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comparison hubArchiveCreator.xml @ 13:25809f699cb3 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
author rmarenco
date Thu, 11 Aug 2016 19:02:29 -0400
parents d05236b15f81
children cbd8982c9f51
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12:747475757cb0 13:25809f699cb3
12 <requirement type="package" version="1.2">samtools</requirement> 12 <requirement type="package" version="1.2">samtools</requirement>
13 <!-- Conda dependencies --> 13 <!-- Conda dependencies -->
14 <requirement type="package" version="332">ucsc-bedtobigbed</requirement> 14 <requirement type="package" version="332">ucsc-bedtobigbed</requirement>
15 <requirement type="package" version="332">ucsc-fatotwobit</requirement> 15 <requirement type="package" version="332">ucsc-fatotwobit</requirement>
16 <requirement type="package" version="324">ucsc-genepredtobed</requirement> 16 <requirement type="package" version="324">ucsc-genepredtobed</requirement>
17 <requirement type="package" version="332">ucsc-genepredtobiggenepred</requirement>
17 <requirement type="package" version="324">ucsc-gff3togenepred</requirement> 18 <requirement type="package" version="324">ucsc-gff3togenepred</requirement>
18 <requirement type="package" version="324">ucsc-gtftogenepred</requirement> 19 <requirement type="package" version="324">ucsc-gtftogenepred</requirement>
19 <requirement type="package" version="324">ucsc-twobitinfo</requirement> 20 <requirement type="package" version="324">ucsc-twobitinfo</requirement>
20 <requirement type="package" version="1.3.1">samtools</requirement> 21 <requirement type="package" version="1.3.1">samtools</requirement>
21 </requirements> 22 </requirements>
97 --data_json '$all_data_json' 98 --data_json '$all_data_json'
98 99
99 ## Retrieve the user email 100 ## Retrieve the user email
100 --user_email $__user_email__ 101 --user_email $__user_email__
101 102
102 -d $__tool_directory__ -e $output.files_path -o $output; 103 -d $__tool_directory__
104
105 -e $output.files_path
106
107 $advanced_options.debug_mode
108
109 -o $output;
103 ]]></command> 110 ]]></command>
104 111
105 <inputs> 112 <inputs>
106 <param 113 <param
107 name="genome_name" 114 name="genome_name"
182 </when> 189 </when>
183 </conditional> 190 </conditional>
184 </when> 191 </when>
185 </conditional> 192 </conditional>
186 </repeat> 193 </repeat>
187 </inputs> 194 <conditional name="advanced_options">
195 <param name="advanced_options_selector" type="select" label="Advanced options">
196 <option value="off" selected="true">Hide advanced options</option>
197 <option value="on">Display advanced options</option>
198 </param>
199 <!-- TODO: Avoid redundancy here -->
200 <when value="on">
201 <param name="debug_mode" type="boolean"
202 label="Activate debug mode" checked="false"
203 truevalue="--debug_mode" falsevalue="">
204 <help>
205 Use this option if you are a G-OnRamp developer
206 </help>
207 </param>
208 </when>
209 <when value="off">
210 <param name="debug_mode" type="hidden"
211 value="">
212 </param>
213 </when>
214 </conditional>
215 </inputs>
188 216
189 <outputs> 217 <outputs>
190 <data format="trackhub" name="output"/> 218 <data format="trackhub" name="output"/>
191 </outputs> 219 </outputs>
192 220