Mercurial > repos > melpetera > batchcorrection
diff BC/macros.xml @ 4:23314e1192d4 draft default tip
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author | melpetera |
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date | Thu, 14 Jan 2021 09:56:58 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BC/macros.xml Thu Jan 14 09:56:58 2021 +0000 @@ -0,0 +1,44 @@ +<?xml version="1.0"?> +<macros> + + <xml name="sm_customisation"> + <section name="smcust" title="Sample metadata file coding parameters" expanded="False"> + <param name="batch_col_name" label="Batch column name" type="text" size="64" value="batch" help="The name of the column containing the batch values."/> + <param name="injection_order_col_name" label="Injection order column name" type="text" size="64" value="injectionOrder" help="The name of the column containing the injection order values."/> + <param name="sample_type_col_name" label="Sample type column name" type="text" size="64" value="sampleType" help="The name of the column containing the sample type values."/> + <param name="sampleTypeTagPool" type="text" size="64" value="pool" label="Set the name used to tag samples as pool in the sample type column."/> + <param name="sampleTypeTagBlank" type="text" size="64" value="blank" label="Set the name used to tag samples as blank in the sample type column."/> + <param name="sampleTypeTagSample" type="text" size="64" value="sample" label="Set the name used to tag samples as real sample in the sample type column."/> + </section> + </xml> + + <token name="@SM_CUSTOM@"> + batch_col_name "$smcust.batch_col_name" + injection_order_col_name "$smcust.injection_order_col_name" + sample_type_col_name "$smcust.sample_type_col_name" + sample_type_tags "blank=$smcust.sampleTypeTagBlank,pool=$smcust.sampleTypeTagPool,sample=$smcust.sampleTypeTagSample" + </token> + + <xml name="foi"> + <param name="ref_factor" label="Factor of interest " type="text" value="batch" help="Column name of a factor of interest in the sampleMatadata table (if none, fill with the batch column name). Used for graphical display only; this factor does not affect correction calculation." /> + </xml> + + <xml name="lll_span"> + <param name="span" type="float" value="1" label="span" help="It is an advanced option; strictly > 0 and maximum to 1."/> + </xml> + + <xml name="lll_options"> + <param name="valnull" label="Unconsistant values" type="select" display="radio" help="What to do of generated negative or infinite values"> + <option value="none">Prevent it: normalisation term reset to adequate minimum one</option> + <option value="0">Consider it as a null intensity ('0')</option> + <option value="NA">Consider it as a missing value ('NA')</option> + </param> + <expand macro="foi"/> + <param name="detail" label="Level of details for plots " type="select" help="Amount of plots in the pdf file output. See Help section for more details."> + <option value="no">basic</option> + <option value="plot">standard</option> + <option value="reg">complete</option> + </param> + </xml> + +</macros>