Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/StripMatrix.xml @ 12:81d5b81fb3c2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
author timpalpant
date Wed, 25 Apr 2012 16:53:48 -0400
parents 4b32ed5d4a1b
children eb53be9a09f4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
1 <tool id="StripMatrix" name="Strip headers" version="1.0.0">
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
2 <description>from an aligned matrix</description>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
3 <command interpreter="sh">galaxyToolRunner.sh visualization.StripMatrix -i $input -o $output</command>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
4 <inputs>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
5 <param format="tabular" name="input" type="data" label="Aligned matrix" />
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
6 </inputs>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
7 <outputs>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
8 <data format="tabular" name="output" metadata="input" />
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
9 </outputs>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
10 <tests>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
11 <test>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
12 <param name="input" value="stripMatrix.input"/>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
13 <output name="output" file="stripMatrix.output"/>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
14 </test>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
15 </tests>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
16
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
17 <help>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
18
12
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
19 This tool is intended to strip the column/row headers off of an aligned matrix (in matrix2png format) for easy import into Matlab or other software where only the data values are required. It removes the first row and first column from a tabular file.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
20
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
21 -----
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
22
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
23 **Example**
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
24
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
25 If the following tabular matrix is used as input ::
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
26
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
27 ID col1 col2 col3
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
28 row1 2 4 5
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
29 row2 5 1 1
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
30
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
31 then the following tabular matrix will be produced as output ::
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
32
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
33 2 4 5
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
34 5 1 1
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
35
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
36 </help>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
37 </tool>