Mercurial > repos > timpalpant > java_genomics_toolkit
annotate galaxy-conf/MatrixAligner.xml @ 15:3e477c7e0e73 draft
Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
| author | timpalpant |
|---|---|
| date | Sat, 09 Jun 2012 16:03:59 -0400 |
| parents | 81d5b81fb3c2 |
| children |
| rev | line source |
|---|---|
| 4 | 1 <tool id="MatrixAligner" name="Align values in a matrix" version="1.0.0"> |
| 2 <description>for a heatmap</description> | |
|
12
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
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3 <command interpreter="sh">galaxyToolRunner.sh visualization.MatrixAligner -i $input -l $loci -m $M -o $output</command> |
| 4 | 4 <inputs> |
| 5 <param format="wig,bigwig" name="input" type="data" label="Sequencing data" /> | |
| 6 <param format="bed" name="loci" type="data" label="List of intervals (with alignment points)" /> | |
| 7 <param type="integer" name="M" value="4000" label="Maximum row length" /> | |
| 8 </inputs> | |
| 9 <outputs> | |
| 10 <data format="tabular" name="output" /> | |
| 11 </outputs> | |
| 12 <!-- TODO:<tests> | |
| 13 <test> | |
| 14 <param name="input" value="test.wig"/> | |
| 15 <param name="loci" value="test.bed"/> | |
| 16 <param name="M" value="4000"/> | |
| 17 <output name="output" file="matrixAligner.output"/> | |
| 18 </test> | |
| 19 <test> | |
| 20 <param name="input" value="test.bw"/> | |
| 21 <param name="loci" value="test.bed"/> | |
| 22 <param name="M" value="4000"/> | |
| 23 <output name="output" file="matrixAligner.output"/> | |
| 24 </test> | |
| 25 <test> | |
| 26 <param name="input" value="test.wig"/> | |
| 27 <param name="loci" value="test2.bed"/> | |
| 28 <param name="M" value="4000"/> | |
| 29 <output name="output" file="matrixAligner.output2"/> | |
| 30 </test> | |
| 31 <test> | |
| 32 <param name="input" value="test.bw"/> | |
| 33 <param name="loci" value="test2.bed"/> | |
| 34 <param name="M" value="4000"/> | |
| 35 <output name="output" file="matrixAligner.output2"/> | |
| 36 </test> | |
| 37 <test> | |
| 38 <param name="input" value="test.wig"/> | |
| 39 <param name="loci" value="test3.bed"/> | |
| 40 <param name="M" value="4000"/> | |
| 41 <output name="output" file="matrixAligner.output3"/> | |
| 42 </test> | |
| 43 <test> | |
| 44 <param name="input" value="test.bw"/> | |
| 45 <param name="loci" value="test3.bed"/> | |
| 46 <param name="M" value="4000"/> | |
| 47 <output name="output" file="matrixAligner.output3"/> | |
| 48 </test> | |
| 49 </tests>--> | |
| 50 | |
| 51 <help> | |
|
12
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
52 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
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. |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
54 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
55 Intervals with alignment points must be provided in the following extended Bed format :: |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
56 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
57 chr low high id alignment strand |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
58 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
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. |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
60 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
61 ----- |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
62 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
63 **Syntax** |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
64 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
65 - **Sequencing data** is the genomic data used to create the matrix |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
66 - **List of intervals** is a list of intervals in Bed format with alignment points |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
67 - **Maximum row length** is the maximum allowed width of the matrix. If aligned intervals extend outside of this width, they will be truncated. |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
68 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
69 ----- |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
70 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
71 .. class:: infomark |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
72 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
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. |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
74 |
| 4 | 75 .. class:: warningmark |
| 76 | |
|
12
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
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. |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
78 |
| 4 | 79 </help> |
| 80 </tool> |