Mercurial > repos > iuc > tag_pileup_frequency
annotate tag_pileup_frequency.xml @ 3:580e8bcb6413 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"
author | iuc |
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date | Fri, 06 Dec 2019 15:32:39 -0500 |
parents | 6432735cdb22 |
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rev | line source |
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3
580e8bcb6413
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"
iuc
parents:
2
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changeset
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1 <tool id="tag_pileup_frequency" name="Tag pileup frequency" version="1.0.2"> |
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> |
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580e8bcb6413
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"
iuc
parents:
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4 <requirement type="package" version="11.0.1">openjdk</requirement> |
0
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents:
diff
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5 </requirements> |
2
6432735cdb22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit ae67f98d61e74e241a6d51378f53a3d5c00967ce
iuc
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6 <command detect_errors="exit_code"><![CDATA[ |
3
580e8bcb6413
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"
iuc
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7 #import re |
580e8bcb6413
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"
iuc
parents:
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8 #set input1_identifier = re.sub('[^\s\w\-]', '_', str($input1.element_identifier)) |
580e8bcb6413
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"
iuc
parents:
2
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9 #set input2_identifier = re.sub('[^\s\w\-]', '_', str($input2.element_identifier)) |
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6432735cdb22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit ae67f98d61e74e241a6d51378f53a3d5c00967ce
iuc
parents:
1
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10 mkdir -p output && |
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580e8bcb6413
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"
iuc
parents:
2
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11 ln -s '${input1}' '${input1_identifier}' && |
580e8bcb6413
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"
iuc
parents:
2
diff
changeset
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12 ln -s '${input2}' '${input2_identifier}' && |
580e8bcb6413
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"
iuc
parents:
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13 ln -s '${input1.metadata.bam_index}' '${input1_identifier}.bai' && |
2
6432735cdb22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit ae67f98d61e74e241a6d51378f53a3d5c00967ce
iuc
parents:
1
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14 java -jar '$__tool_directory__/TagPileup.jar' |
3
580e8bcb6413
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"
iuc
parents:
2
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15 -b '${input1_identifier}' |
580e8bcb6413
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"
iuc
parents:
2
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16 -i '${input1_identifier}.bai' |
580e8bcb6413
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"
iuc
parents:
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17 -c '$input2_identifier' |
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6432735cdb22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit ae67f98d61e74e241a6d51378f53a3d5c00967ce
iuc
parents:
1
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18 -s $tag_shift |
6432735cdb22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit ae67f98d61e74e241a6d51378f53a3d5c00967ce
iuc
parents:
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19 -n $bin_size |
6432735cdb22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit ae67f98d61e74e241a6d51378f53a3d5c00967ce
iuc
parents:
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20 -e $tags_equal |
6432735cdb22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit ae67f98d61e74e241a6d51378f53a3d5c00967ce
iuc
parents:
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21 -r $reads |
6432735cdb22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit ae67f98d61e74e241a6d51378f53a3d5c00967ce
iuc
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22 -p $proper_pe |
6432735cdb22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit ae67f98d61e74e241a6d51378f53a3d5c00967ce
iuc
parents:
1
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23 -a $combine_strands |
6432735cdb22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit ae67f98d61e74e241a6d51378f53a3d5c00967ce
iuc
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24 -t "\${GALAXY_SLOTS:-4}" |
6432735cdb22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit ae67f98d61e74e241a6d51378f53a3d5c00967ce
iuc
parents:
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25 -w $composite_smoothing_window |
6432735cdb22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit ae67f98d61e74e241a6d51378f53a3d5c00967ce
iuc
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26 -m true |
6432735cdb22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit ae67f98d61e74e241a6d51378f53a3d5c00967ce
iuc
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27 -x '$output1' |
6432735cdb22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit ae67f98d61e74e241a6d51378f53a3d5c00967ce
iuc
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28 -h $output_heatmap |
6432735cdb22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit ae67f98d61e74e241a6d51378f53a3d5c00967ce
iuc
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29 #if str($output_heatmap) == "true": |
6432735cdb22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit ae67f98d61e74e241a6d51378f53a3d5c00967ce
iuc
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30 -o output |
6432735cdb22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit ae67f98d61e74e241a6d51378f53a3d5c00967ce
iuc
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31 #end if |
6432735cdb22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit ae67f98d61e74e241a6d51378f53a3d5c00967ce
iuc
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32 1>/dev/null |
6432735cdb22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit ae67f98d61e74e241a6d51378f53a3d5c00967ce
iuc
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33 ]]></command> |
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fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents:
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34 <inputs> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents:
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35 <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
parents:
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36 <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
parents:
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37 <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
parents:
diff
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38 <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
parents:
diff
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39 <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
parents:
diff
changeset
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40 <param name="reads" type="select" label="Reads to examine" help="Selecting combined requires paired-end BAM input"> |
3
580e8bcb6413
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"
iuc
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41 <option value="0" selected="true">Read1</option> |
0
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents:
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42 <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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43 <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
parents:
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44 </param> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents:
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45 <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
parents:
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46 <param name="combine_strands" type="select" label="Combine strands?"> |
3
580e8bcb6413
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"
iuc
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47 <option value="0" selected="true">No</option> |
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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 <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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49 </param> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents:
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50 <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
parents:
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51 <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
parents:
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52 </inputs> |
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents:
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53 <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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54 <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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55 <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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56 <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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57 </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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58 <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
parents:
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59 </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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60 <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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61 <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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62 <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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63 <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
parents:
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64 <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
parents:
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65 <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
parents:
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66 <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
parents:
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67 <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
parents:
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68 <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
parents:
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69 <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
parents:
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70 <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
parents:
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71 <param name="output_heatmap" value="true" /> |
3
580e8bcb6413
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"
iuc
parents:
2
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72 <output name="output1" file="output1.tabular" ftype="tabular" compare="contains"/> |
0
fa82c3c9ced3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents:
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73 <output_collection name="heatmaps" type="list"> |
3
580e8bcb6413
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"
iuc
parents:
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74 <element name="input_bed_input_bam_read1_anti.tabular" file="input2_input1_read1_anti.tabular" ftype="tabular" compare="contains"/> |
580e8bcb6413
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"
iuc
parents:
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75 <element name="input_bed_input_bam_read1_sense.tabular" file="input2_input1_read1_sense.tabular" ftype="tabular" compare="contains"/> |
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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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76 </output_collection> |
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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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77 </test> |
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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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78 </tests> |
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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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79 <help> |
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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 |
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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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81 **What it does** |
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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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82 |
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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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83 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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
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84 |
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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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85 ----- |
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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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86 |
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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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87 **Options** |
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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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88 |
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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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89 **Global transformations** |
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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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90 |
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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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91 - **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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
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92 - **Bin Size (bp)** - bins tags together into specified size, useful for lower resolution data or for especially wide reference windows. |
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93 - **Set Tags to be equal** - standardizes tag count to be equal to genome size, useful for replicate comparisons. |
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94 |
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95 **Read parameters** |
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96 |
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97 - **Reads to Examine** - output data for Read1, Read2, or combined (only for paired end BAM files). |
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98 - **Require Proper PE** - require output reads to be properly paired (only for paired end BAM files). |
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99 - **Combine Strands** - examine reads on a forward/reverse basis (strand separate) or ignoring read orientation (strand combined). |
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100 |
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101 **Run parameters** |
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102 |
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103 - **Composite smoothing window (bp)** - sliding window to smooth composite frequencies. |
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104 - **Output frequencies for heatmap** - generate an additional dataset collection containing frequencies that can be used to generate a heatmap plot. |
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105 |
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106 </help> |
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107 <citations> |
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108 <citation type="bibtex"> |
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109 @unpublished{None, |
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110 author = {Lai, William}, |
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111 title = {None}, |
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112 year = {None}, |
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113 eprint = {None}, |
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114 url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation} |
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115 }</citation> |
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116 </citations> |
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117 </tool> |