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comparison galaxy-conf/MatrixAligner.xml @ 12:81d5b81fb3c2 draft

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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
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11:b1952a90d4bf 12:81d5b81fb3c2
1 <tool id="MatrixAligner" name="Align values in a matrix" version="1.0.0"> 1 <tool id="MatrixAligner" name="Align values in a matrix" version="1.0.0">
2 <description>for a heatmap</description> 2 <description>for a heatmap</description>
3 <command interpreter="sh"> 3 <command interpreter="sh">galaxyToolRunner.sh visualization.MatrixAligner -i $input -l $loci -m $M -o $output</command>
4 galaxyToolRunner.sh visualization.MatrixAligner -i $input -l $loci -m $M -o $output
5 </command>
6 <inputs> 4 <inputs>
7 <param format="wig,bigwig" name="input" type="data" label="Sequencing data" /> 5 <param format="wig,bigwig" name="input" type="data" label="Sequencing data" />
8 <param format="bed" name="loci" type="data" label="List of intervals (with alignment points)" /> 6 <param format="bed" name="loci" type="data" label="List of intervals (with alignment points)" />
9 <param type="integer" name="M" value="4000" label="Maximum row length" /> 7 <param type="integer" name="M" value="4000" label="Maximum row length" />
10 <!-- TODO: Bring back optional markers
11 <conditional name="ladder">
12 <param name="draw" type="boolean" checked="false" falsevalue="false" truevalue="true" label="Include marker ladder across X-axis"/>
13 <when value="true">
14 <param name="spacing" type="integer" value="200" label="Draw marker every N base pairs" />
15 </when>
16 <when value="false">
17 </when>
18 </conditional> -->
19 </inputs> 8 </inputs>
20 <outputs> 9 <outputs>
21 <data format="tabular" name="output" /> 10 <data format="tabular" name="output" />
22 </outputs> 11 </outputs>
23 <!-- TODO:<tests> 12 <!-- TODO:<tests>
58 <output name="output" file="matrixAligner.output3"/> 47 <output name="output" file="matrixAligner.output3"/>
59 </test> 48 </test>
60 </tests>--> 49 </tests>-->
61 50
62 <help> 51 <help>
52
53 This tool aligns sequencing data into a rectangular matrix for creating a heatmap with matrix2png. Data from each interval is lined up on the specified alignment point (column 5 in the Bed file), and flipped if on the - strand so that all intervals are 5'-to-3' from left-to-right.
54
55 Intervals with alignment points must be provided in the following extended Bed format ::
56
57 chr low high id alignment strand
58
59 The heatmap is created by taking each interval in the **List of Intervals**, retrieving the data for that interval from the Wig file, and adding it as a new row in the matrix. Intervals are processed in their original order.
60
61 -----
62
63 **Syntax**
64
65 - **Sequencing data** is the genomic data used to create the matrix
66 - **List of intervals** is a list of intervals in Bed format with alignment points
67 - **Maximum row length** is the maximum allowed width of the matrix. If aligned intervals extend outside of this width, they will be truncated.
68
69 -----
70
71 .. class:: infomark
72
73 **TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in Wig or BigWig format. Use "edit attributes" to set the correct format if it was not detected correctly.
74
63 .. class:: warningmark 75 .. class:: warningmark
64 76
65 Large heatmap matrices may require a long time to generate. To reduce the size of an MxN matrix with large M, rows (N) can be truncated using the maximum row length parameter. Rows are truncated from the alignment point (symmetrically) if possible, or as nearly symmetrically as possible. 77 Large heatmap matrices may require a long time to generate in Galaxy because it validates that the output is in correct tab-delimited format. To reduce the size of an MxN matrix with large M, rows (N) can be truncated using the maximum row length parameter. Rows are truncated from the alignment point (symmetrically) if possible, or as nearly symmetrically as possible.
78
66 </help> 79 </help>
67 </tool> 80 </tool>