Mercurial > repos > bgruening > hicexplorer_chicviewpoint

comparison chicViewpoint.xml @ 4:78b70d78a596 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
author iuc
date Fri, 14 Aug 2020 06:12:45 -0400
parents 8fb584526458
children dbfd2cfc0f66
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3:8fb584526458 4:78b70d78a596
1 <tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.1">
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>
25 --decimalPlaces $decimalPlaces 25 --decimalPlaces $decimalPlaces
26 --threads @THREADS@ 26 --threads @THREADS@
27 --backgroundModelFile '$backgroundModelFile' 27 --backgroundModelFile '$backgroundModelFile'
28 --outputFolder interactionFiles 28 --outputFolder interactionFiles
29 $writeFileNamesToFile 29 $writeFileNamesToFile
30
31 #if $tar:
32 && cd interactionFiles
33 && tar -cvf ../viewpoints.tar .
34 && cd ..
35 && rm -rf interactionFiles
36 #end if
30 37
31 ]]></command> 38 ]]></command>
32 <inputs> 39 <inputs>
33 <expand macro="matrix_h5_cooler_multiple_macro" /> 40 <expand macro="matrix_h5_cooler_multiple_macro" />
34 41
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.'/> 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.'/>
46 <param argument="--decimalPlaces" type="integer" value="12" label="Decimal places for output" help='Decimal places for all floating value in the output.'/> 53 <param argument="--decimalPlaces" type="integer" value="12" label="Decimal places for output" help='Decimal places for all floating value in the output.'/>
47 54
48 <param name='writeFileNamesToFile' type='boolean' truevalue='--writeFileNamesToFile interactionFiles.txt' falsevalue="" checked="false" label="Save interaction file names (batch processing)" 55 <param name='writeFileNamesToFile' type='boolean' truevalue='--writeFileNamesToFile interactionFiles.txt' falsevalue="" checked="false" label="Save interaction file names (batch processing)"
49 help="Set this parameter if you want to use the batch processing mode for the further analysis."/> 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
50 </inputs> 60 </inputs>
51 <outputs> 61 <outputs>
52 <collection name="interactionFilesCollection" type="list" label="Interaction files"> 62 <collection name="interactionFilesCollection" type="list" label="Interaction files">
53 <discover_datasets pattern="__name__" format="interval" directory="interactionFiles" /> 63 <discover_datasets pattern="__name__" format="interval" directory="interactionFiles" />
54 </collection> 64 </collection>
55 <data name="interactionFileNames" from_work_dir="interactionFiles.txt" format="txt" label="${tool.name} interaction file names"> 65 <data name="interactionFileNames" from_work_dir="interactionFiles.txt" format="txt" label="${tool.name} interaction file names">
56 <filter>writeFileNamesToFile</filter> 66 <filter>writeFileNamesToFile</filter>
67 </data>
68 <data name="interactionFilesTar" from_work_dir="viewpoints.tar" format="tar" label="${tool.name} interaction file names tar">
69 <filter>tar</filter>
57 </data> 70 </data>
58 </outputs> 71 </outputs>
59 <tests> 72 <tests>
60 <test> 73 <test>
61 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/> 74 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/>
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"/> 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"/>
102 </output_collection> 115 </output_collection>
103 <!-- <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/> --> 116 <!-- <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/> -->
104 117
105 </test> 118 </test>
119 <test>
120 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/>
121
122 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed"/>
123 <param name="backgroundModelFile" value="cHi-C/background.txt"/>
124 <param name="fixateRange" value="500000"/>
125 <param name="rangeUpstream" value="200000"/>
126 <param name="rangeDownstream" value="200000"/>
127 <param name="writeFileNamesToFile" 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' />
131 <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/>
132
133 </test>
106 </tests> 134 </tests>
107 <help><![CDATA[ 135 <help><![CDATA[
108 136
109 Compute viewpoints for all given reference points 137 Compute viewpoints for all given reference points
110 ================================================= 138 =================================================