Mercurial > repos > geco-team > gmql_queries_composer
comparison gmql_operators_group.xml @ 0:a80c93182db3 draft default tip
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
author | geco-team |
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date | Tue, 26 Jun 2018 09:08:06 -0400 |
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1 <macros> | |
2 <import>gmql_queries_macros.xml</import> | |
3 <xml name="group"> | |
4 <expand macro="input_var" name="input_var" label="Input Dataset" optional="false" /> | |
5 <expand macro="output_var" /> | |
6 <conditional name="add_grouping"> | |
7 <param name="group_type" type="select" label="Additional Grouping Options" | |
8 help="If the defualt option is set, it will group only on the region attributes which represent | |
9 the four genomic coordinates (chr, start, stop, and strand). Inside a single sample, it collapses | |
10 all regions that have equal values in these four coordinates into a single one, thus eliminating duplicate regions" > | |
11 <option value="default">Only default attributes (genomic coordinates)</option> | |
12 <option value="meta">Group also on metadata attributes</option> | |
13 <option value="regions">Group also on other region attributes and/or create new region fields with aggregate functions</option> | |
14 <option value="both">Group also on both metadata and other regions attributes</option> | |
15 </param> | |
16 <when value="default"> | |
17 <!-- do nothing --> | |
18 </when> | |
19 <when value="meta"> | |
20 <expand macro="metadata_options" /> | |
21 </when> | |
22 <when value="regions"> | |
23 <expand macro="region_options" /> | |
24 </when> | |
25 <when value="both"> | |
26 <expand macro="metadata_options" /> | |
27 <expand macro="region_options" /> | |
28 </when> | |
29 </conditional> | |
30 <expand macro="materialize_stm" /> | |
31 </xml> | |
32 <xml name="region_options"> | |
33 <section name="regions" title="Additional grouping options over region attributes" expanded="true" | |
34 help="In each sample, regions found in the same group (i.e., regions with same coordinates and | |
35 grouping attribute values), are combined into a single region; this allows to merge regions that are | |
36 duplicated inside the same sample (based on the values of their coordinates and of other possible | |
37 specified region attributes)"> | |
38 <repeat name="group_regions_atts" min="0" title="Grouping Region Attribute"> | |
39 <param name="attribute" type="text" label="Region Attribute"> | |
40 <expand macro="text_val" /> | |
41 <validator type="expression" message="Coordinate attributes are already used by default">value not in ['chr','left','right','strand']</validator> | |
42 </param> | |
43 </repeat> | |
44 <expand macro="att_generator" title="Aggregate Region Attribute" min="0"/> | |
45 </section> | |
46 </xml> | |
47 <xml name="metadata_options"> | |
48 <section name="metadata" title="Grouping Options over metadata attributes" expanded="true" | |
49 help="GROUP performs the grouping of samples of the input dataset based on one specified metadata | |
50 attribute. If the metadata attribute is multi-value, the grouping identifies different groups of | |
51 samples for each attribute value combination. All metadata in the input samples are conserved, | |
52 with the addition of the _group attribute, whose value is the identifier of the group to which | |
53 the specific sample is assigned. Samples having missing values for any of the grouping metadata | |
54 attributes are assigned all together to one group, identified by the special value _group = 0"> | |
55 <repeat name="group_meta_atts" min="1" title="Grouping Metadata Attribute"> | |
56 <expand macro="metajoin_attribute" name="j_att" optional="true" > | |
57 <expand macro="metajoin_options" /> | |
58 </expand> | |
59 </repeat> | |
60 <conditional name="meta_agg"> | |
61 <param name="meta_agg_flag" type="boolean" label="Create new aggregate attributes?" | |
62 help="It is possible to request the evaluation of aggregate functions on metadata attributes; | |
63 these functions consider the metadata contained in all samples of each group" /> | |
64 <when value="true"> | |
65 <expand macro="att_generator" title="Aggregate Metadata Attribute" min="1" /> | |
66 </when> | |
67 </conditional> | |
68 </section> | |
69 </xml> | |
70 <xml name="att_generator" token_title="@TITLE@" token_min="@MIN@"> | |
71 <repeat name="new_attributes" title="@TITLE@" min="@MIN@"> | |
72 <param name="new_name" type="text" label="New Attribute Name"> | |
73 <expand macro="text_val"/> | |
74 </param> | |
75 <expand macro="aggrFuncs" help="Sum, average, maximum, minimum and standard deviation are only for numerical | |
76 attributes" optional="false" label="Aggregate Function to apply" /> | |
77 <param name="argument" label="Attributes over which apply function" type="text"> | |
78 <expand macro="text_val"/> | |
79 </param> | |
80 </repeat> | |
81 </xml> | |
82 </macros> |