Mercurial > repos > iuc > gff_to_prot

comparison macros.xml @ 6:4a2b9f7491a3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
author iuc
date Tue, 08 Oct 2019 08:23:26 -0400
parents 78c16a7fe346
children e046db34c47a
comparison
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5:78c16a7fe346 6:4a2b9f7491a3
7 </citations> 7 </citations>
8 </xml> 8 </xml>
9 <xml name="requirements"> 9 <xml name="requirements">
10 <requirements> 10 <requirements>
11 <requirement type="package" version="@VERSION@">transit</requirement> 11 <requirement type="package" version="@VERSION@">transit</requirement>
12 <requirement type="package" version="3.7">python</requirement>
12 <yield /> 13 <yield />
13 </requirements> 14 </requirements>
14 </xml> 15 </xml>
15 <token name="@VERSION@">2.5.2</token> 16 <token name="@VERSION@">3.0.1</token>
16 <xml name="outputs"> 17 <xml name="outputs">
17 <yield /> 18 <yield />
18 <data name="sites" from_work_dir="transit_out.txt" format="tabular" label="${tool.name} on ${on_string} Sites" /> 19 <data name="sites" from_work_dir="transit_out.txt" format="tabular" label="${tool.name} on ${on_string} Sites" />
19 </xml> 20 </xml>
20 <xml name="replicates"> 21 <xml name="replicates">
41 </xml> 42 </xml>
42 <xml name="ignore_tas"> 43 <xml name="ignore_tas">
43 <param name="nterm" argument="-iN" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the N terminus." /> 44 <param name="nterm" argument="-iN" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the N terminus." />
44 <param name="cterm" argument="-iC" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the C terminus." /> 45 <param name="cterm" argument="-iC" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the C terminus." />
45 </xml> 46 </xml>
47 <xml name="normal">
48 <param name="normalization" argument="-n" type="select" label="Normalization method" value="TTR">
49 <option value="TTR">TTR</option>
50 <option value="nonorm">No Normalization</option>
51 <option value="nzmean">Non-Zero Mean</option>
52 <option value="totreads">Total read counts</option>
53 <option value="zinfnb">Zero inflated Negative Binomial model</option>
54 <option value="quantile">Quantile Normalization</option>
55 <option value="betageom">Beta-Geometric Correction</option>
56 </param>
57 </xml>
46 <xml name="standard_inputs"> 58 <xml name="standard_inputs">
47 <expand macro="inputs" /> 59 <expand macro="inputs" />
48 <yield /> 60 <yield />
49 <expand macro="ignore_tas" /> 61 <expand macro="ignore_tas" />
62 <expand macro="normal" />
50 </xml> 63 </xml>
51 <token name="@LINK_INPUTS@"> 64 <token name="@LINK_INPUTS@">
52 <![CDATA[ 65 <![CDATA[
53 #if str($mode.replicates) == 'Batch': 66 #if str($mode.replicates) == 'Batch':
54 #set $input_files = $mode.inputs 67 #set $input_files = $mode.inputs
62 ]]> 75 ]]>
63 </token> 76 </token>
64 <token name="@STANDARD_OPTIONS@"> 77 <token name="@STANDARD_OPTIONS@">
65 -iN $nterm 78 -iN $nterm
66 -tC $cterm 79 -tC $cterm
80 -n $normalization
67 </token> 81 </token>
68 </macros> 82 </macros>