Mercurial > repos > iuc > ampvis2_merge_ampvis2
annotate macros.xml @ 4:a14326f1e7df draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
author | iuc |
---|---|
date | Fri, 16 Aug 2024 08:59:54 +0000 |
parents | d8334b328618 |
children |
rev | line source |
---|---|
0
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
1 <macros> |
2
78ff575ef835
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
iuc
parents:
1
diff
changeset
|
2 <token name="@TOOL_VERSION@">2.8.6</token> |
4
a14326f1e7df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
parents:
3
diff
changeset
|
3 <token name="@VERSION_SUFFIX@">2</token> |
0
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
4 <token name="@PROFILE@">22.01</token> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
5 <xml name="header"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
6 <xrefs> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
7 <xref type="bio.tools">ampvis</xref> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
8 </xrefs> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
9 <requirements> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
10 <requirement type="package" version="@TOOL_VERSION@">r-ampvis2</requirement> |
2
78ff575ef835
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
iuc
parents:
1
diff
changeset
|
11 <requirement type="package" version="2.1.5">r-readr</requirement> |
78ff575ef835
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
iuc
parents:
1
diff
changeset
|
12 <requirement type="package" version="1.46.0">bioconductor-phyloseq</requirement> |
0
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
13 </requirements> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
14 <version_command><![CDATA[ |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
15 echo $(R --version | grep "R version")", ampvis2 version" $(R --vanilla --slave -e "library(ampvis2, quietly = TRUE); sessionInfo()\$otherPkgs\$ampvis2\$Version" 2> /dev/null | grep -v -i "WARNING: ") |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
16 ]]></version_command> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
17 |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
18 </xml> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
19 <xml name="citations"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
20 <citations> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
21 <citation type="doi">10.1101/299537</citation> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
22 <yield/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
23 </citations> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
24 </xml> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
25 |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
26 <xml name="rds_input_macro" token_multiple="false"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
27 <param argument="data" type="data" format="ampvis2" multiple="@MULTIPLE@" label="Ampvis2 RDS dataset" help="Generated with ampvis2: load"/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
28 </xml> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
29 |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
30 <xml name="rds_metadata_input_macro" token_metadata_optional="true"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
31 <expand macro="rds_input_macro"/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
32 <param name="metadata_list" type="data" optional="@METADATA_OPTIONAL@" format="tabular" label="Metadata list"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
33 <validator type="expression" message="The metadatalist file must have 3 columns"><![CDATA[value.metadata.columns == 4]]></validator> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
34 </param> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
35 </xml> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
36 |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
37 <token name="@SAVE_TAX_LIST@"><![CDATA[ |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
38 for(level in colnames(data\$tax)){ |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
39 for(u in unique(data\$tax[level])){ |
2
78ff575ef835
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
iuc
parents:
1
diff
changeset
|
40 write(paste(u, level, sep="\t"), file="$taxonomy_list_out", append=T) |
0
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
41 } |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
42 } |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
43 ]]></token> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
44 |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
45 <token name="@SAVE_METADATA_LIST@"><![CDATA[ |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
46 classes <- sapply(data\$metadata, class) |
4
a14326f1e7df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
parents:
3
diff
changeset
|
47 data\$metadata[is.na(data\$metadata)] <- "NA" ##the comparison below fails if NA values are present, see https://stackoverflow.com/questions/7355187/error-in-if-while-condition-missing-value-where-true-false-needed |
0
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
48 for(name in names(data\$metadata)){ |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
49 ## check if it is the column containing the sample names |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
50 ## the additional column in the ist file can the be used |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
51 ## to filter SampleIDs from select inputs |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
52 ## (check for character columns only .. since data in the column is otherwise converted to the corresponding type .. which fails) |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
53 if(classes[[name]] == "character" && all(data\$metadata[[name]] == rownames(data\$metadata))){ |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
54 sample_names <- TRUE; |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
55 }else{ |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
56 sample_names <- FALSE; |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
57 } |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
58 for(m in unique(data\$metadata[[name]])){ |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
59 write(paste(name, m, sample_names, classes[[name]], sep="\t"), file="$metadata_list_out", append=T); |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
60 } |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
61 } |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
62 ]]></token> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
63 |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
64 <!-- defaults can be set by redefining an on option with selected="true" --> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
65 <xml name="taxlevel_macro" token_argument="" token_multiple="false" token_optional="false" token_label="" token_help=""> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
66 <param argument="@ARGUMENT@" type="select" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
67 <option value="OTU">OTU/ASV</option> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
68 <option value="Species">Species</option> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
69 <option value="Genus">Genus</option> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
70 <option value="Family">Family</option> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
71 <option value="Order">Order</option> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
72 <option value="Class">Class</option> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
73 <option value="Phylum">Phylum</option> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
74 <option value="Kingdom">Kingdom</option> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
75 <yield/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
76 </param> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
77 </xml> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
78 |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
79 <xml name="tax_empty_macro"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
80 <param argument="tax_empty" type="select" label="How to show OTUs without taxonomic information"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
81 <option value="remove">Remove OTUs without taxonomic information</option> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
82 <option value="best" selected="true">Use the best classification possible</option> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
83 <option value="OTU">Display the OTU name</option> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
84 </param> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
85 </xml> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
86 |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
87 <token name="@TAX_SHOW@"><![CDATA[ |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
88 #if $tax_show_cond.tax_show_sel == "number" |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
89 tax_show = $tax_show_cond.tax_show, |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
90 #else |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
91 #set tax_show_list='c("' + '", "'.join(str($tax_show_cond.tax_show).split(",")) + '")' |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
92 tax_show = $tax_show_list |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
93 #end if |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
94 ]]></token> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
95 <xml name="tax_show_macro" token_value=""> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
96 <conditional name="tax_show_cond"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
97 <param name="tax_show_sel" type="select" label="Limit the number of shown taxa"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
98 <option value="number">Select a number of taxa to show</option> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
99 <option value="explicit">Manually select taxa to show</option> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
100 </param> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
101 <when value="number"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
102 <param argument="tax_show" type="integer" value="@VALUE@" min="1" label="Number of taxa to show"/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
103 </when> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
104 <when value="explicit"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
105 <param name="taxonomy_list" format="tabular" type="data" optional="false" label="Taxonomy list" help="Generated with ampvis2: load"/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
106 <param argument="tax_show" type="select" multiple="true" optional="false" label="Taxa to show"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
107 <options from_dataset="taxonomy_list"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
108 <column name="name" index="0"/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
109 <column name="value" index="0"/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
110 <!-- TODO filter by tax_aggregate level? --> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
111 </options> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
112 </param> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
113 </when> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
114 </conditional> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
115 </xml> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
116 |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
117 <xml name="metadata_select" token_quote="__" tokens="argument,label" token_an="argument" token_optional="true" token_multiple="false" token_help=""> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
118 <param __AN__="__ARGUMENT__" type="select" optional="__OPTIONAL__" multiple="__MULTIPLE__" label="__LABEL__" help="In order to select values a metadata list needs to be selected first. __HELP__"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
119 <options from_dataset="metadata_list"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
120 <column name="name" index="0"/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
121 <column name="value" index="0"/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
122 <filter type="unique_value" column="0"/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
123 <yield name="options"/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
124 </options> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
125 <yield/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
126 </param> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
127 </xml> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
128 |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
129 <xml name="metadata_select_discrete" tokens="argument,label" token_optional="true" token_multiple="false" token_help=""> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
130 <expand macro="metadata_select" argument="@ARGUMENT@" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
131 <token name="options"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
132 <filter type="static_value" column="3" value="numeric" keep="false"/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
133 </token> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
134 <yield/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
135 </expand> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
136 </xml> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
137 |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
138 <xml name="metadata_select_numeric" tokens="argument,label" token_optional="true" token_multiple="false" token_help=""> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
139 <expand macro="metadata_select" argument="@ARGUMENT@" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
140 <token name="options"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
141 <filter type="static_value" column="3" value="character" keep="false"/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
142 <filter type="static_value" column="3" value="Date" keep="false"/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
143 </token> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
144 <yield/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
145 </expand> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
146 </xml> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
147 |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
148 <xml name="metadata_select_date" tokens="argument,label" token_optional="true" token_multiple="false" token_help=""> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
149 <expand macro="metadata_select" argument="@ARGUMENT@" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
150 <token name="options"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
151 <filter type="static_value" column="3" value="Date" keep="true"/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
152 </token> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
153 <yield/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
154 </expand> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
155 </xml> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
156 |
2
78ff575ef835
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
iuc
parents:
1
diff
changeset
|
157 <!-- metadata_sample_or_variable_select is currently unused (heatmap is documented to allow normalize by |
78ff575ef835
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
iuc
parents:
1
diff
changeset
|
158 sample or variable, but only sample seems possible https://github.com/KasperSkytte/ampvis2/issues/168 |
78ff575ef835
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
iuc
parents:
1
diff
changeset
|
159 leaving it for now in case it can be fixed .. then metadata_sample_select could be removed) --> |
0
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
160 <xml name="metadata_sample_select" token_argument=""> |
2
78ff575ef835
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
iuc
parents:
1
diff
changeset
|
161 <param argument="@ARGUMENT@" type="select" optional="true"> |
78ff575ef835
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
iuc
parents:
1
diff
changeset
|
162 <options from_dataset="metadata_list"> |
78ff575ef835
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
iuc
parents:
1
diff
changeset
|
163 <column name="name" index="1"/> |
78ff575ef835
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
iuc
parents:
1
diff
changeset
|
164 <column name="value" index="1"/> |
78ff575ef835
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
iuc
parents:
1
diff
changeset
|
165 <filter type="static_value" value="TRUE" column="2"/> <!-- filter samples --> |
78ff575ef835
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
iuc
parents:
1
diff
changeset
|
166 <filter type="unique_value" column="1"/> |
78ff575ef835
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
iuc
parents:
1
diff
changeset
|
167 </options> |
78ff575ef835
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
iuc
parents:
1
diff
changeset
|
168 </param> |
78ff575ef835
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
iuc
parents:
1
diff
changeset
|
169 </xml> |
78ff575ef835
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
iuc
parents:
1
diff
changeset
|
170 <xml name="metadata_sample_or_variable_select" token_argument=""> |
0
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
171 <conditional name="@ARGUMENT@_cond"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
172 <param name="@ARGUMENT@_sel" type="select"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
173 <option value="no">No</option> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
174 <option value="variable">Metadata variable</option> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
175 <option value="sample">Specific sample</option> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
176 </param> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
177 <when value="no"/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
178 <when value="variable"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
179 <expand macro="metadata_select" argument="@ARGUMENT@" label="Metadata variable"/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
180 </when> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
181 <when value="sample"> |
2
78ff575ef835
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
iuc
parents:
1
diff
changeset
|
182 <expand macro="metadata_sample_select"/> |
0
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
183 </when> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
184 </conditional> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
185 </xml> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
186 |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
187 <xml name="taxonomy_select_macro" token_argument="" token_optional="false" token_multiple="true"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
188 <param argument="@ARGUMENT@" type="select" optional="@OPTIONAL@" multiple="@MULTIPLE@"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
189 <options from_dataset="taxonomy_list"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
190 <column name="name" index="0"/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
191 <column name="value" index="0"/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
192 <filter type="unique_value" column="0"/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
193 </options> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
194 <yield/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
195 </param> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
196 </xml> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
197 |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
198 <xml name="facet_scales_macro" token_argument="" token_label="Scales of the facets" token_help=""> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
199 <param argument="@ARGUMENT@" type="select" optional="true" label="@LABEL@" help="@HELP@"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
200 <option value="fixed">Same scale</option> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
201 <option value="free">Free scale</option> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
202 <option value="free_x">Free x-scale</option> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
203 <option value="free_y">Free y-scale</option> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
204 </param> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
205 </xml> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
206 |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
207 <token name="@OUTPUT_TOKEN@"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
208 ggsave("$plot", |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
209 print(plot), |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
210 device="$output_options.out_format" |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
211 #if str($output_options.plot_width) != '' |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
212 , width = $output_options.plot_width |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
213 #end if |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
214 #if str($output_options.plot_height) != '' |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
215 , height = $output_options.plot_height |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
216 #end if |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
217 ) |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
218 </token> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
219 <xml name="out_macro" token_name="plot" token_label=""> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
220 <data name="@NAME@" format="pdf" label="${tool.name} on ${on_string}@LABEL@"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
221 <yield/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
222 <change_format> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
223 <when input="output_options.out_format" value="png" format="png" /> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
224 <when input="output_options.out_format" value="svg" format="svg" /> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
225 </change_format> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
226 </data> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
227 </xml> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
228 <xml name="out_format_macro"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
229 <section name="output_options" title="Output options" expanded="false"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
230 <param name="out_format" type="select" label="Output format"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
231 <option value="pdf" selected="true">PDF</option> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
232 <option value="png">PNG</option> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
233 <option value="svg">SVG</option> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
234 <yield/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
235 </param> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
236 <param name="plot_width" type="float" value="" min="1" optional="true" label="Plot width in cm"/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
237 <param name="plot_height" type="float" value="" min="1" optional="true" label="Plot height in cm"/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
238 </section> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
239 </xml> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
240 |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
241 <token name="@RAREFY_TOKEN@"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
242 #if str($rarefy) != "" |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
243 , rarefy = $rarefy |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
244 #end if |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
245 </token> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
246 <xml name="rarefy_macro" token_help=""> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
247 <param argument="rarefy" type="integer" optional="true" value="" min="0" label="Rarefy species richness to this value" help="@HELP@"/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
248 </xml> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
249 |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
250 <xml name="normalise_macro" token_checked="false"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
251 <param argument="normalise" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="@CHECKED@" label="Normalise read counts" help="Transform the OTU read counts to be in percent per sample."/> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
252 </xml> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
253 |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
254 <token name="@HELP_RDS_INPUT@"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
255 An ampvis2 RDS dataset obtained by the ``ampvis2: load`` tool (or ``ampvis2: mergereplicates`` or one of the |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
256 ``ampvis2: subset ...`` tools). |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
257 </token> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
258 <token name="@HELP_METADATA_LIST_INPUT@"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
259 The metadata list output of the ``ampvis2: load`` tool (or ``ampvis2: mergereplicates`` or the |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
260 ``ampvis2: subset sample`` tool). This input is only used for providing |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
261 values to the parameters alowing to select metadata variables or values. |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
262 </token> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
263 |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
264 <token name="@HELP_RELATIVE_ABUNDANCES@"> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
265 Preserving relative abundances in a subset of larger data |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
266 ========================================================= |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
267 |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
268 By default the raw read counts in the abundance matrix are normalised |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
269 (transformed to percentages) by some ampvis2 plotting tools (for |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
270 example ``ampvis2: heatmap``, ``ampvis2: timeseries``, and more). |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
271 If this is applied to data generated by one of the ``ampvis2: subset ...`` tools |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
272 this means that the relative |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
273 abundances shown will be calculated based on the remaining taxa after the |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
274 subset, not including the removed taxa, if any. To circumvent this, enable |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
275 ``normalise`` when subsetting with the ``ampvis2: subset ...``` tools, |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
276 and then disable ``normalise`` in the plotting tool. This will |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
277 transform the OTU counts to relative abundances BEFORE the subset. |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
278 </token> |
028ba7c0b400
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
iuc
parents:
diff
changeset
|
279 </macros> |