comparison multigps.xml @ 26:0c48a4ed47a0 draft

Uploaded

25:b3eef7e04ea9

inputs_path = sys.argv[1]
params = json.load(open(inputs_path, 'r'))
condition_repeat = params['condition_repeat']
fh = open('design.tabular', 'w')
fh.write('%s\n' % str(params))
"""
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.file_name, '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.file_name, '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="signal_repeat" title="Signal" min="1">
                <param name="signal" type="data" format="bam,bed,scidx" label="Select signal" help="Supported formats are bam, bed and scidx">
                    <validator type="unspecified_build" />
                </param>
                <expand macro="param_experiment_type" />
                <param name="replicate_name" type="text" label="Replicate name" />
                <expand macro="cond_fixedreadcount" />
            </repeat>
            <repeat name="control_repeat" title="Control" min="0">
                <param name="control" type="data" format="bam,bed,scidx" label="Select control" help="Optional, supported formats are bam, bed and scidx">
                    <validator type="unspecified_build" />
                </param>
                <expand macro="param_experiment_type" />
                <conditional name="specify_replicate_name_cond">
                    <param  name="specify_replicate_name" type="select" label="Specify replicate name?" help="Optional for control.  If used, the control will only be used for the corresponding named signal replicate">
                        <option value="no" selected="True">No</option>
                        <option value="yes">Yes</option>
                    </param>

            title = {Normalization of ChIP-seq data with control},
            year = {2012},}
        </citation>
    </citations>
</tool>

26:0c48a4ed47a0

inputs_path = sys.argv[1]
params = json.load(open(inputs_path, 'r'))
condition_repeat = params['condition_repeat']
fh = open('design.tabular', 'w')
fh.write('%s\n' % str(params))
for condition_items in condition_repeat:
    for signal_items in condition_items['signal_repeat']:
        signal = signal_items['signal']
        condition_name = signal_items['condition_name']
        replicate_name = signal_items['replicate_name']
        experiment_type = signal['experiment_type']
        line_items = [signal.file_name, 'Signal', signal.ext.upper(), condition_name, 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']
        condition_name = control_items['condition_name']
        line_items = [control.file_name, 'Control', control.ext.upper(), condition_name]
        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="signal_repeat" title="Signal" min="1">
                <param name="signal" type="data" format="bam,bed,scidx" label="Select signal" help="Supported formats are bam, bed and scidx">
                    <validator type="unspecified_build" />
                </param>
                <expand macro="param_experiment_type" />
                <param name="condition_name" type="text" label="Condition name" />
                <param name="replicate_name" type="text" label="Replicate name" />
                <expand macro="cond_fixedreadcount" />
            </repeat>
            <repeat name="control_repeat" title="Control" min="0">
                <param name="control" type="data" format="bam,bed,scidx" label="Select control" help="Optional, supported formats are bam, bed and scidx">
                    <validator type="unspecified_build" />
                </param>
                <expand macro="param_experiment_type" />
                <param name="condition_name" type="text" label="Condition name" />
                <conditional name="specify_replicate_name_cond">
                    <param  name="specify_replicate_name" type="select" label="Specify replicate name?" help="Optional for control.  If used, the control will only be used for the corresponding named signal replicate">
                        <option value="no" selected="True">No</option>
                        <option value="yes">Yes</option>
                    </param>

            title = {Normalization of ChIP-seq data with control},
            year = {2012},}
        </citation>
    </citations>
</tool>