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annotate macros.xml @ 0:5412208882fc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
author dave
date Mon, 05 Nov 2018 12:53:04 -0500
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children 39dcc05e4b60
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5412208882fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
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1 <?xml version="1.0"?>
5412208882fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
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2 <macros>
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3 <xml name="citations">
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4 <citations>
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5 <citation type="doi">10.1371/journal.pcbi.1004401</citation>
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6 <yield />
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7 </citations>
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8 </xml>
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9 <xml name="requirements">
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10 <requirements>
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11 <requirement type="package" version="@VERSION@">transit</requirement>
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12 <yield />
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13 </requirements>
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14 </xml>
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15 <token name="@VERSION@">2.3.1</token>
5412208882fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
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16 <xml name="outputs">
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17 <yield />
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18 <data name="output" from_work_dir="transit_out.txt" format="tabular" label="${tool.name} on ${on_string}: Output" />
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19 <data name="genes" from_work_dir="transit_out_genes.txt" format="tabular" label="${tool.name} on ${on_string}: Genes" />
5412208882fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
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20 </xml>
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21 <xml name="inputs">
5412208882fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
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22 <param name="inputs" type="data" format="wig" multiple="true" label="Input .wig files" />
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23 <param name="annotation" type="data" format="gff3" label="Input annotation" />
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24 </xml>
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25 <xml name="replicates">
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26 <param name="replicates" type="select" label="How to handle replicates">
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27 <option value="Mean">Mean</option>
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28 <option value="Sum">Sum</option>
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29 </param>
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30 </xml>
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31 <xml name="ignore_tas">
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32 <param name="nterm" argument="-iN" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the N terminus." />
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33 <param name="cterm" argument="-iC" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the C terminus." />
5412208882fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
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34 </xml>
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35 <xml name="standard_inputs">
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36 <expand macro="inputs" />
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37 <expand macro="replicates" />
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38 <yield />
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39 <expand macro="ignore_tas" />
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40 </xml>
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41 <token name="@LINK_INPUTS@">
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42 <![CDATA[
5412208882fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
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43 #set $input_files = ','.join(['input_file_%d.wig' % idx for idx, _ in enumerate(str($inputs).split(','))])
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44 #for idx, filename in enumerate(str($inputs).split(',')):
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45 ln -s '$filename' input_file_${idx}.wig &&
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46 #end for
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47 ln -s '$annotation' annotation.dat &&
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48 ]]>
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49 </token>
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50 <token name="@FILES@">
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51 <![CDATA[
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52 $input_files
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53 annotation.dat
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54 'transit_out.txt'
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55 ]]>
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56 </token>
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57 <token name="@STANDARD_OPTIONS@">
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58 -r $replicates
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59 -iN $nterm
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60 -tC $cterm
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61 </token>
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62 </macros>