Mercurial > repos > bgruening > deeptools
comparison deepTools_macros.xml @ 30:2e5b92e7f3cb draft
Uploaded
| author | bgruening |
|---|---|
| date | Tue, 28 Jan 2014 13:54:34 -0500 |
| parents | 60788be7b346 |
| children | 934b9fccabd4 |
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| 29:60788be7b346 | 30:2e5b92e7f3cb |
|---|---|
| 1 <macros> | 1 <macros> |
| 2 <xml name="bamCorrelate_mode_actions"> | 2 <xml name="bamCorrelate_mode_actions"> |
| 3 <param name="region" type="text" value="" | |
| 4 label="Region of the genome to limit the operation to" | |
| 5 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"" /> | |
| 6 | |
| 3 <conditional name="advancedOpt"> | 7 <conditional name="advancedOpt"> |
| 4 <param name="showAdvancedOpt" type="select" label="Show advanced options" > | 8 <param name="showAdvancedOpt" type="select" label="Show advanced options" > |
| 5 <option value="no" selected="true">no</option> | 9 <option value="no" selected="true">no</option> |
| 6 <option value="yes">yes</option> | 10 <option value="yes">yes</option> |
| 7 </param> | 11 </param> |
| 8 <when value="no" /> | 12 <when value="no" /> |
| 9 <when value="yes"> | 13 <when value="yes"> |
| 10 <param name="region" type="text" value="" | |
| 11 label="Region of the genome to limit the operation to" | |
| 12 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"" /> | |
| 13 | |
| 14 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" | 14 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" |
| 15 label="Do not extend paired ends" | 15 label="Do not extend paired ends" |
| 16 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/> | 16 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/> |
| 17 | 17 |
| 18 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" | 18 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" |
| 41 <xml name="requirements"> | 41 <xml name="requirements"> |
| 42 <requirements> | 42 <requirements> |
| 43 <requirement type="package" >samtools</requirement> | 43 <requirement type="package" >samtools</requirement> |
| 44 <requirement type="package" >deepTools</requirement> | 44 <requirement type="package" >deepTools</requirement> |
| 45 <requirement type="package" >ucsc_tools</requirement> | 45 <requirement type="package" >ucsc_tools</requirement> |
| 46 <requirement type="package" version="1.5.4_e5c75f3e967be0fa1d6dbcbb63a0f992e1cdcd61">deepTools</requirement> | 46 <requirement type="package" version="1.5.4_eabc1c3842f4b6367fb41904061a3b95c9a0ce0c">deepTools</requirement> |
| 47 <requirement type="package" version="0.1">ucsc_tools</requirement> | 47 <requirement type="package" version="0.1">ucsc_tools</requirement> |
| 48 <requirement type="package" version="1.7.1">numpy</requirement> | 48 <requirement type="package" version="1.7.1">numpy</requirement> |
| 49 <requirement type="package" version="0.7.7">pysam</requirement> | 49 <requirement type="package" version="0.7.7">pysam</requirement> |
| 50 <requirement type="package" version="0.12.0">scipy</requirement> | 50 <requirement type="package" version="0.12.0">scipy</requirement> |
| 51 <requirement type="package" version="1.2.1">matplotlib</requirement> | 51 <requirement type="package" version="1.2.1">matplotlib</requirement> |