Mercurial > repos > geco-team > gmql_queries_composer
annotate gmql_operators_merge_union_diff.xml @ 0:a80c93182db3 draft default tip
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
author | geco-team |
---|---|
date | Tue, 26 Jun 2018 09:08:06 -0400 |
parents | |
children |
rev | line source |
---|---|
0
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
1 <macros> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
2 <import>gmql_queries_macros.xml</import> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
3 <xml name="merge"> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
4 <expand macro="input_var" name="input_var" label="Input Dataset" optional="false" /> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
5 <expand macro="output_var" /> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
6 <section name="groupby" title="Group Samples" expanded="true" |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
7 help="Grouping metadata attributes can be specified: the samples are then partitioned in groups, |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
8 each with a distinct value of the grouping metadata attributes, and the MERGE operation is applied to each |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
9 group separately, yielding to one sample in the result dataset for each group. Samples without the grouping |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
10 metadata attributes are disregarded"> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
11 <repeat name="group_meta_atts" min="0" title="Metadata Attribute"> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
12 <expand macro="metajoin_attribute" name="j_att" optional="true" > |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
13 <expand macro="metajoin_options" /> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
14 </expand> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
15 </repeat> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
16 </section> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
17 <expand macro="materialize_stm" /> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
18 </xml> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
19 <xml name="union"> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
20 <expand macro="input_var" name="input_var_first" label="First Dataset to be unified" optional="false" /> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
21 <expand macro="input_var" name="input_var_second" label="Second Dataset to be unified" optional="false" /> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
22 <expand macro="output_var" /> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
23 <expand macro="materialize_stm" /> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
24 </xml> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
25 <xml name="difference"> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
26 <param name="input_var_reference" label="Reference Dataset" type="text" |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
27 help="It is he dataset which is copied in the output and from which regions of DS neg are “subtracted”. |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
28 Must be a dataset variable already defined as output of a previous operation."> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
29 <expand macro="text_val" /> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
30 </param> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
31 <param name="input_var_negative" label="Dataset to subtract from Reference" type="text" |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
32 help="If any reference region is found to have intersection with a region in this dataset, it is removed from |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
33 the output dataset. Must be a dataset variable already defined as output of a previous operation."> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
34 <expand macro="text_val" /> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
35 </param> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
36 <param name="exact_flag" label="Exact matching?" type="boolean" help="If selected, regions are not kept in |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
37 the result only if they exactly matches regions in the reference dataset." /> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
38 <section name="joinby" title="Joinby Conditions" expanded="true" |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
39 help="If attributes are specified, only samples that have the same value for each attributeare considered |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
40 when performing the DIFFERENCE."> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
41 <repeat name="group_meta_atts" min="0" title="Metadata Attribute"> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
42 <expand macro="metajoin_attribute" name="j_att" optional="true" > |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
43 <expand macro="metajoin_options" /> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
44 </expand> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
45 </repeat> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
46 </section> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
47 <expand macro="output_var" /> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
48 <expand macro="materialize_stm" /> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
49 </xml> |
a80c93182db3
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
geco-team
parents:
diff
changeset
|
50 </macros> |