Mercurial > repos > bgruening > hicexplorer_chicviewpoint

annotate chicViewpoint.xml @ 6:dbfd2cfc0f66 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 15:06:55 +0000
parents 78b70d78a596
children f881c94fb3b3
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dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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1 <tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>computes viewpoints with the given reference points and a background model.</description>
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3 <macros>
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4 <token name="@BINARY@">chicViewpoint</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 #import re
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6d76e532b669 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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11 mkdir interactionFiles &&
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12 #for $m in $matrix_h5_cooler_multiple:
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13 #set identifier = @ESCAPE_IDENTIFIER_M@
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14 ln -s '$m' '$identifier' &&
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15 #end for
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16 #set $m = ' '.join([ '\'%s\'' % @ESCAPE_IDENTIFIER_MATRIX@ for $matrix in $matrix_h5_cooler_multiple ])
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17
0
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18 @BINARY@
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19 --matrices $m
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20 --range $rangeUpstream $rangeDownstream
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21 --referencePoints '$referencePoints'
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22 --averageContactBin $averageContactBin
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23 --fixateRange $fixateRange
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24 --decimalPlaces $decimalPlaces
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25 --threads @THREADS@
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26 --backgroundModelFile '$backgroundModelFile'
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27 --outputFolder interactionFiles
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28 $writeFileNamesToFile
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29
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30 #if $tar:
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31 && cd interactionFiles
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32 && tar -cvf ../viewpoints.tar .
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33 && cd ..
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34 && rm -rf interactionFiles
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35 #end if
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36
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37 ]]> </command>
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38 <inputs>
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39 <expand macro="matrix_h5_cooler_multiple_macro" />
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40
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41 <param argument="--referencePoints" type="data" format='interval' label="Reference points" help="Bed file contains all reference points which should be used to create viewpoints." />
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42 <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.' />
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43 <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.' />
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44
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45 <param argument="--backgroundModelFile" type="data" format='tabular' label="Background model" help="The background file computed by chicViewpointBackgroundModel" />
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46 <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.' />
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47 <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.' />
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48 <param argument="--decimalPlaces" type="integer" value="12" label="Decimal places for output" help='Decimal places for all floating value in the output.' />
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49
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50 <param name='writeFileNamesToFile' type='boolean' truevalue='--writeFileNamesToFile interactionFiles.txt' falsevalue="" checked="false" label="Save interaction file names (batch processing)" help="Set this parameter if you want to use the batch processing mode for the further analysis." />
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51 <param name='tar' type='boolean' checked="false" 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." />
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52
0
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53 </inputs>
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54 <outputs>
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55 <collection name="interactionFilesCollection" type="list" label="Interaction files">
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56 <discover_datasets pattern="__name__" format="interval" directory="interactionFiles" />
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57 </collection>
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58 <data name="interactionFileNames" from_work_dir="interactionFiles.txt" format="txt" label="${tool.name} interaction file names">
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59 <filter>writeFileNamesToFile</filter>
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60 </data>
4
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61 <data name="interactionFilesTar" from_work_dir="viewpoints.tar" format="tar" label="${tool.name} interaction file names tar">
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62 <filter>tar</filter>
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63 </data>
0
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64 </outputs>
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65 <tests>
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66 <test>
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67 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" />
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68 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed" />
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69 <param name="backgroundModelFile" value="cHi-C/background.txt" />
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70 <param name="fixateRange" value="500000" />
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71 <param name="rangeUpstream" value="200000" />
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72 <param name="rangeDownstream" value="200000" />
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73 <param name="writeFileNamesToFile" value="True" />
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74
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75 <output_collection name="interactionFilesCollection" type="list" count="6">
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76 <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" />
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77 <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" />
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diff changeset
78 <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval">
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
79 <assert_contents>
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
80 <has_text text="18895000" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
81 <has_text text="chr1" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
82 <has_text text="Tfap2d" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
83 <has_text text="interactions" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
84 <has_text text="472.0" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
85 </assert_contents>
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
86 </element>
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
87 <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" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
88 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval">
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
89 <assert_contents>
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
90 <has_text text="14100000" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
91 <has_text text="chr1" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
92 <has_text text="Eya1" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
93 <has_text text="interactions" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
94 <has_text text="832.0" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
95 </assert_contents>
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
96 </element>
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
97 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval">
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
98 <assert_contents>
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
99 <has_text text="4455000" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
100 <has_text text="chr1" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
101 <has_text text="Sox17" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
102 <has_text text="interactions" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
103 <has_text text="978.0" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
104 <has_text text="-30000" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
105 </assert_contents>
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
106 </element>
0
6d76e532b669 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
107 </output_collection>
6
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
108 <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0' />
0
6d76e532b669 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
109 </test>
1
68c92dfd03d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents: 0
diff changeset
110 <test>
6
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
111 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
112 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
113 <param name="backgroundModelFile" value="cHi-C/background.txt" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
114 <param name="fixateRange" value="500000" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
115 <param name="rangeUpstream" value="200000" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
116 <param name="rangeDownstream" value="200000" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
117 <param name="writeFileNamesToFile" value="False" />
1
68c92dfd03d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents: 0
diff changeset
118 <output_collection name="interactionFilesCollection" type="list" count="6">
6
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
119 <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" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
120 <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" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
121 <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval">
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
122 <assert_contents>
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
123 <has_text text="18893000" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
124 <has_text text="chr1" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
125 <has_text text="Tfap2d" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
126 <has_text text="interactions" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
127 <has_text text="472.0" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
128 </assert_contents>
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
129 </element>
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
130 <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" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
131 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval">
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
132 <assert_contents>
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
133 <has_text text="14103000" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
134 <has_text text="chr1" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
135 <has_text text="Eya1" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
136 <has_text text="interactions" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
137 <has_text text="832.0" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
138 <has_text text="-199000" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
139 </assert_contents>
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
140 </element>
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
141 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval">
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
142 <assert_contents>
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
143 <has_text text="4455000" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
144 <has_text text="chr1" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
145 <has_text text="Sox17" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
146 <has_text text="interactions" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
147 <has_text text="978.0" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
148 <has_text text="-30000" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
149 </assert_contents>
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
150 </element>
1
68c92dfd03d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents: 0
diff changeset
151 </output_collection>
68c92dfd03d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents: 0
diff changeset
152 <!-- <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/> -->
68c92dfd03d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents: 0
diff changeset
153 </test>
4
78b70d78a596 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
parents: 3
diff changeset
154 <test>
6
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
155 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" />
dbfd2cfc0f66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 4
diff changeset
156 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed" />
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157 <param name="backgroundModelFile" value="cHi-C/background.txt" />
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158 <param name="fixateRange" value="500000" />
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159 <param name="rangeUpstream" value="200000" />
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160 <param name="rangeDownstream" value="200000" />
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161 <param name="writeFileNamesToFile" value="True" />
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162 <param name='tar' value='True' />
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163 <output name="interactionFilesTar" file="cHi-C/chicViewpoint/viewpoints.tar" ftype='tar' compare="sim_size" delta='40000' />
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164 <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0' />
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165 </test>
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166 </tests>
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167 <help><![CDATA[
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168
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169 Compute viewpoints for all given reference points
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170 =================================================
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171
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172 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
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173 are named by the name of the reference point, the sample name and the location of the reference point:
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174
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175 gene_matrix_name_chr_start_end.txt
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176
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177 If multiple reference points are used and the processing downstream should be automated via batch processing mode, please activate `--writeFileNamesToFile`. In this
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178 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.
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179
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180 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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181
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182 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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183 ]]> </help>
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184 <expand macro="citations" />
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185 </tool>