Mercurial > repos > bgruening > deeptools_multi_bam_summary
comparison multiBamSummary.xml @ 26:a1a84914d00d draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
| author | bgruening |
|---|---|
| date | Mon, 18 Feb 2019 17:21:57 -0500 |
| parents | ebc070a847a4 |
| children | d9e59cf2fdf6 |
comparison
equal
deleted
inserted
replaced
| 25:89c5b63a954d | 26:a1a84914d00d |
|---|---|
| 21 | 21 |
| 22 #if $outRawCounts: | 22 #if $outRawCounts: |
| 23 --outRawCounts '$outFileRawCounts' | 23 --outRawCounts '$outFileRawCounts' |
| 24 #end if | 24 #end if |
| 25 | 25 |
| 26 #if $scalingFactors: | |
| 27 --scalingFactors '$scalingFactorsFile' | |
| 28 #end if | |
| 29 | |
| 26 #if $mode.modeOpt == "bins": | 30 #if $mode.modeOpt == "bins": |
| 27 --binSize '$mode.binSize' | 31 --binSize '$mode.binSize' |
| 28 --distanceBetweenBins '$mode.distanceBetweenBins' | 32 --distanceBetweenBins '$mode.distanceBetweenBins' |
| 29 #else: | 33 #else: |
| 30 --BED $mode.region_file | 34 --BED $mode.region_file |
| 42 ]]> | 46 ]]> |
| 43 </command> | 47 </command> |
| 44 | 48 |
| 45 <inputs> | 49 <inputs> |
| 46 <expand macro="multiple_input_bams" MIN="2"/> | 50 <expand macro="multiple_input_bams" MIN="2"/> |
| 51 <expand macro="custom_sample_labels" /> | |
| 47 | 52 |
| 48 <conditional name="mode"> | 53 <conditional name="mode"> |
| 49 <param name="modeOpt" type="select" label="Choose computation mode" | 54 <param name="modeOpt" type="select" label="Choose computation mode" |
| 50 help="In the bins mode, the coverage is computed for equally | 55 help="In the bins mode, the coverage is computed for equally |
| 51 sized bins. \nIn BED file mode, a list of genomic regions | 56 sized bins. \nIn BED file mode, a list of genomic regions |
| 77 <expand macro="gtf_options" /> | 82 <expand macro="gtf_options" /> |
| 78 <expand macro="blacklist" /> | 83 <expand macro="blacklist" /> |
| 79 </expand> | 84 </expand> |
| 80 | 85 |
| 81 <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to file" help=""/> | 86 <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to file" help=""/> |
| 87 <param argument="--scalingFactors" type="boolean" label="Save scaling factors" help="Scaling factors calculated as in DESeq2 and made directly compatible with bamCoverage."/> | |
| 82 | 88 |
| 83 </inputs> | 89 </inputs> |
| 84 <outputs> | 90 <outputs> |
| 85 <data format="deeptools_coverage_matrix" name="outFile" label="${tool.name} on ${on_string}: correlation matrix" /> | 91 <data format="deeptools_coverage_matrix" name="outFile" label="${tool.name} on ${on_string}: correlation matrix" /> |
| 86 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts"> | 92 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts"> |
| 87 <filter>outRawCounts is True</filter> | 93 <filter>outRawCounts is True</filter> |
| 94 </data> | |
| 95 <data format="tabular" name="scalingFactorsFile" label="${tool.name} on ${on_string}: scaling factors"> | |
| 96 <filter>scalingFactors is True</filter> | |
| 88 </data> | 97 </data> |
| 89 </outputs> | 98 </outputs> |
| 90 <tests> | 99 <tests> |
| 91 <test> | 100 <test> |
| 92 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" /> | 101 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" /> |