = params['condition_repeat']
fh = open('design.tabular', 'w')

for cond_i, condition_items in enumerate(condition_repeat):
    for signal_items in condition_items['signal_repeat']:
        signal = signal_items['signal']
        replicate_name = signal_items['replicate_name']
        experiment_type = signal['experiment_type']
        line_items = [signal, 'Signal', signal.ext.upper(), cond_i, replicate_name, experiment_type]
        fixedreadcount_cond = signal_items['fixedreadcount_cond']
        fixedreadcount_select = fixedreadcount_cond['fixedreadcount_select']
        if fixedreadcount_select == 'yes':
            line_items.append(fixedreadcount_cond['fixedreadcount'])
        fh.write('%s\n' % '\t'.join(line_items)
    for control_items in condition_items['control_repeat']:
        control = control_items['control']
        experiment_type = control_items['experiment_type']
        line_items = [control, 'Control', control.ext.upper(), cond_i]
        specify_replicate_name_cond = control_items['specify_replicate_name_cond']
        specify_replicate_name = specify_replicate_name_cond['specify_replicate_name']
        if specify_replicate_name == 'yes':
            line_items.append(specify_replicate_name_cond['replicate_name'])
        line_items.append(experiment_type)
        fixedreadcount_cond = control_items['fixedreadcount_cond']
        fixedreadcount_select = fixedreadcount_cond['fixedreadcount_select']
        if fixedreadcount_select) == 'yes':
            line_items.append(fixedreadcount_cond['fixedreadcount'])
        fh.write('%s\n' % '\t'.join(line_items)
fh.close()
]]>
        </configfile>
    </configfiles>
    <inputs>
        <repeat name="condition_repeat" title="Condition" min="1">