Mercurial > repos > iuc > cwpair2
annotate cwpair2.xml @ 6:c4b926c9831c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit ca66053a0d915edba3d7f1d4ce014718e7f4f0f2
| author | iuc |
|---|---|
| date | Thu, 02 May 2019 08:30:22 -0400 |
| parents | 71188f3f4b76 |
| children |
| rev | line source |
|---|---|
|
0
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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1 <?xml version="1.0"?> |
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6
c4b926c9831c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit ca66053a0d915edba3d7f1d4ce014718e7f4f0f2
iuc
parents:
5
diff
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2 <tool id="cwpair2" name="CWPair2" version="1.1.1"> |
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0
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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3 <description>find matched pairs and unmatched orphans</description> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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4 <macros> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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5 <import>cwpair2_macros.xml</import> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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6 </macros> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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7 <expand macro="requirements" /> |
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5
71188f3f4b76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
iuc
parents:
3
diff
changeset
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8 <command detect_errors="aggressive"><![CDATA[ |
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71188f3f4b76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
iuc
parents:
3
diff
changeset
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9 python '$__tool_directory__/cwpair2.py' |
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71188f3f4b76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
iuc
parents:
3
diff
changeset
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10 #for $i in $input: |
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71188f3f4b76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
iuc
parents:
3
diff
changeset
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11 --input '${i}' '${i.hid}' |
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71188f3f4b76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
iuc
parents:
3
diff
changeset
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12 #end for |
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71188f3f4b76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
iuc
parents:
3
diff
changeset
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13 --up_distance $up_distance |
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71188f3f4b76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
iuc
parents:
3
diff
changeset
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14 --down_distance $down_distance |
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71188f3f4b76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
iuc
parents:
3
diff
changeset
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15 --method $method |
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71188f3f4b76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
iuc
parents:
3
diff
changeset
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16 --binsize $binsize |
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71188f3f4b76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
iuc
parents:
3
diff
changeset
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17 --threshold_format $threshold_format_cond.threshold_format |
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71188f3f4b76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
iuc
parents:
3
diff
changeset
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18 #if str($threshold_format_cond.threshold_format) == "absolute_threshold": |
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71188f3f4b76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
iuc
parents:
3
diff
changeset
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19 --absolute_threshold $threshold_format_cond.absolute_threshold |
|
71188f3f4b76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
iuc
parents:
3
diff
changeset
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20 #elif str($threshold_format_cond.threshold_format) == "relative_threshold": |
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71188f3f4b76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
iuc
parents:
3
diff
changeset
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21 --relative_threshold $threshold_format_cond.relative_threshold |
|
71188f3f4b76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
iuc
parents:
3
diff
changeset
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22 #end if |
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71188f3f4b76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
iuc
parents:
3
diff
changeset
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23 --output_files $output_files |
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71188f3f4b76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
iuc
parents:
3
diff
changeset
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24 --statistics_output '$statistics_output' |
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71188f3f4b76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
iuc
parents:
3
diff
changeset
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25 ]]></command> |
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0
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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26 <inputs> |
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5
71188f3f4b76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
iuc
parents:
3
diff
changeset
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27 <param name="input" type="data" format="gff" multiple="true" label="Find matched pairs on" /> |
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0
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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28 <param name="up_distance" type="integer" value="50" min="0" label="Distance upstream from a peak to allow a pair" help="The maximum distance upstream or 5’ to the primary peak"/> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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29 <param name="down_distance" type="integer" value="100" min="0" label="Distance downstream from a peak to allow a pair" help="The maximum distance downstream or 3’ to the primary peak"/> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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30 <param name="method" type="select" label="Method of finding a match"> |
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5
71188f3f4b76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
iuc
parents:
3
diff
changeset
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31 <option value="mode" selected="true">Mode</option> |
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0
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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32 <option value="closest">Closest</option> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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33 <option value="largest">Largest</option> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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34 <option value="all">All</option> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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35 </param> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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36 <param name="binsize" type="integer" value="1" min="0" label="Width of bins for frequency plots and mode calculation" help="Value 1 implies no bins" /> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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37 <conditional name="threshold_format_cond"> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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38 <param name="threshold_format" type="select" label="Filter using"> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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39 <option value="relative_threshold" selected="True">Relative threshold</option> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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40 <option value="absolute_threshold">Absolute threshold</option> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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41 </param> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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42 <when value="relative_threshold"> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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43 <param name="relative_threshold" type="float" value="0.0" min="0.0" label="Percentage of the 95 percentile value to filter below" help="Value 0 results in no filtering" /> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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44 </when> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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45 <when value="absolute_threshold"> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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46 <param name="absolute_threshold" type="float" value="0.0" min="0.0" label="Absolute value to filter below" /> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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47 </when> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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48 </conditional> |
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1
d4db13c9dd7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
0
diff
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49 <param name="output_files" type="select" label="Select output" help="Statistics will always be generated." > |
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d4db13c9dd7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
0
diff
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50 <option value="all" selected="True">everything (C,D,F,O,P,MP)</option> |
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0
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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51 <option value="matched_pair">matched pairs only (MP)</option> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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52 <option value="matched_pair_orphan">matched pairs and orphans only (O,MP)</option> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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53 <option value="matched_pair_orphan_detail">matched pairs, orphans and details only (D,O,MP)</option> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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54 </param> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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55 </inputs> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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56 <outputs> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
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57 <data name="statistics_output" format="tabular" label="Statistics Table: ${tool.name} on ${on_string}" /> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
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58 <collection name="H" type="list" label="Statistics Histogram: ${tool.name} on ${on_string}"> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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59 <filter>output_files == "all"</filter> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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60 <discover_datasets pattern="(?P<designation>.*)" directory="H" ext="pdf" visible="false" /> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
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61 </collection> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
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62 <collection name="D" type="list" label="Data D: ${tool.name} on ${on_string}"> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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63 <filter>output_files in ["all", "matched_pair_orphan_detail"]</filter> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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64 <discover_datasets pattern="(?P<designation>.*)" directory="data_D" ext="tabular" visible="false" /> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
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65 </collection> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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66 <collection name="O" type="list" label="Data O: ${tool.name} on ${on_string}"> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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67 <filter>output_files in ["all", "matched_pair_orphan", "matched_pair_orphan_detail"]</filter> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
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68 <discover_datasets pattern="(?P<designation>.*)" directory="data_O" ext="tabular" visible="false" /> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
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69 </collection> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
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70 <collection name="MP" type="list" label="Data MP: ${tool.name} on ${on_string}"> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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71 <discover_datasets pattern="(?P<designation>.*)" directory="data_MP" ext="gff" visible="false" /> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
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72 </collection> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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73 </outputs> |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
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74 <tests> |
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8600bfe7ed52
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75 <test> |
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76 <param name="input" value="cwpair2_input1.gff" /> |
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77 <param name="up_distance" value="25" /> |
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78 <param name="down_distance" value="100" /> |
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79 <param name="method" value="all" /> |
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80 <param name="binsize" value="1" /> |
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81 <param name="threshold_format" value="relative_threshold" /> |
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82 <param name="relative_threshold" value="0.0" /> |
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83 <param name="output_files" value="matched_pair" /> |
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84 <output name="statistics_output" file="statistics1.tabular" ftype="tabular" /> |
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85 <output_collection name="MP" type="list"> |
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86 <element name="data_MP_closest_f0u25d100_on_data_1.gff" file="closest_mp_output1.gff" ftype="gff" /> |
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87 <element name="data_MP_largest_f0u25d100_on_data_1.gff" file="largest_mp_output1.gff" ftype="gff" /> |
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88 <element name="data_MP_mode_f0u25d100_on_data_1.gff" file="mode_mp_output1.gff" ftype="gff" /> |
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89 </output_collection> |
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90 </test> |
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91 <test> |
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92 <param name="input" value="cwpair2_input1.gff" /> |
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93 <param name="up_distance" value="50" /> |
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94 <param name="down_distance" value="100" /> |
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95 <param name="method" value="all" /> |
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96 <param name="binsize" value="1" /> |
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97 <param name="threshold_format" value="relative_threshold" /> |
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98 <param name="relative_threshold" value="0.0" /> |
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99 <param name="output_files" value="all" /> |
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100 <output name="statistics_output" file="statistics2.tabular" ftype="tabular" /> |
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101 <output_collection name="H" type="list"> |
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102 <element name="histogram_C_mode_f0u50d100_on_data_1.pdf" file="magic.pdf" ftype="pdf" compare="contains" /> |
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103 <element name="histogram_F_closest_f0u50d100_on_data_1.pdf" file="magic.pdf" ftype="pdf" compare="contains" /> |
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104 <element name="histogram_F_largest_f0u50d100_on_data_1.pdf" file="magic.pdf" ftype="pdf" compare="contains" /> |
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105 <element name="histogram_F_mode_f0u50d100_on_data_1.pdf" file="magic.pdf" ftype="pdf" compare="contains" /> |
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106 <element name="histogram_P_mode_f0u50d100_on_data_1.pdf" file="magic.pdf" ftype="pdf" compare="contains" /> |
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107 </output_collection> |
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108 <output_collection name="D" type="list"> |
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109 <element name="data_D_closest_f0u50d100_on_data_1.tabular" file="closest_d_output2.tabular" ftype="tabular" /> |
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110 <element name="data_D_largest_f0u50d100_on_data_1.tabular" file="largest_d_output2.tabular" ftype="tabular" /> |
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111 <element name="data_D_mode_f0u50d100_on_data_1.tabular" file="mode_d_output2.tabular" ftype="tabular" /> |
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0
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112 </output_collection> |
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113 <output_collection name="O" type="list"> |
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114 <element name="data_O_closest_f0u50d100_on_data_1.tabular" file="closest_o_output2.tabular" ftype="tabular" /> |
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115 <element name="data_O_largest_f0u50d100_on_data_1.tabular" file="largest_o_output2.tabular" ftype="tabular" /> |
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116 <element name="data_O_mode_f0u50d100_on_data_1.tabular" file="mode_o_output2.tabular" ftype="tabular" /> |
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117 </output_collection> |
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118 <output_collection name="MP" type="list"> |
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119 <element name="data_MP_closest_f0u50d100_on_data_1.gff" file="closest_mp_output2.gff" ftype="gff" /> |
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120 <element name="data_MP_largest_f0u50d100_on_data_1.gff" file="largest_mp_output2.gff" ftype="gff" /> |
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121 <element name="data_MP_mode_f0u50d100_on_data_1.gff" file="mode_mp_output2.gff" ftype="gff" /> |
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122 </output_collection> |
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123 </test> |
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124 </tests> |
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125 <help> |
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126 **What it does** |
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127 |
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128 CWPair accepts one or more gff files as input and takes the peak location to be the midpoint between the |
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129 exclusion zone start and end coordinate (columns D and E). CWPair starts with the highest peak (primary peak) |
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130 in the dataset, and then looks on the opposite strand for another peak located within the distance defined by |
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131 a combination of the tool's **Distance upstream from a peak to allow a pair** (the distance upstream or 5’ to |
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132 the primary peak) and **Distance downstream from a peak to allow a pair** (the distance downstream or 3’ to the |
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133 primary peak) parameters. So "upstream" value 30 "downstream" value 20 makes the tool look 30 bp upstream and |
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134 20 bp downstream (inclusive). Consequently, the search space would be 51 bp, since it includes the primary peak |
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135 coordinate. The use of a negative number changes the direction of the search limits. So, "upstream" -30 and |
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136 "downstream" 20 produces an 11 bp downstream search window (20-30 bp downstream, inclusive). |
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137 |
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138 .. image:: $PATH_TO_IMAGES/cwpair2.png |
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139 |
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140 When encountering multiple candidate peaks within the search window, CWPair uses the resolution method defined by |
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141 the tool's **Method of finding a match** parameter as follows: |
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142 |
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143 |
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144 * **mode** - This is an iterative process in which all peak-pair distances within the search window are determined, and the mode calculated. The pair whose distance apart is closest to the mode is then selected. |
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145 * **closest** - Pairs the peak that has the closest absolute distance from the primary peak. |
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146 * **largest** - Pairs the peak that has the highest tag count. |
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147 * **all** - Runs all three methods, producing separate outputs for each. |
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148 |
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149 When considering the candidate peaks for pairing to a primary peak, a tag-count threshold may also be set using |
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150 the tool's **Filter using relative/absolute threshold** parameter. A relative threshold determines the tag counts |
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151 at the 95th percentile of peak occupancy (i.e. top 5% in terms of tag counts), then uses a tag count threshold at |
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152 the specified percentage of this 95th percentile. So if the peak at the 95th percentile has 200 tags, and "relative |
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153 threshold" 50 is used, then it will not consider any peak having less than 100 tags. |
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154 |
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155 ----- |
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156 |
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157 **Options** |
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158 |
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159 * **Method of finding match** - Method of finding matched pair, mode, closest, largest, or all (run with each method). |
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160 * **Distance upstream from a peak to allow a pair** - The maximum distance (inclusive) upstream on the opposite strand from the primary peak to locate another peak, resulting in a pair. |
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161 * **Distance downstream from a peak to allow a pair** - The maximum distance (inclusive) downstream on the opposite strand from the primary peak to locate another peak, resulting in a pair. |
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162 * **Percentage of the 95 percentile value to filter below** - Percentage of the 95 percentile value below which to filter when using a relative threshold. |
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163 * **Absolute value to filter below** - Absolute value below which to filter when using an absolute threshold. |
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164 * **Output files** - Restrict output dataset collections to matched pairs only or one of several combinations of collection types. |
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165 |
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166 ----- |
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167 |
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168 **Output Data Files** |
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169 |
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170 * **closest/largest/mode MP** - gff file containing the Matched Pairs and includes the peak-pair midpoint coordinate (column D) and the coordinate +1 (column E). The tag count sum is reported in column F, along with the C-W distance in bp in column I. |
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171 * **closest/largest/mode O** - tabular file containing the Orphans (all peaks that are not in pairs). |
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172 * **closest/largest/mode D** - tabular file containing the Details, which lists + and – strand information separately. The start and end represent the lower and higher coordinates of the exclusion zone from GeneTrack, and “Value” is the tag count sum within the exclusion zone. The peak pair midpoint is calculated along with the distance between the two paired peaks (midpoint-to-midpoint or C-W distance). |
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173 |
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174 **Output Statistics Files** |
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175 |
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176 * **closest/largest/mode C** - pdf file that provides the frequency distribution of peak pair distances. |
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177 * **closest/largest/mode P** - pdf file that provides the preview plots graph (the initial iteration of the process for finding the mode). |
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178 * **closest/largest/mode F** - pdf file that provides the final plots graph. |
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179 * **Statistics Table** - provides the number of peaks in pairs (dividing this by 2 provides the number of peak-pairs). |
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180 </help> |
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181 <expand macro="citations" /> |
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182 </tool> |