Mercurial > repos > timpalpant > java_genomics_toolkit
annotate galaxy-conf/ValueDistribution.xml @ 16:35031c567ece draft
Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
| author | timpalpant |
|---|---|
| date | Sat, 09 Jun 2012 16:06:25 -0400 |
| parents | 3e477c7e0e73 |
| children |
| rev | line source |
|---|---|
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3e477c7e0e73
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.
timpalpant
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1 <tool id="WigValueDistribution" name="Compute the value distribution" version="1.1.0"> |
| 10 | 2 <description>of a (Big)Wig file</description> |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
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3 <command interpreter="sh">galaxyToolRunner.sh wigmath.ValueDistribution -i $input |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
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4 #if str( $min ) != '' |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
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5 --min $min |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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6 #end if |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
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7 |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
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8 #if str( $max ) != '' |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
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9 --max $max |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
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10 #end if |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
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changeset
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11 |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
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12 -n $bins -o $output |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
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13 </command> |
| 10 | 14 <inputs> |
| 15 <param format="bigwig,wig" name="input" type="data" label="(Big)Wig file" /> | |
| 11 | 16 <param name="min" type="float" optional="true" label="Minimum bin value (optional)" /> |
| 17 <param name="max" type="float" optional="true" label="Maximum bin value (optional)" /> | |
| 10 | 18 <param name="bins" type="integer" value="40" label="Number of bins" /> |
| 19 </inputs> | |
| 20 <outputs> | |
| 21 <data format="txt" name="output" /> | |
| 22 </outputs> | |
| 23 | |
| 24 <help> | |
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12
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
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25 |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
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26 This tool computes a histogram of the values in a Wig file, as well as the moments of the distribution. |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
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changeset
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27 |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
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28 ----- |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
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changeset
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29 |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
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30 **Syntax** |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
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31 |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
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32 - **Input data** is the genomic data used to compute the histogram. |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
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33 - **Minimum bin value** is the smallest bin. If unset, it is equal to the minimum value in the input data |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
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34 - **Maximum bin value** is the largest bin. If unset, it is equal to the maximum value in the input data |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
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35 - **Number of bins** is the number of bins to use. The bin size will be equal to (max - min) / (# bins). |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
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36 |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
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37 ----- |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
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38 |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
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39 **Output** |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
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40 |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
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41 The output is in 2-column tabular format, where the first column represents the lower edge of a bin inteval and the second column represents the number of values that fell in that bin. For example if the **minimum bin value** is 0, the **maximum bin value** is 0.3, and the **number of bins** is 3, then the following output might be produced :: |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
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42 |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
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43 bin count |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
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44 <0 3 |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
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45 0 1 |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
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46 0.1 10 |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
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47 0.2 4 |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
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48 >0.3 12 |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
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49 |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
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50 where there were 3 values in (-inf, 0), 1 value in [0, 0.1), 10 values in [0.1, 0.2), 4 values in [0.2, 0.3), and 12 values in [0.3, inf). |
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81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
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51 |
| 10 | 52 </help> |
| 53 </tool> |