Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/IntervalLengthDistribution.xml @ 15:3e477c7e0e73 draft

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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 eb53be9a09f4
children
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1 <tool id="IntervalLengthDistribution" name="Make histogram" version="1.0.0">
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2 <description>of read lengths</description>
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3 <command interpreter="sh">galaxyToolRunner.sh ngs.IntervalLengthDistribution -i $input $freq -o $output</command>
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4 <inputs>
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5 <param name="input" type="data" format="sam,bam,bed,bedgraph,gff" label="Reads/Intervals" />
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6 <param name="freq" type="boolean" checked="false" truevalue="-f" falsevalue="" label="Output normalized frequencies rather than counts" />
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7 </inputs>
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8 <outputs>
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9 <data format="tabular" name="output" />
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10 </outputs>
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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.
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11 <tests>
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12 <test>
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13 <param name="input" value="test.bed"/>
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.
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14 <param name="freq" value="false"/>
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15 <output name="output" file="intervallengthdistribution1.txt"/>
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16 </test>
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.
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17 <test>
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.
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18 <param name="input" value="test.bed"/>
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.
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19 <param name="freq" value="true"/>
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20 <output name="output" file="intervallengthdistribution2.txt"/>
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21 </test>
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22 <test>
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23 <param name="input" value="test2.bed"/>
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24 <param name="freq" value="false"/>
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25 <output name="output" file="intervallengthdistribution3.txt"/>
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26 </test>
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27 </tests>
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29 <help>
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31 This tool calculates the distribution of interval lengths from a list of intervals or reads in SAM, BAM, Bed, BedGraph, or GFF format.
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33 .. class:: warningmark
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35 For paired-end sequencing reads, the length is the length of the fragment (5' end of read 1 to 5' end of read 2)
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37 </help>
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38 </tool>