Mercurial > repos > iuc > transit_resampling

comparison macros.xml @ 4:7288ac4e8583 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit b8111d3ebede6ee71b18fbbabc708cdeab340912-dirty
author dave
date Wed, 03 Apr 2019 14:43:41 -0400
parents 173bf0f6ca1e
children 3fcb70c1ca78
comparison
equal deleted inserted replaced
3:b33af081b02e 4:7288ac4e8583
22 <option value="Mean">Mean</option> 22 <option value="Mean">Mean</option>
23 <option value="Sum">Sum</option> 23 <option value="Sum">Sum</option>
24 </param> 24 </param>
25 </xml> 25 </xml>
26 <xml name="inputs"> 26 <xml name="inputs">
27 <param name="inputs" type="data" format="wig,tabular" multiple="true" label="Input .wig files" /> 27 <conditional name="mode">
28 <param name="replicates" type="select" label="Operation mode" help="If set to 'Batch', transit will run and produce one output for each input file. If set to 'Replicates', transit will run once on all the input files.">
29 <option value="Batch">Batch</option>
30 <option value="Replicates">Replicates</option>
31 </param>
32 <when value="Batch">
33 <param name="inputs" type="data" format="wig,tabular" multiple="false" label="Input .wig files" />
34 </when>
35 <when value="Replicates">
36 <param name="inputs" type="data" format="wig,tabular" multiple="true" label="Input .wig files" />
37 </when>
38 </conditional>
28 <yield /> 39 <yield />
29 <param name="annotation" type="data" format="gff3,tabular" label="Input annotation" /> 40 <param name="annotation" type="data" format="gff3,tabular" label="Input annotation" />
30 </xml> 41 </xml>
31 <xml name="ignore_tas"> 42 <xml name="ignore_tas">
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." /> 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." />
37 <yield /> 48 <yield />
38 <expand macro="ignore_tas" /> 49 <expand macro="ignore_tas" />
39 </xml> 50 </xml>
40 <token name="@LINK_INPUTS@"> 51 <token name="@LINK_INPUTS@">
41 <![CDATA[ 52 <![CDATA[
42 #set $input_files = ','.join(['input_file_%d.wig' % idx for idx, _ in enumerate(str($inputs).split(','))]) 53 #if str($mode.replicates) == 'Batch':
43 #for idx, filename in enumerate(str($inputs).split(',')): 54 #set $input_files = $mode.inputs
44 ln -s '$filename' input_file_${idx}.wig && 55 #else:
45 #end for 56 #set $input_files = ','.join(['input_file_%d.wig' % idx for idx, _ in enumerate(str($mode.inputs).split(','))])
57 #for idx, filename in enumerate(str($mode.inputs).split(',')):
58 ln -s '$filename' input_file_${idx}.wig &&
59 #end for
60 #end if
46 ln -s '$annotation' annotation.dat && 61 ln -s '$annotation' annotation.dat &&
47 ]]> 62 ]]>
48 </token> 63 </token>
49 <token name="@STANDARD_OPTIONS@"> 64 <token name="@STANDARD_OPTIONS@">
50 -iN $nterm 65 -iN $nterm