Mercurial > repos > melpetera > batchcorrection
comparison BC/macros.xml @ 4:23314e1192d4 draft default tip
Uploaded
author | melpetera |
---|---|
date | Thu, 14 Jan 2021 09:56:58 +0000 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
3:73892ef177e3 | 4:23314e1192d4 |
---|---|
1 <?xml version="1.0"?> | |
2 <macros> | |
3 | |
4 <xml name="sm_customisation"> | |
5 <section name="smcust" title="Sample metadata file coding parameters" expanded="False"> | |
6 <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."/> | |
7 <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."/> | |
8 <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."/> | |
9 <param name="sampleTypeTagPool" type="text" size="64" value="pool" label="Set the name used to tag samples as pool in the sample type column."/> | |
10 <param name="sampleTypeTagBlank" type="text" size="64" value="blank" label="Set the name used to tag samples as blank in the sample type column."/> | |
11 <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."/> | |
12 </section> | |
13 </xml> | |
14 | |
15 <token name="@SM_CUSTOM@"> | |
16 batch_col_name "$smcust.batch_col_name" | |
17 injection_order_col_name "$smcust.injection_order_col_name" | |
18 sample_type_col_name "$smcust.sample_type_col_name" | |
19 sample_type_tags "blank=$smcust.sampleTypeTagBlank,pool=$smcust.sampleTypeTagPool,sample=$smcust.sampleTypeTagSample" | |
20 </token> | |
21 | |
22 <xml name="foi"> | |
23 <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." /> | |
24 </xml> | |
25 | |
26 <xml name="lll_span"> | |
27 <param name="span" type="float" value="1" label="span" help="It is an advanced option; strictly > 0 and maximum to 1."/> | |
28 </xml> | |
29 | |
30 <xml name="lll_options"> | |
31 <param name="valnull" label="Unconsistant values" type="select" display="radio" help="What to do of generated negative or infinite values"> | |
32 <option value="none">Prevent it: normalisation term reset to adequate minimum one</option> | |
33 <option value="0">Consider it as a null intensity ('0')</option> | |
34 <option value="NA">Consider it as a missing value ('NA')</option> | |
35 </param> | |
36 <expand macro="foi"/> | |
37 <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."> | |
38 <option value="no">basic</option> | |
39 <option value="plot">standard</option> | |
40 <option value="reg">complete</option> | |
41 </param> | |
42 </xml> | |
43 | |
44 </macros> |