Mercurial > repos > pjbriggs > rnachipintegrator
comparison rnachipintegrator_macros.xml @ 0:0abe6bac47a6 draft
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
| author | pjbriggs |
|---|---|
| date | Wed, 24 Feb 2016 09:25:18 -0500 |
| parents | |
| children | d37526cd12aa |
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| -1:000000000000 | 0:0abe6bac47a6 |
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| 1 <macros> | |
| 2 <token name="@VERSION@">1.0.0</token> | |
| 3 <xml name="requirements"> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="0.8.4">python_xlsxwriter</requirement> | |
| 6 <requirement type="package" version="1.0.0">rnachipintegrator</requirement> | |
| 7 </requirements> | |
| 8 </xml> | |
| 9 <xml name="version_command"> | |
| 10 <version_command>RnaChipIntegrator --version</version_command> | |
| 11 </xml> | |
| 12 <xml name="analysis_options"> | |
| 13 <param name="cutoff" type="integer" value="1000000" optional="true" | |
| 14 label="Maximum distance between a gene/peak pair | |
| 15 before it is omitted from the analyses (bp)" | |
| 16 help="Leave blank for no limit (--cutoff)" /> | |
| 17 <param name="number" type="integer" value="4" optional="true" | |
| 18 label="Maximum number of gene/peak pairs to report from | |
| 19 the analyses" | |
| 20 help="Leave blank for no limit (--number)" /> | |
| 21 <param name="promoter_start" type="integer" value="-1000" optional="true" | |
| 22 label="Start of promoter region with respect to gene TSS" /> | |
| 23 <param name="promoter_end" type="integer" value="100" optional="true" | |
| 24 label="End of promoter region with respect to gene TSS" /> | |
| 25 <param name="edge" type="select" | |
| 26 label="Gene 'edges' to consider in distance calculations" | |
| 27 help="(--edge)"> | |
| 28 <option value="tss" selected="true">TSS only</option> | |
| 29 <option value="both">Nearest of TSS or TES</option> | |
| 30 </param> | |
| 31 </xml> | |
| 32 <xml name="output_options"> | |
| 33 <conditional name="output"> | |
| 34 <param name="compact_format" type="boolean" checked="true" | |
| 35 truevalue="true" falsevalue="false" | |
| 36 label="Use 'compact' output format" | |
| 37 help="Puts all hits for each peak or gene on a single line | |
| 38 (--compact)" /> | |
| 39 <when value="true"> | |
| 40 </when> | |
| 41 <when value="false"> | |
| 42 <param name="pad_output" type="boolean" checked="false" | |
| 43 truevalue="--pad" falsevalue="" | |
| 44 label="Output same number of lines for each peak" | |
| 45 help="Add blank lines in output for peaks with fewer than | |
| 46 maximum number of hits (--pad)" /> | |
| 47 <param name="summary" type="boolean" checked="false" | |
| 48 truevalue="true" falsevalue="false" | |
| 49 label="Output additional 'summary' datasets" | |
| 50 help="Summaries contain only the top hits for each peak | |
| 51 or feature (--summary)" /> | |
| 52 </when> | |
| 53 </conditional> | |
| 54 </xml> | |
| 55 <xml name="citations"> | |
| 56 <citations> | |
| 57 <citation type="bibtex">@misc{Briggs2016, | |
| 58 author = {Briggs PJ, Donaldson IJ, Zeef LAH}, | |
| 59 title = {RnaChipIntegrator}, | |
| 60 publisher = {GitHub}, | |
| 61 journal = {GitHub repository}, | |
| 62 year = {2016}, | |
| 63 howpublished = {\url{https://github.com/fls-bioinformatics-core/RnaChipIntegrator}}, | |
| 64 version = {1.0.0} | |
| 65 }</citation> | |
| 66 </citations> | |
| 67 </xml> | |
| 68 </macros> |