Mercurial > repos > bgruening > hicexplorer_chicviewpoint

comparison chicViewpoint.xml @ 5:7403e41df69e 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 14:06:17 +0000
parents 544440b09b16
children ec40077337e3
comparison
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4:058d756f85a3 5:7403e41df69e
1 <tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.1"> 1 <tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>computes viewpoints with the given reference points and a background model.</description> 2 <description>computes viewpoints with the given reference points and a background model.</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">chicViewpoint</token> 4 <token name="@BINARY@">chicViewpoint</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
14 ln -s '$m' '$identifier' && 14 ln -s '$m' '$identifier' &&
15 #end for 15 #end for
16 #set $m = ' '.join([ '\'%s\'' % @ESCAPE_IDENTIFIER_MATRIX@ for $matrix in $matrix_h5_cooler_multiple ]) 16 #set $m = ' '.join([ '\'%s\'' % @ESCAPE_IDENTIFIER_MATRIX@ for $matrix in $matrix_h5_cooler_multiple ])
17 17
18 @BINARY@ 18 @BINARY@
19
20 --matrices $m 19 --matrices $m
21 --range $rangeUpstream $rangeDownstream 20 --range $rangeUpstream $rangeDownstream
22 --referencePoints '$referencePoints' 21 --referencePoints '$referencePoints'
23 --averageContactBin $averageContactBin 22 --averageContactBin $averageContactBin
24 --fixateRange $fixateRange 23 --fixateRange $fixateRange
33 && tar -cvf ../viewpoints.tar . 32 && tar -cvf ../viewpoints.tar .
34 && cd .. 33 && cd ..
35 && rm -rf interactionFiles 34 && rm -rf interactionFiles
36 #end if 35 #end if
37 36
38 ]]></command> 37 ]]> </command>
39 <inputs> 38 <inputs>
40 <expand macro="matrix_h5_cooler_multiple_macro" /> 39 <expand macro="matrix_h5_cooler_multiple_macro" />
41 40
42 <param argument="--referencePoints" type="data" format='interval' 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." />
43 label="Reference points" 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.' />
44 help="Bed file contains all reference points which should be used to create viewpoints." /> 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.' />
45 <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.' />
46 <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.' />
47 44
48 <param argument="--backgroundModelFile" type="data" format='tabular' 45 <param argument="--backgroundModelFile" type="data" format='tabular' label="Background model" help="The background file computed by chicViewpointBackgroundModel" />
49 label="Background model" 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.' />
50 help="The background file computed by chicViewpointBackgroundModel" /> 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.' />
51 <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.'/> 48 <param argument="--decimalPlaces" type="integer" value="12" label="Decimal places for output" help='Decimal places for all floating value in the output.' />
52 <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.'/> 49
53 <param argument="--decimalPlaces" type="integer" value="12" label="Decimal places for output" help='Decimal places for all floating value in the output.'/> 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." />
54 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." />
55 <param name='writeFileNamesToFile' type='boolean' truevalue='--writeFileNamesToFile interactionFiles.txt' falsevalue="" checked="false" label="Save interaction file names (batch processing)" 52
56 help="Set this parameter if you want to use the batch processing mode for the further analysis."/>
57 <param name='tar' type='boolean' checked="false" label="tar output to one file"
58 help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large."/>
59
60 </inputs> 53 </inputs>
61 <outputs> 54 <outputs>
62 <collection name="interactionFilesCollection" type="list" label="Interaction files"> 55 <collection name="interactionFilesCollection" type="list" label="Interaction files">
63 <discover_datasets pattern="__name__" format="interval" directory="interactionFiles" /> 56 <discover_datasets pattern="__name__" format="interval" directory="interactionFiles" />
64 </collection> 57 </collection>
65 <data name="interactionFileNames" from_work_dir="interactionFiles.txt" format="txt" label="${tool.name} interaction file names"> 58 <data name="interactionFileNames" from_work_dir="interactionFiles.txt" format="txt" label="${tool.name} interaction file names">
66 <filter>writeFileNamesToFile</filter> 59 <filter>writeFileNamesToFile</filter>
67 </data> 60 </data>
68 <data name="interactionFilesTar" from_work_dir="viewpoints.tar" format="tar" label="${tool.name} interaction file names tar"> 61 <data name="interactionFilesTar" from_work_dir="viewpoints.tar" format="tar" label="${tool.name} interaction file names tar">
69 <filter>tar</filter> 62 <filter>tar</filter>
70 </data> 63 </data>
71 </outputs> 64 </outputs>
72 <tests> 65 <tests>
73 <test> 66 <test>
74 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/> 67 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" />
75 68 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed" />
76 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed"/> 69 <param name="backgroundModelFile" value="cHi-C/background.txt" />
77 <param name="backgroundModelFile" value="cHi-C/background.txt"/> 70 <param name="fixateRange" value="500000" />
78 <param name="fixateRange" value="500000"/> 71 <param name="rangeUpstream" value="200000" />
79 <param name="rangeUpstream" value="200000"/> 72 <param name="rangeDownstream" value="200000" />
80 <param name="rangeDownstream" value="200000"/> 73 <param name="writeFileNamesToFile" value="True" />
81 <param name="writeFileNamesToFile" value="True"/>
82
83 74
84 <output_collection name="interactionFilesCollection" type="list" count="6"> 75 <output_collection name="interactionFilesCollection" type="list" count="6">
85 <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"/> 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" />
86 <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"/> 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" />
87 <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"/> 78 <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval">
88 79 <assert_contents>
89 <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"/> 80 <has_text text="18895000" />
90 <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"/> 81 <has_text text="chr1" />
91 <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"/> 82 <has_text text="Tfap2d" />
83 <has_text text="interactions" />
84 <has_text text="472.0" />
85 </assert_contents>
86 </element>
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" />
88 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval">
89 <assert_contents>
90 <has_text text="14100000" />
91 <has_text text="chr1" />
92 <has_text text="Eya1" />
93 <has_text text="interactions" />
94 <has_text text="832.0" />
95 </assert_contents>
96 </element>
97 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval">
98 <assert_contents>
99 <has_text text="4455000" />
100 <has_text text="chr1" />
101 <has_text text="Sox17" />
102 <has_text text="interactions" />
103 <has_text text="978.0" />
104 <has_text text="-30000" />
105 </assert_contents>
106 </element>
92 </output_collection> 107 </output_collection>
93 <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/> 108 <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0' />
94
95 </test> 109 </test>
96 <test> 110 <test>
97 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/> 111 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" />
98 112 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed" />
99 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed"/> 113 <param name="backgroundModelFile" value="cHi-C/background.txt" />
100 <param name="backgroundModelFile" value="cHi-C/background.txt"/> 114 <param name="fixateRange" value="500000" />
101 <param name="fixateRange" value="500000"/> 115 <param name="rangeUpstream" value="200000" />
102 <param name="rangeUpstream" value="200000"/> 116 <param name="rangeDownstream" value="200000" />
103 <param name="rangeDownstream" value="200000"/> 117 <param name="writeFileNamesToFile" value="False" />
104 <param name="writeFileNamesToFile" value="False"/>
105
106
107 <output_collection name="interactionFilesCollection" type="list" count="6"> 118 <output_collection name="interactionFilesCollection" type="list" count="6">
108 <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"/> 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" />
109 <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"/> 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" />
110 <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"/> 121 <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval">
111 122 <assert_contents>
112 <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"/> 123 <has_text text="18893000" />
113 <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"/> 124 <has_text text="chr1" />
114 <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"/> 125 <has_text text="Tfap2d" />
126 <has_text text="interactions" />
127 <has_text text="472.0" />
128 </assert_contents>
129 </element>
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" />
131 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval">
132 <assert_contents>
133 <has_text text="14103000" />
134 <has_text text="chr1" />
135 <has_text text="Eya1" />
136 <has_text text="interactions" />
137 <has_text text="832.0" />
138 <has_text text="-199000" />
139 </assert_contents>
140 </element>
141 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval">
142 <assert_contents>
143 <has_text text="4455000" />
144 <has_text text="chr1" />
145 <has_text text="Sox17" />
146 <has_text text="interactions" />
147 <has_text text="978.0" />
148 <has_text text="-30000" />
149 </assert_contents>
150 </element>
115 </output_collection> 151 </output_collection>
116 <!-- <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/> --> 152 <!-- <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/> -->
117
118 </test> 153 </test>
119 <test> 154 <test>
120 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/> 155 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" />
121 156 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed" />
122 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed"/> 157 <param name="backgroundModelFile" value="cHi-C/background.txt" />
123 <param name="backgroundModelFile" value="cHi-C/background.txt"/> 158 <param name="fixateRange" value="500000" />
124 <param name="fixateRange" value="500000"/> 159 <param name="rangeUpstream" value="200000" />
125 <param name="rangeUpstream" value="200000"/> 160 <param name="rangeDownstream" value="200000" />
126 <param name="rangeDownstream" value="200000"/> 161 <param name="writeFileNamesToFile" value="True" />
127 <param name="writeFileNamesToFile" value="True"/> 162 <param name='tar' value='True' />
128 <param name='tar' value='True'/>
129
130 <output name="interactionFilesTar" file="cHi-C/chicViewpoint/viewpoints.tar" ftype='tar' compare="sim_size" delta='40000' /> 163 <output name="interactionFilesTar" file="cHi-C/chicViewpoint/viewpoints.tar" ftype='tar' compare="sim_size" delta='40000' />
131 <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/> 164 <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0' />
132
133 </test> 165 </test>
134 </tests> 166 </tests>
135 <help><![CDATA[ 167 <help><![CDATA[
136 168
137 Compute viewpoints for all given reference points 169 Compute viewpoints for all given reference points
146 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. 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.
147 179
148 For more information about HiCExplorer please consider our documentation on readthedocs.io_ 180 For more information about HiCExplorer please consider our documentation on readthedocs.io_
149 181
150 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 182 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
151 ]]></help> 183 ]]> </help>
152 <expand macro="citations" /> 184 <expand macro="citations" />
153 </tool> 185 </tool>