Mercurial > repos > bgruening > deeptools_multi_bigwig_summary

comparison multiBigwigSummary.xml @ 33:8aa73e204ada draft default tip

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9
author bgruening
date Thu, 01 Jun 2023 10:22:06 +0000
parents 6f32d646433b
children
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32:c21b4362b0ae 33:8aa73e204ada
1 <tool id="deeptools_multi_bigwig_summary" name="multiBigwigSummary" version="@WRAPPER_VERSION@.0"> 1 <tool id="deeptools_multi_bigwig_summary" name="multiBigwigSummary" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
2 <description>calculates average scores for a list of two or more bigwig files</description> 2 <description>calculates average scores for a list of two or more bigwig files</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">multiBigwigSummary</token> 4 <token name="@BINARY@">multiBigwigSummary</token>
5 <import>deepTools_macros.xml</import> 5 <import>deepTools_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 #set files=[] 10 #set files=[]
11 #set labels=[] 11 #set labels=[]
12 12
13 @multiple_input_bigwigs@ 13 @multiple_input_bigwigs@
14
15 @BINARY@ 14 @BINARY@
16 $mode.modeOpt 15 $mode.modeOpt
17 16
18 @THREADS@ 17 @THREADS@
19 18
20 --outFileName $outFile 19 --outFileName $outFile
21 20
22 --bwfiles #echo ' '.join($files)# 21 --bwfiles #echo ' '.join($files)#
23 --labels #echo ' '.join($labels)# 22
24 23 #if $custom_sample_labels_conditional.custom_labels_select == 'Yes'
24 --labels #echo ' '.join($custom_sample_labels_conditional.labels)#
25 #end if
25 #if $outRawCounts: 26 #if $outRawCounts:
26 --outRawCounts '$outFileRawCounts' 27 --outRawCounts '$outFileRawCounts'
27 #end if 28 #end if
28 29
29 #if $mode.modeOpt == "bins": 30 #if $mode.modeOpt == "bins":
41 @ADVANCED_OPTS_GTF@ 42 @ADVANCED_OPTS_GTF@
42 @blacklist@ 43 @blacklist@
43 #end if 44 #end if
44 ]]> 45 ]]>
45 </command> 46 </command>
46
47 <inputs> 47 <inputs>
48 <expand macro="multiple_input_bigwigs" MIN="2" LABEL="Bigwig files" TITLE="BigWig files"/> 48 <expand macro="multiple_input_bigwigs" MIN="2" LABEL="Bigwig files" TITLE="BigWig files"/>
49 <expand macro="custom_sample_labels" /> 49 <expand macro="custom_sample_labels" />
50 50
51 <conditional name="mode"> 51 <conditional name="mode">
68 <param name="region_file" type="data" format="bed,gtf" 68 <param name="region_file" type="data" format="bed,gtf"
69 label="Region file in BED format" 69 label="Region file in BED format"
70 help="Correlation is computed for the number of reads that overlap such regions."/> 70 help="Correlation is computed for the number of reads that overlap such regions."/>
71 </when> 71 </when>
72 </conditional> 72 </conditional>
73
74 <expand macro="region_limit_operation" /> 73 <expand macro="region_limit_operation" />
75 <param argument="--outRawCounts" type="boolean" label="Save raw counts (scores) to file" help=""/> 74 <param argument="--outRawCounts" type="boolean" label="Save raw counts (scores) to file" help=""/>
76 75
77 <expand macro="advancedOpt_scaffold"> 76 <expand macro="advancedOpt_scaffold">
78 <expand macro="gtf_options" /> 77 <expand macro="gtf_options" />
89 <tests> 88 <tests>
90 <test> 89 <test>
91 <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" /> 90 <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
92 <param name="modeOpt" value="bins" /> 91 <param name="modeOpt" value="bins" />
93 <param name="binSize" value="10" /> 92 <param name="binSize" value="10" />
94 <param name="corMethod" value="spearman" />
95 <output name="outFile" file="multiBigwigSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" /> 93 <output name="outFile" file="multiBigwigSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
96 </test> 94 </test>
97 <!--test> 95 <test>
98 <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" /> 96 <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
99 <param name="modeOpt" value="BED-file" /> 97 <param name="modeOpt" value="bins" />
100 <param name="region_file" value="multiBamSummary_regions.bed" /> 98 <param name="binSize" value="10" />
101 <param name="corMethod" value="pearson" />
102 <param name="outRawCounts" value="True" /> 99 <param name="outRawCounts" value="True" />
100 <conditional name="custom_sample_labels_conditional">
101 <param name="custom_labels_select" value="Yes"/>
102 <param name="labels" value="sample1 sample2"/>
103 </conditional>
103 <output name="outFileRawCounts" file="multiBigwigSummary_result2.tabular" ftype="tabular" /> 104 <output name="outFileRawCounts" file="multiBigwigSummary_result2.tabular" ftype="tabular" />
104 <output name="outFileName" file="multiBigwigSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" /> 105 <output name="outFile" file="multiBigwigSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
105 </test--> 106 </test>
106 </tests> 107 </tests>
107 <help> 108 <help>
108 <![CDATA[ 109 <![CDATA[
109 110
110 What it does 111 What it does