Mercurial > repos > devteam > column_maker
annotate column_maker.xml @ 7:e7c273e8d4d6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
author | devteam |
---|---|
date | Mon, 25 Jan 2021 09:59:49 +0000 |
parents | 0aeda7a81b46 |
children | 227e82286a0e |
rev | line source |
---|---|
7
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
1 <tool id="Add_a_column1" name="Compute" version="1.5"> |
6
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
2 <description>an expression on every row</description> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
3 <requirements> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
4 <requirement type="package" version="3.8">python</requirement> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
5 <requirement type="package" version="1.19.1">numpy</requirement> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
6 </requirements> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
7 <command detect_errors="aggressive"><![CDATA[ |
7
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
8 ln -s '$input' data && |
6
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
9 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
10 ## inject colums and column_types metadata into inputs json |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
11 #import json |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
12 #set inputs_dict = json.load(open($inputs)) |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
13 #set inputs_dict['columns'] = $input.metadata.columns |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
14 #set inputs_dict['column_types'] = $input.metadata.column_types |
7
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
15 ## flatten conditional |
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
16 #if $header_lines_conditional.header_lines_select == "yes": |
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
17 #set inputs_dict['header_new_column_name'] = str($header_lines_conditional.header_new_column_name) |
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
18 #end if |
6
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
19 #set x = json.dump($inputs_dict, open($inputs, 'w')) |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
20 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
21 python '$__tool_directory__/column_maker.py' |
7
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
22 data '$out_file1' |
6
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
23 --load_json '$inputs' |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
24 ]]></command> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
25 <configfiles> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
26 <inputs name="inputs"/> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
27 </configfiles> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
28 <inputs> |
7
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
29 <param name="cond" type="text" value="c3-c2" label="Add expression"> |
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
30 <sanitizer> |
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
31 <valid initial="default"> |
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
32 <add value="<" /> |
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
33 <add value=">" /> |
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
34 <add value=""" /> |
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
35 <add value="'" /> |
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
36 </valid> |
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
37 </sanitizer> |
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
38 </param> |
6
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
39 <param format="tabular" name="input" type="data" label="as a new column to" help="Dataset missing? See TIP below"/> |
7
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
40 <param name="round" type="boolean" truevalue="yes" falsevalue="no" label="Round result?" /> |
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
41 <param name="avoid_scientific_notation" type="boolean" truevalue="yes" falsevalue="no" |
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
42 label="Avoid scientific notation" |
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
43 help="If yes, use fully expanded decimal representation when writing new columns (use only if expression produces decimal numbers)." /> |
6
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
44 <conditional name="header_lines_conditional"> |
7
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
45 <param name="header_lines_select" type="select" |
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
46 label="Input has a header line with column names?" |
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
47 help="Select Yes to be able to specify a name for the new column and have it added to the header line. If you select No, the first line will be treated as a regular line: If it is empty or starts with a # character it will be skipped, otherwise the tool will attempt to compute the specified expression on it." > |
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
48 <option value="no" >No</option> |
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
49 <option value="yes" >Yes</option> |
6
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
50 </param> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
51 <when value="no"> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
52 </when> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
53 <when value="yes"> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
54 <param name="header_new_column_name" type="text" value="New Column" label="The new column name" /> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
55 </when> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
56 </conditional> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
57 </inputs> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
58 <outputs> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
59 <data format_source="input" name="out_file1" metadata_source="input"/> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
60 </outputs> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
61 <tests> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
62 <test> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
63 <param name="cond" value="c3-c2"/> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
64 <param name="input" value="1.bed"/> |
7
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
65 <param name="round" value="false"/> |
6
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
66 <output name="out_file1" file="column_maker_out1.interval"/> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
67 </test> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
68 <test> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
69 <param name="cond" value="c4*1"/> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
70 <param name="input" value="1.interval"/> |
7
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
71 <param name="round" value="false"/> |
6
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
72 <output name="out_file1" file="column_maker_out2.interval"/> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
73 </test> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
74 <test> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
75 <param name="cond" value="c4*1"/> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
76 <param name="input" value="1.header.tsv"/> |
7
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
77 <param name="round" value="false"/> |
6
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
78 <conditional name="header_lines_conditional"> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
79 <param name="header_lines_select" value="yes" /> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
80 <param name="header_new_column_name" value="value1_again" /> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
81 </conditional> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
82 <output name="out_file1" file="column_maker_out2.header.tsv"/> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
83 </test> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
84 <test> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
85 <param name="cond" value="c4*1"/> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
86 <param name="input" value="1.interval"/> |
7
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
87 <param name="round" value="true"/> |
6
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
88 <output name="out_file1" file="column_maker_out3.interval"/> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
89 </test> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
90 <test> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
91 <param name="cond" value="float(.0000000000001)"/> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
92 <param name="input" value="1.bed"/> |
7
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
93 <param name="round" value="false"/> |
6
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
94 <output name="out_file1"> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
95 <assert_contents> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
96 <has_text text="CCDS10397" /> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
97 <has_text text="1e-13" /> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
98 </assert_contents> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
99 </output> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
100 </test> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
101 <test> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
102 <param name="cond" value="float(.0000000000001)"/> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
103 <param name="input" value="1.bed"/> |
7
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
104 <param name="round" value="false"/> |
e7c273e8d4d6
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
6
diff
changeset
|
105 <param name="avoid_scientific_notation" value="true"/> |
6
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
106 <output name="out_file1"> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
107 <assert_contents> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
108 <has_text text="CCDS10397" /> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
109 <has_text text=".0000000000001" /> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
110 <not_has_text text="1e-13" /> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
111 </assert_contents> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
112 </output> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
113 </test> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
114 </tests> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
115 <help> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
116 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
117 .. class:: infomark |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
118 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
119 **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
120 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
121 ----- |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
122 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
123 **What it does** |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
124 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
125 This tool computes an expression for every row of a dataset and appends the result as a new column (field). |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
126 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
127 - Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
128 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
129 - **c3-c2** will add a length column to the dataset if **c2** and **c3** are start and end position |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
130 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
131 ----- |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
132 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
133 **Example** |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
134 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
135 If this is your input:: |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
136 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
137 chr1 151077881 151077918 2 200 - |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
138 chr1 151081985 151082078 3 500 + |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
139 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
140 computing "c4*c5" will produce:: |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
141 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
142 chr1 151077881 151077918 2 200 - 400.0 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
143 chr1 151081985 151082078 3 500 + 1500.0 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
144 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
145 if, at the same time, "Round result?" is set to **YES** results will look like this:: |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
146 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
147 chr1 151077881 151077918 2 200 - 400 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
148 chr1 151081985 151082078 3 500 + 1500 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
149 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
150 You can also use this tool to evaluate expressions. For example, computing "c3>=c2" for Input will result in the following:: |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
151 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
152 chr1 151077881 151077918 2 200 - True |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
153 chr1 151081985 151082078 3 500 + True |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
154 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
155 or computing "type(c2)==type('') for Input will return:: |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
156 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
157 chr1 151077881 151077918 2 200 - False |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
158 chr1 151081985 151082078 3 500 + False |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
159 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
160 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
161 The following built-in functions are available:: |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
162 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
163 abs | all | any | bin | bool | chr | ceil | cmp | complex |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
164 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
165 divmod | exp | float | log | log10 | floor | hex | int | len | long |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
166 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
167 max | min | oct | ord | pow | range | reversed |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
168 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
169 round | sorted | sqrt | str | sum | type | unichr | unicode | |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
170 |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
171 </help> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
172 <citations /> |
0aeda7a81b46
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
5
diff
changeset
|
173 </tool> |