Mercurial > repos > iuc > tag_pileup_frequency
annotate tag_pileup_frequency.xml @ 0:fa82c3c9ced3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
author | iuc |
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date | Tue, 17 May 2016 14:15:39 -0400 |
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children | b7d7ae3963aa |
rev | line source |
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0
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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1 <tool id="tag_pileup_frequency" name="Tag pileup frequency" version="1.0.0"> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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2 <description></description> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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3 <requirements> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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4 <requirement type="package" version="8.0.45">java-jdk</requirement> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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5 </requirements> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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6 <command> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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7 <![CDATA[ |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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8 mkdir -p output && |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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9 ln -f -s "${input1.metadata.bam_index}" "${input1}.bai" && |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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10 java -jar $__tool_directory__/TagPileup.jar |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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11 -b "$input1" |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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12 -i "${input1}.bai" |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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13 -c "$input2" |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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14 -s $tag_shift |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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15 -n $bin_size |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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16 -e $tags_equal |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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17 -r $reads |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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18 -p $proper_pe |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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19 -a $combine_strands |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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20 -t "\${GALAXY_SLOTS:-4}" |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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21 -w $composite_smoothing_window |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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22 -m "true" |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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23 -x "$output1" |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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24 -h $output_heatmap |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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25 #if str($output_heatmap) == "true": |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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26 -o output |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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27 #end if |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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28 1>/dev/null |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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29 ]]> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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30 </command> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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31 <inputs> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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32 <param name="input1" type="data" format="bam" label="BAM file" /> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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33 <param name="input2" type="data" format="bed" label="Bed file" /> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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34 <param name="tag_shift" type="integer" value="0" min="0" label="5' to 3' Tag Shift (bp)" /> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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35 <param name="bin_size" type="integer" value="1" min="1" label="Bin Size (bp)" /> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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36 <param name="tags_equal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set Tags to be equal?" /> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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37 <param name="reads" type="select" label="Reads to examine" help="Selecting combined requires paired-end BAM input"> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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38 <option value="0" selected="True">Read1</option> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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39 <option value="1">Read2</option> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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40 <option value="2">combined</option> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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41 </param> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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42 <param name="proper_pe" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require proper PE?" help="Requires paired-end BAM input"/> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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43 <param name="combine_strands" type="select" label="Combine strands?"> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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44 <option value="0" selected="True">No</option> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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45 <option value="1">Yes</option> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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46 </param> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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47 <param name="composite_smoothing_window" type="integer" value="0" min="0" label="Composite smoothing window (bp)" /> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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48 <param name="output_heatmap" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Output frequencies heatmap?" /> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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49 </inputs> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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50 <outputs> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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51 <collection name="heatmaps" type="list" label="Heatmap frequencies: ${tool.name} on ${on_string}"> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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52 <discover_datasets pattern="(?P<designation>.*)" directory="output" ext="tabular" visible="false" /> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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53 <filter>output_heatmap == true</filter> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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54 </collection> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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55 <data name="output1" format="tabular"/> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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56 </outputs> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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57 <tests> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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58 <test> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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59 <param name="input1" value="input.bam" ftype="bam"/> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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60 <param name="input2" value="input.bed" ftype="bed"/> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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61 <param name="tag_shift" value="0" /> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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62 <param name="bin_size" value="1" /> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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63 <param name="tags_equal" value="false" /> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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64 <param name="reads" value="0" /> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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65 <param name="proper_pe" value="false" /> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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66 <param name="combine_strands" value="0" /> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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67 <param name="composite_smoothing_window" value="0" /> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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68 <param name="output_heatmap" value="true" /> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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69 <output name="output1" file="output1.tabular" ftype="tabular"/> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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70 <output_collection name="heatmaps" type="list"> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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71 <element name="dataset_2_dataset_1_read1_anti.tabular" file="input2_input1_read1_anti.tabular" ftype="tabular" compare="contains"/> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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72 <element name="dataset_2_dataset_1_read1_sense.tabular" file="input2_input1_read1_sense.tabular" ftype="tabular" compare="contains"/> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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73 </output_collection> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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74 </test> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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75 </tests> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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76 <help> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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77 |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
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78 **What it does** |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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79 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
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80 Generates a frequency pileup of the 5' ends of aligned reads in a BAM file relative to reference points in a BED file. |
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81 |
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82 ----- |
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83 |
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84 **Options** |
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85 |
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86 **Global transformations** |
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87 |
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88 - **5' to 3' tag shift (bp)** - moves all tags from the 5' to the 3' direction given a specified distance in base pairs. |
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89 - **Bin Size (bp)** - bins tags together into specified size, useful for lower resolution data or for especially wide reference windows. |
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90 - **Set Tags to be equal** - standardizes tag count to be equal to genome size, useful for replicate comparisons. |
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91 |
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92 **Read parameters** |
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93 |
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94 - **Reads to Examine** - output data for Read1, Read2, or combined (only for paired end BAM files). |
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95 - **Require Proper PE** - require output reads to be properly paired (only for paired end BAM files). |
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96 - **Combine Strands** - examine reads on a forward/reverse basis (strand separate) or ignoring read orientation (strand combined). |
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97 |
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98 **Run parameters** |
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99 |
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100 - **Composite smoothing window (bp)** - sliding window to smooth composite frequencies. |
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101 - **Output frequencies for heatmap** - generate an additional dataset collection containing frequencies that can be used to generate a heatmap plot. |
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102 |
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103 </help> |
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104 <citations> |
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105 <citation type="bibtex"> |
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106 @unpublished{None, |
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107 author = {Lai, William}, |
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108 title = {None}, |
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109 year = {None}, |
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110 eprint = {None}, |
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111 url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation} |
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112 }</citation> |
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113 </citations> |
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114 </tool> |