Mercurial > repos > bgruening > hicexplorer_chicsignificantinteractions
annotate chicSignificantInteractions.xml @ 6:6001400eed99 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
| author | iuc |
|---|---|
| date | Tue, 16 Mar 2021 15:33:42 +0000 |
| parents | 38fa8a72ece6 |
| children | 640e0e45518a |
| rev | line source |
|---|---|
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
1 <tool id="hicexplorer_chicsignificantinteractions" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
2 <description>computes viewpoints with the given reference points and a background model</description> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
3 <macros> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
4 <token name="@BINARY@">chicSignificantInteractions</token> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
5 <import>macros.xml</import> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
6 </macros> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
7 <expand macro="requirements" /> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
8 <command detect_errors="exit_code"><![CDATA[ |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
9 #import re |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
10 |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
11 mkdir interactionFiles && |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
12 mkdir targetFolder && |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
13 mkdir significantFilesFolder && |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
14 |
|
4
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
15 #if $tar_input_conditional.tar_input_selector == 'tar_input': |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
16 ln -s '$tar_input_conditional.interactionFiles' viewpoints.tar && |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
17 tar -C interactionFiles -xvf viewpoints.tar && |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
18 #else: |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
19 #for $file in $tar_input_conditional.interactionFiles: |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
20 #set identifier = @ESCAPE_IDENTIFIER_FILE@ |
|
4
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
21 ln -s '$file' 'interactionFiles/$identifier' && |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
22 #end for |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
23 #end if |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
24 |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
25 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
26 #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ]) |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
27 #end if |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
28 @BINARY@ |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
29 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
30 --interactionFile $interactonfileslist |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
31 --computeSampleNumber $batchmode_conditional.computeSampleNumber |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
32 #else: |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
33 --interactionFile '$batchmode_conditional.interactionFilesOrderFile' |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
34 --interactionFileFolder interactionFiles |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
35 --batchMode |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
36 --targetFileList targetListFile.txt |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
37 --writeFileNamesToFile significantFiles.txt |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
38 --computeSampleNumber $batchmode_conditional.computeSampleNumber |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
39 #end if |
|
2
3df84bb4486c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
1
diff
changeset
|
40 |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
41 --pValue $pvalue |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
42 |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
43 #if $filter_conditional.filter_selector == 'optionXfold': |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
44 --xFoldBackground $filter_conditional.xfold |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
45 #else: |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
46 --loosePValue $filter_conditional.loosePvalue |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
47 |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
48 #end if |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
49 --backgroundModelFile '$backgroundModelFile' |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
50 --resolution $resolution |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
51 --peakInteractionsThreshold $peakInteractionsThreshold |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
52 --range $rangeUpstream $rangeDownstream |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
53 --targetFolder targetFolder |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
54 --outputFolder significantFilesFolder |
|
3
7668fac6cc3a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents:
2
diff
changeset
|
55 $truncateZeroPvalues |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
56 --fixateRange $fixateRange |
|
2
3df84bb4486c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
1
diff
changeset
|
57 -suffix significant_interactions.txt |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
58 --threads @THREADS@ |
|
4
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
59 |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
60 #if $tar: |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
61 && cd targetFolder |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
62 && tar -cvf ../targetFolder.tar * |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
63 && cd .. |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
64 && rm -rf targetFolder |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
65 |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
66 && cd significantFilesFolder |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
67 && tar -cvf ../significantFilesFolder.tar * |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
68 && cd .. |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
69 && rm -rf significantFilesFolder |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
70 |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
71 #end if |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
72 ]]> </command> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
73 <inputs> |
|
4
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
74 <conditional name="tar_input_conditional"> |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
75 <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode"> |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
76 <option value="tar_input">Tar file</option> |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
77 <option value="interval_input" selected="True">Interval files</option> |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
78 </param> |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
79 <when value="tar_input"> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
80 <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false" /> |
|
4
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
81 </when> |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
82 <when value="interval_input"> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
83 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true" /> |
|
4
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
84 </when> |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
85 </conditional> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
86 <conditional name="batchmode_conditional"> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
87 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode"> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
88 <option value="optionBatchmode">Batch processing</option> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
89 <option value="optionSinglemode" selected="True">Single file processing</option> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
90 </param> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
91 <when value="optionBatchmode"> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
92 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
93 <param name='computeSampleNumber' type="integer" value='2' label="Create one target file for n consecutive files." /> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
94 </when> |
|
2
3df84bb4486c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
1
diff
changeset
|
95 <when value="optionSinglemode"> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
96 <param name='computeSampleNumber' type="integer" value='2' label="Create one target file for n consecutive files." /> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
97 </when> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
98 </conditional> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
99 <param name='pvalue' type="float" value='0.05' label="P-value of interaction to be accepted as significant" /> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
100 <conditional name="filter_conditional"> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
101 <param name="filter_selector" type="select" label="List of chromosomes or a BED file containg regions"> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
102 <option value="optionXfold">x-fold over mean background</option> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
103 <option value="optionLoosePvalue" selected="True">Loose p-value (NB background)</option> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
104 </param> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
105 <when value="optionXfold"> |
|
2
3df84bb4486c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
1
diff
changeset
|
106 <param name='xfold' type="float" value='2.0' label="X-fold over mean background to be accepted." help='Filter x-fold over background. Used to merge neighboring bins with a broader peak but |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
107 less significant interactions to one peak with high significance. Used only for pValue option.' /> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
108 </when> |
|
2
3df84bb4486c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
1
diff
changeset
|
109 <when value="optionLoosePvalue"> |
|
3df84bb4486c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
1
diff
changeset
|
110 <param name='loosePvalue' type="float" value='0.3' label="Loose p-value" help='loose p-value threshold value to filter target regions in a first round. |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
111 Used to merge neighboring bins with a broader peak but less significant interactions to one peak with high significance. |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
112 Used only for pValue option.' /> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
113 </when> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
114 </conditional> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
115 <param argument="--backgroundModelFile" type="data" format='tabular' label="Background model" help="The background file computed by chicViewpointBackgroundModel" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
116 <param argument="--peakInteractionsThreshold" type="integer" value="5" label="Minimum interactions" help='The minimum number of interactions a detected peaks needs to have to be considered.' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
117 <param argument="--resolution" type="integer" value="1000" label="Bin resolution of the used data" help='Resolution of the bin in genomic units. Values are usually e.g. 1000 for a 1kb, 5000 for a 5kb or 10000 for a 10kb resolution. |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
118 This value is used to merge neighboring bins.' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
119 <param name="rangeUpstream" type="integer" value="500000" label="Upstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
120 <param name="rangeDownstream" type="integer" value="500000" label="Downstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
121 <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
122 <param name='truncateZeroPvalues' type='boolean' truevalue='--truncateZeroPvalues' falsevalue="" checked="false" label="Truncate zeros by setting them to one." help="Sets all p-values which are equal to zero to one. This has the effect that the associated positions are not part of the significance decision." /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
123 <param name='tar' type='boolean' checked="false" truevalue='True' label="tar output to one file" help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large." /> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
124 </inputs> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
125 <outputs> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
126 <collection name="significantFilesCollection" type="list" label="Significant files"> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
127 <discover_datasets pattern="__name__" format="interval" directory="significantFilesFolder" /> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
128 </collection> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
129 <collection name="targetFilesCollection" type="list" label="Target files"> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
130 <discover_datasets pattern="__name__" format="interval" directory="targetFolder" /> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
131 </collection> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
132 <data name="significantFileNames" from_work_dir="significantFiles.txt" format="txt" label="${tool.name} significant file names"> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
133 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
134 </data> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
135 <data name="targetFileNames" from_work_dir="targetListFile.txt" format="txt" label="${tool.name} target file names"> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
136 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
137 </data> |
|
4
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
138 <data name="targetFolderTar" from_work_dir="targetFolder.tar" format="tar" label="Target files tar"> |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
139 <filter>tar</filter> |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
140 </data> |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
141 <data name="significantFilesFolderTar" from_work_dir="significantFilesFolder.tar" format="tar" label="Significant files tar"> |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
142 <filter>tar</filter> |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
143 </data> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
144 </outputs> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
145 <tests> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
146 <test> |
|
4
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
147 <conditional name="tar_input_conditional"> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
148 <param name="tar_input_selector" value='interval_input' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
149 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" /> |
|
4
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
150 </conditional> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
151 <conditional name="batchmode_conditional"> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
152 <param name="batchmode_selector" value='optionBatchmode' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
153 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
154 <param name="computeSampleNumber" value='2' /> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
155 </conditional> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
156 <param name="pvalue" value='0.2' /> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
157 |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
158 <conditional name="filter_conditional"> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
159 <param name="filter_selector" value='optionLoosePvalue' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
160 <param name="loosePvalue" value='0.5' /> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
161 </conditional> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
162 |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
163 <param name="backgroundModelFile" value="cHi-C/background.txt" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
164 <param name="rangeUpstream" value="200000" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
165 <param name="rangeDownstream" value="200000" /> |
|
2
3df84bb4486c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
1
diff
changeset
|
166 |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
167 <output_collection name="significantFilesCollection" type="list" count="6"> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
168 <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" ftype="interval"> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
169 <assert_contents> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
170 <has_text text="4480000" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
171 <has_text text="chr1" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
172 <has_text text="Sox17" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
173 <has_text text="810.0" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
174 <has_text text="interactions" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
175 </assert_contents> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
176 </element> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
177 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" ftype="interval"> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
178 <assert_contents> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
179 <has_text text="14274000" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
180 <has_text text="chr1" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
181 <has_text text="Eya1" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
182 <has_text text="interactions" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
183 </assert_contents> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
184 </element> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
185 <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" ftype="interval" lines_diff="4" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
186 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" ftype="interval"> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
187 <assert_contents> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
188 <has_text text="4480000" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
189 <has_text text="chr1" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
190 <has_text text="Sox17" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
191 <has_text text="interactions" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
192 <has_text text="93000" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
193 <has_text text="978.0" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
194 </assert_contents> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
195 </element> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
196 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" ftype="interval" lines_diff="4" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
197 <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" ftype="interval"> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
198 <assert_contents> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
199 <has_text text="19077000" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
200 <has_text text="chr1" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
201 <has_text text="Tfap2d" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
202 <has_text text="interactions" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
203 <has_text text="-15000" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
204 </assert_contents> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
205 </element> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
206 </output_collection> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
207 <output_collection name="targetFilesCollection" type="list" count="3"> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
208 <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt" ftype="interval"> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
209 <assert_contents> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
210 <has_text text="4555000" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
211 <has_text text="chr1" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
212 <has_text text="p-value" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
213 <has_text text="interactions" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
214 </assert_contents> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
215 </element> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
216 <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" file="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" ftype="interval" lines_diff="4" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
217 <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt" ftype="interval"> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
218 <assert_contents> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
219 <has_text text="19143000" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
220 <has_text text="chr1" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
221 <has_text text="p-value" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
222 <has_text text="19150000" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
223 </assert_contents> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
224 </element> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
225 </output_collection> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
226 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
227 <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" /> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
228 </test> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
229 <test> |
|
4
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
230 <conditional name="tar_input_conditional"> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
231 <param name="tar_input_selector" value='interval_input' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
232 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" /> |
|
4
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
233 </conditional> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
234 <conditional name="batchmode_conditional"> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
235 <param name="batchmode_selector" value='optionSinglemode' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
236 <param name="computeSampleNumber" value="1" /> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
237 </conditional> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
238 <param name="pvalue" value='0.2' /> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
239 |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
240 <conditional name="filter_conditional"> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
241 <param name="filter_selector" value='optionXfold' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
242 <param name="xfold" value='1.5' /> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
243 </conditional> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
244 |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
245 <param name="backgroundModelFile" value="cHi-C/background.txt" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
246 <param name="rangeUpstream" value="200000" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
247 <param name="rangeDownstream" value="200000" /> |
|
2
3df84bb4486c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
1
diff
changeset
|
248 |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
249 <output_collection name="significantFilesCollection" type="list" count="2"> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
250 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt" ftype="interval" lines_diff="4" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
251 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" ftype="interval"> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
252 <assert_contents> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
253 <has_text text="14295000" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
254 <has_text text="chr1" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
255 <has_text text="Eya1" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
256 <has_text text="interactions" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
257 </assert_contents> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
258 </element> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
259 </output_collection> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
260 <output_collection name="targetFilesCollection" type="list" count="2"> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
261 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt" file="cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt" ftype="interval" lines_diff="4" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
262 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" file="cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" ftype="interval" lines_diff="4" /> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
263 </output_collection> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
264 </test> |
|
4
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
265 |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
266 <test> |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
267 <conditional name="tar_input_conditional"> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
268 <param name="tar_input_selector" value='interval_input' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
269 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" /> |
|
4
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
270 </conditional> |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
271 <conditional name="batchmode_conditional"> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
272 <param name="batchmode_selector" value='optionBatchmode' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
273 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
274 <param name="computeSampleNumber" value='2' /> |
|
4
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
275 </conditional> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
276 <param name="pvalue" value='0.2' /> |
|
4
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
277 |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
278 <conditional name="filter_conditional"> |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
279 <param name="filter_selector" value='optionLoosePvalue' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
280 <param name="loosePvalue" value='0.5' /> |
|
4
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
281 </conditional> |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
282 |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
283 <param name="backgroundModelFile" value="cHi-C/background.txt" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
284 <param name="rangeUpstream" value="200000" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
285 <param name="rangeDownstream" value="200000" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
286 |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
287 <param name='tar' value='True' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
288 |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
289 <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype='tar' compare="sim_size" delta='40000' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
290 <output name="significantFilesFolderTar" file="cHi-C/chicSignificantInteractions/significantFilesFolder.tar" ftype='tar' compare="sim_size" delta='40000' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
291 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
292 <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
293 </test> |
|
4
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
294 |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
295 <test> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
296 <conditional name="tar_input_conditional"> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
297 <param name="tar_input_selector" value='tar_input' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
298 <param name="interactionFiles" value="cHi-C/chicViewpoint/viewpoints.tar" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
299 </conditional> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
300 <conditional name="batchmode_conditional"> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
301 <param name="batchmode_selector" value='optionBatchmode' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
302 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
303 <param name="computeSampleNumber" value='2' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
304 </conditional> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
305 <param name="pvalue" value='0.2' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
306 |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
307 <conditional name="filter_conditional"> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
308 <param name="filter_selector" value='optionLoosePvalue' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
309 <param name="loosePvalue" value='0.5' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
310 </conditional> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
311 |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
312 <param name="backgroundModelFile" value="cHi-C/background.txt" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
313 <param name="rangeUpstream" value="200000" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
314 <param name="rangeDownstream" value="200000" /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
315 |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
316 <param name='tar' value='True' /> |
|
4
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
317 |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
318 <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype='tar' compare="sim_size" delta='40000' /> |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
319 <output name="significantFilesFolderTar" file="cHi-C/chicSignificantInteractions/significantFilesFolder.tar" ftype='tar' compare="sim_size" delta='40000' /> |
|
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
320 |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
321 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta='40000' /> |
|
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
322 <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" compare="sim_size" delta='40000' /> |
|
4
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents:
3
diff
changeset
|
323 </test> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
324 </tests> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
325 <help><![CDATA[ |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
326 |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
327 Significant interaction detection |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
328 ================================= |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
329 |
|
2
3df84bb4486c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
1
diff
changeset
|
330 Significant interactions are detected by this tool for each viewpoint based on the background model. chicSignificantInteractions outputs for each viewpoint a file containing all recorded significant interactions and |
|
3df84bb4486c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
1
diff
changeset
|
331 a target file. The target file is especially useful in the batch mode context, as it merges for two consecutive listed control and treatment viewpoint the significant interactions which can then be used |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
332 to test for a differential interaction scheme. |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
333 |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
334 chicSignificantInteractions supports two modes to detect significant interactions, either by an x-fold over the average background or a loose p-value. In both cases neighboring significant peaks are merged together and an additional |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
335 p-value based on the sum of interactions for this neighborhood is computed. Only interactions with a higher p-value as specified by the threshold `--pValue` are accepted as a significant interaction. |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
336 |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
337 For more information about HiCExplorer please consider our documentation on readthedocs.io_ |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
338 |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
339 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html |
|
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
4
diff
changeset
|
340 ]]> </help> |
|
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
341 <expand macro="citations" /> |
|
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff
changeset
|
342 </tool> |