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