Mercurial > repos > bgruening > join_files_on_column_fuzzy

annotate join_files_on_column_fuzzy.xml @ 0:5b667b17923a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
author bgruening
date Sun, 26 Nov 2017 16:12:46 -0500
parents
children 0dc3fa8c94e8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
1 <tool id="join_files_on_column_fuzzy" name="Join two files" version="1.0.0">
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
2 <description>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
3 on column allowing a small difference
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
4 </description>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
5 <requirements>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
6 <requirement type="package" version="3.6">python</requirement>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
7 </requirements>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
8 <command>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
9 <![CDATA[
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
10 python '$__tool_directory__/join_files_on_column_fuzzy.py'
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
11 --f1 '$f1'
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
12 --f2 '$f2'
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
13 --c1 $c1
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
14 --c2 $c2
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
15 --outfile '$merged_file'
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
16 $header
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
17 $add_distance
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
18 #if $merge_mode.merge_mode_select == 'closest':
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
19 --closest
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
20 #else:
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
21 --distance $merge_mode.distance
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
22 --unit $merge_mode.units
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
23 #end if
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
24 ]]>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
25 </command>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
26 <inputs>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
27 <param argument="--f1" type="data" optional="true" format="tabular" label="1st file"
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
28 help=""/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
29 <param argument="--c1" type="data_column" data_ref="f1" label="Column to use from 1st file" help="The file needs to be sorted by this column, ascending."/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
30 <param argument="--f2" type="data" optional="true" format="tabular" label="2nd file"
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
31 help=""/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
32 <param argument="--c2" type="data_column" data_ref="f2" label="Column to use from 2nd file" help="The file needs to be sorted by this column, ascending."/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
33
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
34 <param argument="--header" type="boolean" checked="false" truevalue="--header" falsevalue="" label="Does the input files contain a header line" />
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
35 <param argument="--add_distance" type="boolean" checked="false" truevalue="--add_distance" falsevalue="" label="Add an addional column with the calculated distance." />
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
36
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
37 <conditional name="merge_mode">
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
38 <param name="merge_mode_select" type="select" label="Choose the mode of merging.">
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
39 <option value="closest" selected="True">Best match (in case of multiple best matches, only the first one is reported)</option>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
40 <option value="distance">Matching with a defined distance</option>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
41 </param>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
42 <when value="closest"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
43 <when value="distance">
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
44 <param name="units" display="radio" type="select" value="ppm_value" label="Choose the metrics of your distance"
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
45 help="ppm is useful for very small differences">
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
46 <option value="absolute" selected="True">Absolute distance</option>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
47 <option value="ppm" >Distance in ppm</option>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
48 </param>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
49 <param name="distance" value="0.2" type="float" label="Allowed distance between the two values that will trigger a merge" help=""/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
50 </when>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
51 </conditional>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
52 </inputs>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
53 <outputs>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
54 <data name="merged_file" format="tabular" />
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
55 </outputs>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
56
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
57 <tests>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
58 <test>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
59 <param name="f1" value="file1.tab" ftype="tabular"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
60 <param name="f2" value="file2.tab" ftype="tabular"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
61 <param name="c1" value="1"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
62 <param name="c2" value="1"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
63 <param name="merge_mode_select" value="distance"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
64 <param name="distance" value="0.1"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
65 <param name="units" value="absolute"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
66 <output name="merged_file" file="no_header_result1.tab" />
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
67 </test>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
68 <test>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
69 <param name="f1" value="file1_header.tab" ftype="tabular"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
70 <param name="f2" value="file2_header.tab" ftype="tabular"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
71 <param name="c1" value="1"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
72 <param name="c2" value="1"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
73 <param name="merge_mode_select" value="distance"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
74 <param name="distance" value="0.2"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
75 <param name="units" value="absolute"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
76 <param name="header" value="true"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
77 <output name="merged_file" file="header_result2.tab" />
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
78 </test>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
79 <test>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
80 <param name="f1" value="file1_header.tab" ftype="tabular"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
81 <param name="f2" value="file2_header.tab" ftype="tabular"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
82 <param name="c1" value="1"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
83 <param name="c2" value="1"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
84 <param name="header" value="true"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
85 <param name="closest" value="true"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
86 <output name="merged_file" file="header_closest_result3.tab" />
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
87 </test>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
88 <test>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
89 <param name="f1" value="file1_ppm.tab" ftype="tabular"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
90 <param name="f2" value="file2_ppm.tab" ftype="tabular"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
91 <param name="c1" value="1"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
92 <param name="c2" value="1"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
93 <param name="header" value="false"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
94 <param name="merge_mode_select" value="distance"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
95 <param name="distance" value="100"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
96 <param name="units" value="ppm"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
97 <output name="merged_file" file="no_header_ppm_result4.tab" />
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
98 </test>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
99 <test>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
100 <param name="f1" value="file1_header.tab" ftype="tabular"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
101 <param name="f2" value="file2_header.tab" ftype="tabular"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
102 <param name="c1" value="1"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
103 <param name="c2" value="1"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
104 <param name="header" value="true"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
105 <param name="closest" value="true"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
106 <param name="add_distance" value="true"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
107 <output name="merged_file" file="header_closest_result5.tab" />
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
108 </test>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
109 <test>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
110 <param name="f1" value="file1_ppm.tab" ftype="tabular"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
111 <param name="f2" value="file2_ppm.tab" ftype="tabular"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
112 <param name="c1" value="1"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
113 <param name="c2" value="1"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
114 <param name="header" value="false"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
115 <param name="merge_mode_select" value="distance"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
116 <param name="distance" value="100"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
117 <param name="units" value="ppm"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
118 <param name="add_distance" value="true"/>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
119 <output name="merged_file" file="no_header_ppm_result6.tab" />
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
120 </test>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
121 </tests>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
122 <help>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
123 <![CDATA[
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
124
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
125 Join two files on a common column. It is possible to provide an allowed difference between both values (currently only numbers)
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
126 as the absolute differece or as PPM.
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
127
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
128 Two modes are available:
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
129
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
130 1. In the **best match** mode only the rows are merged for the most similar (or identical) values. In case of multiple best matches, only the first one is reported.
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
131
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
132 1. The **Matching with a defined distance** option will offer you the possibility
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
133 to provide a distance between the two values of the columns. Is the calculates distance smaller or equal than the given distance the columns will be joined. You can specify the allowed distance as an absolute distance or as PPM.
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
134
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
135
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
136 ]]>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
137 </help>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
138 <citations>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
139 </citations>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
140 </tool>
5b667b17923a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
diff changeset
141