Mercurial > repos > bgruening > deeptools_bigwig_compare
comparison bigwigCompare.xml @ 8:aec7ca832043 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
| author | bgruening |
|---|---|
| date | Mon, 19 Sep 2016 17:33:20 -0400 |
| parents | 48f35873bbb1 |
| children | f90c8a697ee9 |
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| 7:18f46b571982 | 8:aec7ca832043 |
|---|---|
| 32 --binSize $advancedOpt.binSize | 32 --binSize $advancedOpt.binSize |
| 33 | 33 |
| 34 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": | 34 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": |
| 35 --plotTitle '$advancedOpt.plotTitle' | 35 --plotTitle '$advancedOpt.plotTitle' |
| 36 #end if | 36 #end if |
| 37 @blacklist@ | |
| 37 | 38 |
| 38 #end if | 39 #end if |
| 39 ]]> | 40 ]]> |
| 40 </command> | 41 </command> |
| 41 <inputs> | 42 <inputs> |
| 42 <param name="bigwigFile1" format="bigwig" type="data" label="Treatment bigwig file" /> | 43 <param name="bigwigFile1" format="bigwig" type="data" label="Treatment bigwig file" /> |
| 43 <param name="bigwigFile2" format="bigwig" type="data" label="bigWig file" /> | 44 <param name="bigwigFile2" format="bigwig" type="data" label="bigWig file" /> |
| 44 | 45 |
| 45 <conditional name="comparison"> | 46 <conditional name="comparison"> |
| 46 <param name="comparison_select" type="select" | 47 <param name="comparison_select" type="select" |
| 47 label="How to compare the two files" | 48 label="How to compare the two files" |
| 48 help="The default is to output the log2ratio between the two samples. | 49 help="The default is to output the log2ratio between the two samples. |
| 49 The reciprocal ratio returns the negative of the inverse of the ratio if | 50 The reciprocal ratio returns the negative of the inverse of the ratio if |
| 50 the ratio is less than 0. The resulting values are interpreted as negative fold changes. (--ratio)"> | 51 the ratio is less than 0. The resulting values are interpreted as negative |
| 51 <option value="log2" selected="true">compute log2 of the number of reads ratio</option> | 52 fold changes. To output the scaled values from the first or second BAM file, |
| 52 <option value="ratio">compute the ratio of the number of reads</option> | 53 select 'first' or 'second'."> |
| 53 <option value="subtract">compute difference (subtract input from treatment) of the number of reads</option> | 54 <option value="log2" selected="true">Compute log2 of the number of reads ratio</option> |
| 54 <option value="add">compute the sum over all reads</option> | 55 <option value="ratio">Compute the ratio of the number of reads</option> |
| 56 <option value="subtract">Compute difference (subtract input from treatment) of the number of reads</option> | |
| 57 <option value="add">Compute the sum of number of reads</option> | |
| 55 <option value="reciprocal_ratio">Computes the fold change. If the fold change is less than 1, the negative of the inverse is reported. E.g. A fold change of 10 to 5 would be reported not as 0.5 but as -2</option> | 58 <option value="reciprocal_ratio">Computes the fold change. If the fold change is less than 1, the negative of the inverse is reported. E.g. A fold change of 10 to 5 would be reported not as 0.5 but as -2</option> |
| 59 <option value="first">Returns the scaled value of the first BAM file</option> | |
| 60 <option value="second">Returns the scaled value of the second BAM file</option> | |
| 56 </param> | 61 </param> |
| 57 <when value="log2"> | 62 <when value="log2"> |
| 58 <expand macro="pseudocount" /> | 63 <expand macro="pseudocount" /> |
| 59 </when> | 64 </when> |
| 60 <when value="ratio"> | 65 <when value="ratio"> |
| 61 <expand macro="pseudocount" /> | 66 <expand macro="pseudocount" /> |
| 62 </when> | 67 </when> |
| 63 <when value="subtract" /> | 68 <when value="subtract" /> |
| 64 <when value="add" /> | 69 <when value="add" /> |
| 70 <when value="first" /> | |
| 71 <when value="second" /> | |
| 65 <when value="reciprocal_ratio"> | 72 <when value="reciprocal_ratio"> |
| 66 <expand macro="pseudocount" /> | 73 <expand macro="pseudocount" /> |
| 67 </when> | 74 </when> |
| 68 </conditional> | 75 </conditional> |
| 69 | 76 |
| 86 help="Size of the bins in bases for the output of the bigwig/bedgraph file."/> | 93 help="Size of the bins in bases for the output of the bigwig/bedgraph file."/> |
| 87 | 94 |
| 88 <expand macro="skipNAs" /> | 95 <expand macro="skipNAs" /> |
| 89 <expand macro="scaleFactors" /> | 96 <expand macro="scaleFactors" /> |
| 90 <expand macro="plotTitle" /> | 97 <expand macro="plotTitle" /> |
| 98 <expand macro="blacklist" /> | |
| 91 </when> | 99 </when> |
| 92 </conditional> | 100 </conditional> |
| 93 </inputs> | 101 </inputs> |
| 94 <outputs> | 102 <outputs> |
| 95 <data format="bigwig" name="outFileName"> | 103 <data format="bigwig" name="outFileName"> |