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comparison cwpair2.xml @ 6:ea1c1ab897af draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
author iuc
date Mon, 06 Nov 2017 23:16:47 -0500
parents 6109a90ab0d6
children 076fae29bb39
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5:37ea888d7765 6:ea1c1ab897af
3 <description>find matched pairs and unmatched orphans</description> 3 <description>find matched pairs and unmatched orphans</description>
4 <macros> 4 <macros>
5 <import>cwpair2_macros.xml</import> 5 <import>cwpair2_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="aggressive"> 8 <command detect_errors="aggressive"><![CDATA[
9 <![CDATA[ 9 python '$__tool_directory__/cwpair2.py'
10 python $__tool_directory__/cwpair2.py 10 #for $i in $input:
11 #for $i in $input: 11 --input '${i}' '${i.hid}'
12 --input "${i}" "${i.hid}" 12 #end for
13 #end for 13 --up_distance $up_distance
14 --up_distance $up_distance 14 --down_distance $down_distance
15 --down_distance $down_distance 15 --method $method
16 --method $method 16 --binsize $binsize
17 --binsize $binsize 17 --threshold_format $threshold_format_cond.threshold_format
18 --threshold_format $threshold_format_cond.threshold_format 18 #if str($threshold_format_cond.threshold_format) == "absolute_threshold":
19 #if str($threshold_format_cond.threshold_format) == "absolute_threshold": 19 --absolute_threshold $threshold_format_cond.absolute_threshold
20 --absolute_threshold $threshold_format_cond.absolute_threshold 20 #elif str($threshold_format_cond.threshold_format) == "relative_threshold":
21 #elif str($threshold_format_cond.threshold_format) == "relative_threshold": 21 --relative_threshold $threshold_format_cond.relative_threshold
22 --relative_threshold $threshold_format_cond.relative_threshold 22 #end if
23 #end if 23 --output_files $output_files
24 --output_files $output_files 24 --statistics_output '$statistics_output'
25 --statistics_output "$statistics_output" 25 ]]></command>
26 ]]>
27 </command>
28 <inputs> 26 <inputs>
29 <param name="input" type="data" format="gff" multiple="True" label="Find matched pairs on" /> 27 <param name="input" type="data" format="gff" multiple="true" label="Find matched pairs on" />
30 <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"/> 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"/>
31 <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"/> 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"/>
32 <param name="method" type="select" label="Method of finding a match"> 30 <param name="method" type="select" label="Method of finding a match">
33 <option value="mode" selected="True">Mode</option> 31 <option value="mode" selected="true">Mode</option>
34 <option value="closest">Closest</option> 32 <option value="closest">Closest</option>
35 <option value="largest">Largest</option> 33 <option value="largest">Largest</option>
36 <option value="all">All</option> 34 <option value="all">All</option>
37 </param> 35 </param>
38 <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" /> 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" />
177 175
178 * **closest/largest/mode C** - pdf file that provides the frequency distribution of peak pair distances. 176 * **closest/largest/mode C** - pdf file that provides the frequency distribution of peak pair distances.
179 * **closest/largest/mode P** - pdf file that provides the preview plots graph (the initial iteration of the process for finding the mode). 177 * **closest/largest/mode P** - pdf file that provides the preview plots graph (the initial iteration of the process for finding the mode).
180 * **closest/largest/mode F** - pdf file that provides the final plots graph. 178 * **closest/largest/mode F** - pdf file that provides the final plots graph.
181 * **Statistics Table** - provides the number of peaks in pairs (dividing this by 2 provides the number of peak-pairs). 179 * **Statistics Table** - provides the number of peaks in pairs (dividing this by 2 provides the number of peak-pairs).
182
183 </help> 180 </help>
184 <expand macro="citations" /> 181 <expand macro="citations" />
185 </tool> 182 </tool>