Mercurial > repos > bgruening > deeptools_bigwig_compare
comparison bigwigCompare.xml @ 11:f90c8a697ee9 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca
author | bgruening |
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date | Tue, 24 Jan 2017 04:51:01 -0500 |
parents | aec7ca832043 |
children | 78e60b236515 |
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10:163f2951146c | 11:f90c8a697ee9 |
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47 <param name="comparison_select" type="select" | 47 <param name="comparison_select" type="select" |
48 label="How to compare the two files" | 48 label="How to compare the two files" |
49 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. |
50 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 |
51 the ratio is less than 0. The resulting values are interpreted as negative | 51 the ratio is less than 0. The resulting values are interpreted as negative |
52 fold changes. To output the scaled values from the first or second BAM file, | 52 fold changes. To output the scaled values from the first or second bigWig file, |
53 select 'first' or 'second'."> | 53 select 'first' or 'second'."> |
54 <option value="log2" selected="true">Compute log2 of the number of reads ratio</option> | 54 <option value="log2" selected="true">Compute log2 of the signal ratio</option> |
55 <option value="ratio">Compute the ratio of the number of reads</option> | 55 <option value="ratio">Compute the ratio signals</option> |
56 <option value="subtract">Compute difference (subtract input from treatment) of the number of reads</option> | 56 <option value="subtract">Compute difference (subtract input from treatment) of the signal</option> |
57 <option value="add">Compute the sum of number of reads</option> | 57 <option value="add">Compute the sum of the signals</option> |
58 <option value="mean">Compute the mean of the signal in the two files</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="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="first">Returns the scaled value of the first bigWig file</option> |
60 <option value="second">Returns the scaled value of the second BAM file</option> | 61 <option value="second">Returns the scaled value of the second bigWig file</option> |
61 </param> | 62 </param> |
62 <when value="log2"> | 63 <when value="log2"> |
63 <expand macro="pseudocount" /> | 64 <expand macro="pseudocount" /> |
64 </when> | 65 </when> |
65 <when value="ratio"> | 66 <when value="ratio"> |
66 <expand macro="pseudocount" /> | 67 <expand macro="pseudocount" /> |
67 </when> | 68 </when> |
68 <when value="subtract" /> | 69 <when value="subtract" /> |
69 <when value="add" /> | 70 <when value="add" /> |
71 <when value="mean" /> | |
70 <when value="first" /> | 72 <when value="first" /> |
71 <when value="second" /> | 73 <when value="second" /> |
72 <when value="reciprocal_ratio"> | 74 <when value="reciprocal_ratio"> |
73 <expand macro="pseudocount" /> | 75 <expand macro="pseudocount" /> |
74 </when> | 76 </when> |