Mercurial > repos > bgruening > hicexplorer_chicviewpoint
annotate chicViewpoint.xml @ 2:32f3666332f8 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
| author | iuc |
|---|---|
| date | Tue, 24 Mar 2020 17:31:50 +0000 (2020-03-24) |
| parents | 7a659307d3ff |
| children | 544440b09b16 |
| rev | line source |
|---|---|
|
0
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
1 <tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0"> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
2 <description>computes viewpoints with the given reference points and a background model.</description> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
3 <macros> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
4 <token name="@BINARY@">chicViewpoint</token> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
5 <import>macros.xml</import> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
6 </macros> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
7 <expand macro="requirements" /> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
8 <command detect_errors="exit_code"><![CDATA[ |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
9 #import re |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
10 |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
11 mkdir interactionFiles && |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
12 #for $m in $matrix_h5_cooler_multiple: |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
13 #set identifier = @ESCAPE_IDENTIFIER_M@ |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
14 ln -s '$m' '$identifier' && |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
15 #end for |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
16 #set $m = ' '.join([ '\'%s\'' % @ESCAPE_IDENTIFIER_MATRIX@ for $matrix in $matrix_h5_cooler_multiple ]) |
|
1
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
17 |
|
0
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
18 @BINARY@ |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
19 |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
20 --matrices $m |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
21 --range $rangeUpstream $rangeDownstream |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
22 --referencePoints '$referencePoints' |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
23 --averageContactBin $averageContactBin |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
24 --fixateRange $fixateRange |
|
2
32f3666332f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents:
1
diff
changeset
|
25 --decimalPlaces $decimalPlaces |
|
0
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
26 --threads @THREADS@ |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
27 --backgroundModelFile '$backgroundModelFile' |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
28 --outputFolder interactionFiles |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
29 $writeFileNamesToFile |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
30 |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
31 ]]></command> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
32 <inputs> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
33 <expand macro="matrix_h5_cooler_multiple_macro" /> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
34 |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
35 <param argument="--referencePoints" type="data" format='interval' |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
36 label="Reference points" |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
37 help="Bed file contains all reference points which should be used to create viewpoints." /> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
38 <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.' /> |
|
1
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
39 <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.' /> |
|
0
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
40 |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
41 <param argument="--backgroundModelFile" type="data" format='tabular' |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
42 label="Background model" |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
43 help="The background file computed by chicViewpointBackgroundModel" /> |
|
1
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
44 <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.'/> |
|
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
45 <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.'/> |
|
2
32f3666332f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents:
1
diff
changeset
|
46 <param argument="--decimalPlaces" type="integer" value="12" label="Decimal places for output" help='Decimal places for all floating value in the output.'/> |
|
32f3666332f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
parents:
1
diff
changeset
|
47 |
|
0
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
48 <param name='writeFileNamesToFile' type='boolean' truevalue='--writeFileNamesToFile interactionFiles.txt' falsevalue="" checked="false" label="Save interaction file names (batch processing)" |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
49 help="Set this parameter if you want to use the batch processing mode for the further analysis."/> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
50 </inputs> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
51 <outputs> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
52 <collection name="interactionFilesCollection" type="list" label="Interaction files"> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
53 <discover_datasets pattern="__name__" format="interval" directory="interactionFiles" /> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
54 </collection> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
55 <data name="interactionFileNames" from_work_dir="interactionFiles.txt" format="txt" label="${tool.name} interaction file names"> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
56 <filter>writeFileNamesToFile</filter> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
57 </data> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
58 </outputs> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
59 <tests> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
60 <test> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
61 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/> |
|
1
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
62 |
|
0
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
63 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed"/> |
|
1
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
64 <param name="backgroundModelFile" value="cHi-C/background.txt"/> |
|
0
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
65 <param name="fixateRange" value="500000"/> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
66 <param name="rangeUpstream" value="200000"/> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
67 <param name="rangeDownstream" value="200000"/> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
68 <param name="writeFileNamesToFile" value="True"/> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
69 |
|
1
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
70 |
|
0
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
71 <output_collection name="interactionFilesCollection" type="list" count="6"> |
|
1
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
72 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval" lines_diff="3"/> |
|
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
73 <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3"/> |
|
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
74 <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval" lines_diff="3"/> |
|
0
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
75 |
|
1
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
76 <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval" lines_diff="3"/> |
|
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
77 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval" lines_diff="3"/> |
|
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
78 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3"/> |
|
0
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
79 </output_collection> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
80 <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/> |
|
1
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
81 |
|
0
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
82 </test> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
83 <test> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
84 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/> |
|
1
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
85 |
|
0
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
86 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed"/> |
|
1
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
87 <param name="backgroundModelFile" value="cHi-C/background.txt"/> |
|
0
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
88 <param name="fixateRange" value="500000"/> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
89 <param name="rangeUpstream" value="200000"/> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
90 <param name="rangeDownstream" value="200000"/> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
91 <param name="writeFileNamesToFile" value="False"/> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
92 |
|
1
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
93 |
|
0
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
94 <output_collection name="interactionFilesCollection" type="list" count="6"> |
|
1
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
95 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval" lines_diff="3"/> |
|
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
96 <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3"/> |
|
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
97 <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval" lines_diff="3"/> |
|
0
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
98 |
|
1
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
99 <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval" lines_diff="3"/> |
|
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
100 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval" lines_diff="3"/> |
|
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
101 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3"/> |
|
0
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
102 </output_collection> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
103 <!-- <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/> --> |
|
1
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
104 |
|
0
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
105 </test> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
106 </tests> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
107 <help><![CDATA[ |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
108 |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
109 Compute viewpoints for all given reference points |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
110 ================================================= |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
111 |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
112 Computes per input matrix all viewpoints which are defined in the reference points file. All files are stored in the folder defined by `--outputFolder`, the files |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
113 are named by the name of the reference point, the sample name and the location of the reference point: |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
114 |
|
1
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
115 gene_matrix_name_chr_start_end.txt |
|
0
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
116 |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
117 If multiple reference points are used and the processing downstream should be automated via batch processing mode, please activate `--writeFileNamesToFile`. In this |
|
1
7a659307d3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents:
0
diff
changeset
|
118 file, all the file names will be written to; in the case of multiple samples two consecutive lines are considered as treatment vs control in the differential analysis. |
|
0
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
119 |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
120 For more information about HiCExplorer please consider our documentation on readthedocs.io_ |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
121 |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
122 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
123 ]]></help> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
124 <expand macro="citations" /> |
|
5d431baabba3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff
changeset
|
125 </tool> |