Mercurial > repos > bgruening > deeptools
annotate bigwigCompare.xml @ 71:106cd88dc9da draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
| author | bgruening |
|---|---|
| date | Fri, 18 Sep 2015 07:34:39 -0400 |
| parents | 1dbd76a58d8b |
| children |
| rev | line source |
|---|---|
| 61 | 1 <tool id="deeptools_bigwigCompare" name="bigwigCompare" version="@WRAPPER_VERSION@.0"> |
| 2 <description>normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference</description> | |
| 3 <macros> | |
| 4 <token name="@BINARY@">bigwigCompare</token> | |
| 5 <import>deepTools_macros.xml</import> | |
| 6 </macros> | |
|
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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7 <expand macro="requirements"/> |
| 61 | 8 <command> |
| 9 <![CDATA[ | |
| 10 bigwigCompare | |
| 11 | |
| 12 @THREADS@ | |
| 13 | |
| 14 --bigwig1 '$bigwigFile1' | |
| 15 --bigwig2 '$bigwigFile2' | |
| 16 | |
| 17 --outFileName '$outFileName' | |
| 18 --outFileFormat '$outFileFormat' | |
| 19 | |
| 20 --ratio $comparison.comparison_select | |
| 21 | |
| 22 #if $comparison.comparison_select in ['ratio','log2']: | |
| 23 --pseudocount $comparison.pseudocount | |
| 24 #end if | |
| 25 | |
| 26 #if str($region).strip() != '': | |
| 27 --region '$region' | |
| 28 #end if | |
| 29 | |
| 30 #if $advancedOpt.showAdvancedOpt == "yes": | |
| 31 | |
| 32 --missingDataAsZero $advancedOpt.missingDataAsZero | |
| 33 --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2' | |
| 34 --binSize $advancedOpt.binSize | |
| 35 | |
|
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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36 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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37 --plotTitle '$advancedOpt.plotTitle' |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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38 #end if |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
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39 |
| 61 | 40 #end if |
| 41 ]]> | |
| 42 </command> | |
| 43 <inputs> | |
| 44 <param name="bigwigFile1" format="bigwig" type="data" label="Treatment bigwig file" /> | |
| 45 <param name="bigwigFile2" format="bigwig" type="data" label="bigWig file" /> | |
| 46 | |
| 47 <conditional name="comparison"> | |
| 48 <param name="comparison_select" type="select" | |
|
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
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49 label="How to compare the two files" |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
galaxyp
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50 help="The default is to output the log2ratio between the two samples. |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
galaxyp
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51 The reciprocal ratio returns the negative of the inverse of the ratio if |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
galaxyp
parents:
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changeset
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52 the ratio is less than 0. The resulting values are interpreted as negative fold changes. (--ratio)"> |
| 61 | 53 <option value="log2" selected="true">compute log2 of the number of reads ratio</option> |
| 54 <option value="ratio">compute the ratio of the number of reads</option> | |
| 55 <option value="subtract">compute difference (subtract input from treatment) of the number of reads</option> | |
| 56 <option value="add">compute the sum over all reads</option> | |
|
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
galaxyp
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57 <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> |
| 61 | 58 </param> |
| 59 <when value="log2"> | |
| 60 <expand macro="pseudocount" /> | |
| 61 </when> | |
| 62 <when value="ratio"> | |
| 63 <expand macro="pseudocount" /> | |
| 64 </when> | |
| 65 <when value="subtract" /> | |
| 66 <when value="add" /> | |
|
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
galaxyp
parents:
65
diff
changeset
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67 <when value="reciprocal_ratio"> |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
galaxyp
parents:
65
diff
changeset
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68 <expand macro="pseudocount" /> |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
galaxyp
parents:
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diff
changeset
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69 </when> |
| 61 | 70 </conditional> |
| 71 | |
| 72 <param name="outFileFormat" type="select" label="Coverage file format"> | |
| 73 <option value="bigwig" selected="true">bigwig</option> | |
| 74 <option value="bedgraph">bedgraph</option> | |
| 75 </param> | |
| 76 | |
| 77 <expand macro="region_limit_operation" /> | |
| 78 | |
| 79 <conditional name="advancedOpt"> | |
| 80 <param name="showAdvancedOpt" type="select" label="Show advanced options" > | |
| 81 <option value="no" selected="true">no</option> | |
| 82 <option value="yes">yes</option> | |
| 83 </param> | |
| 84 <when value="no" /> | |
| 85 <when value="yes"> | |
| 86 <param name="binSize" type="integer" value="50" min="1" | |
| 87 label="Length, in base pairs, of the non-overlapping bin for averaging the score over the regions length" | |
| 88 help="Size of the bins in bp for the output of the bigwig/bedgraph file. (--binSize)"/> | |
| 89 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True" | |
| 90 label ="Treat missing data as zero" | |
|
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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91 help ="This parameter determines if missing data should be replaced with a zero. |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
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92 If set to "no", missing data will be ignored and will not be included in the |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
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diff
changeset
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93 output file at all. Missing data is defined as those regions for which no value exists in |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
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changeset
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94 *any* of the bigwig files. The decision to include or exclude missing data depends on |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
61
diff
changeset
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95 the interpretation of the data. Missing data in a bigwig file may mean that there is no |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
61
diff
changeset
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96 information available for certain regions, for example a repetitive region that is not |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
61
diff
changeset
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97 being considered. In the same file regions with low coverage may get zero read counts. |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
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diff
changeset
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98 If missing data is replaced by zero, this would convert the excluded repetitive regions |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
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changeset
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99 into regions of low coverage. (--missingDataAsZero)" /> |
| 61 | 100 <expand macro="scaleFactor" /> |
|
65
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
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diff
changeset
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101 <expand macro="plotTitle" /> |
| 61 | 102 </when> |
| 103 </conditional> | |
| 104 </inputs> | |
| 105 <outputs> | |
| 106 <data format="bigwig" name="outFileName"> | |
| 107 <change_format> | |
| 108 <when input="outFileFormat" value="bigwig" format="bigwig" /> | |
| 109 <when input="outFileFormat" value="bedgraph" format="bedgraph" /> | |
| 110 </change_format> | |
| 111 </data> | |
| 112 </outputs> | |
| 113 <tests> | |
| 114 <test> | |
|
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
galaxyp
parents:
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115 <param name="bigwigFile1" value="test.bw" ftype="bigwig" /> |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
galaxyp
parents:
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116 <param name="bigwigFile2" value="test.bw" ftype="bigwig" /> |
| 61 | 117 <param name="showAdvancedOpt" value="no" /> |
| 118 <param name="outFileFormat" value="bigwig" /> | |
| 119 <param name="binSize" value="5" /> | |
| 120 <param name="comparison_select" value="ratio" /> | |
| 121 <output name="outFileName" file="bigwigCompare_result1.bw" ftype="bigwig" /> | |
| 122 </test> | |
| 123 <test> | |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
galaxyp
parents:
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124 <param name="bigwigFile1" value="test.bw" ftype="bigwig" /> |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
galaxyp
parents:
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diff
changeset
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125 <param name="bigwigFile2" value="test.bw" ftype="bigwig" /> |
| 61 | 126 <param name="showAdvancedOpt" value="no" /> |
| 127 <param name="outFileFormat" value="bedgraph" /> | |
| 128 <param name="binSize" value="10" /> | |
| 129 <param name="comparison_select" value="ratio" /> | |
| 130 <output name="outFileName" file="bigwigCompare_result2.bg" ftype="bedgraph" /> | |
| 131 </test> | |
| 132 </tests> | |
| 133 <help> | |
| 134 <![CDATA[ | |
| 135 **What it does** | |
| 136 | |
| 137 This tool compares two bigwig files based on the number of mapped reads. To | |
| 138 compare the bigwig files the genome is partitioned into bins of equal size, | |
| 139 then the number of reads found in each BAM file are counted for such bins and | |
| 140 finally a summarizing value is reported. This value can be the ratio of the | |
| 141 number of reads per bin, the log2 of the ratio, the sum or the difference. | |
| 142 | |
| 143 | |
| 144 ----- | |
| 145 | |
| 146 @REFERENCES@ | |
| 147 ]]> | |
| 148 </help> | |
| 149 <expand macro="citations" /> | |
| 150 </tool> |