Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/LogTransform.xml @ 22:727fbba02ef7 draft

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Fix a bug in GeneTrackToWig where +/- strands were not merged correctly. Add option to vary the chunk size of tools that process chromosomes in chunks.
author timpalpant
date Tue, 19 Jun 2012 22:09:23 -0400
parents 9d56b5b85740
children b43c420a6135
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1 <tool id="WigLogTransform" name="Log transform" version="1.1.0">
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2 <description>a (Big)Wig file</description>
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3 <command interpreter="sh">galaxyToolRunner.sh wigmath.LogTransform -i $input -b $base -o $output</command>
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4 <inputs>
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5 <param format="bigwig,wig" name="input" type="data" label="(Big)Wig file" />
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6 <param name="base" type="integer" value="2" label="Logarithm base" />
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7 </inputs>
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8 <outputs>
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9 <data format="wig" name="output" metadata_source="input" />
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10 </outputs>
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11 <tests>
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12 <test>
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13 <param name="input" value="wigmath1.wig"/>
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14 <param name="base" value="2"/>
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15 <output name="output" file="logger1.wig"/>
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16 </test>
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17 <test>
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18 <param name="input" value="wigmath2.wig"/>
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19 <param name="base" value="3"/>
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20 <output name="output" file="logger2.wig"/>
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21 </test>
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22 <test>
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23 <param name="input" value="wigmath3.wig"/>
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24 <param name="base" value="10"/>
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25 <output name="output" file="logger3.wig"/>
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26 </test>
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27 <test>
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28 <param name="input" value="wigmath1.bw"/>
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29 <param name="base" value="2"/>
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30 <output name="output" file="logger4.wig"/>
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31 </test>
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32 <test>
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33 <param name="input" value="wigmath2.bw"/>
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34 <param name="base" value="3"/>
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35 <output name="output" file="logger5.wig"/>
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36 </test>
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37 <test>
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38 <param name="input" value="wigmath3.bw"/>
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39 <param name="base" value="10"/>
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40 <output name="output" file="logger6.wig"/>
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41 </test>
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42 </tests>
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43
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44 <help>
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45
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46 .. class:: infomark
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47
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48 **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.
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49
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50 </help>
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51 </tool>