Mercurial > repos > bgruening > deeptools_multi_bigwig_summary
comparison multiBigwigSummary.xml @ 28:d580d6acd1df draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit e7e3025eb4fffe5deb34c12a6d402d79241d9ed5
author | bgruening |
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date | Fri, 19 May 2023 08:37:10 +0000 |
parents | 6e33cebc6063 |
children | d9ce4897dbb2 |
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27:459cfa861f0b | 28:d580d6acd1df |
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1 <tool id="deeptools_multi_bigwig_summary" name="multiBigwigSummary" version="@WRAPPER_VERSION@.0"> | 1 <tool id="deeptools_multi_bigwig_summary" name="multiBigwigSummary" version="@WRAPPER_VERSION@.1"> |
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 |