Mercurial > repos > yating-l > jbrowsearchivecreator

comparison jbrowseArchiveCreator.xml @ 7:5d5fdcb798da draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
author yating-l
date Fri, 20 Apr 2018 13:51:23 -0400
parents 237707a6b74d
children 56d9d10b4990
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6:237707a6b74d 7:5d5fdcb798da
1 <tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.0.1"> 1 <tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.1.1">
2 <description> 2 <description>
3 This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse with Apollo plugin 3 This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse with Apollo plugin
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
8 <requirements> 8 <requirements>
9 <requirement type="package" version="1.2">samtools</requirement> 9 <requirement type="package" version="1.2">samtools</requirement>
10 <requirement type="package" version="1.9">numpy</requirement> 10 <requirement type="package" version="1.9">numpy</requirement>
11 <requirement type="package" version="1.68">biopython</requirement> 11 <requirement type="package" version="1.68">biopython</requirement>
12 <requirement type="package" version="340">ucsc_hac</requirement> 12 <requirement type="package" version="340">ucsc_hac</requirement>
13 <requirement type="package" version="1.12.4">jbrowse_tools</requirement> 13 <requirement type="package" version="1.13.1">jbrowse_tools</requirement>
14 <requirement type="package" version="1.0">gff3sort</requirement>
14 </requirements> 15 </requirements>
15 16
16 <stdio> 17 <stdio>
17 </stdio> 18 </stdio>
18 19
146 #silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)}) 147 #silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)})
147 148
148 #silent $data_parameter_dict.update({"extra_files_path": str($output.extra_files_path)}) 149 #silent $data_parameter_dict.update({"extra_files_path": str($output.extra_files_path)})
149 150
150 #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)}) 151 #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)})
152
153 #silent $data_parameter_dict.update({"feature_tracks_type": str($advanced_options.feature_tracks_type)})
151 154
152 with open(file_path, 'w') as f: 155 with open(file_path, 'w') as f:
153 json.dump($data_parameter_dict, f) 156 json.dump($data_parameter_dict, f)
154 </configfile> 157 </configfile>
155 </configfiles> 158 </configfiles>
326 <conditional name="advanced_options"> 329 <conditional name="advanced_options">
327 <param name="advanced_options_selector" type="select" label="Advanced options"> 330 <param name="advanced_options_selector" type="select" label="Advanced options">
328 <option value="off" selected="true">Hide advanced options</option> 331 <option value="off" selected="true">Hide advanced options</option>
329 <option value="on">Display advanced options</option> 332 <option value="on">Display advanced options</option>
330 </param> 333 </param>
331 <!-- TODO: Avoid redundancy here -->
332 <when value="on"> 334 <when value="on">
333 <param name="debug_mode" type="select" label="Activate debug mode"> 335 <param name="feature_tracks_type" type="select" label="Choose JBrowse feature tracks type">
336 <option value="CanvasFeatures" selected="true">CanvasFeatures</option>
337 <option value="HTMLFeatures">HTMLFeatures (Create a large number of range-indexed static JSON files. Don't choose this option if you want to upload/transfer output JBrowse hub to CyVerse Data Store!)
338 </option>
339 </param>
340 <param name="debug_mode" type="select" label="Activate debug mode">
334 <option value="false" selected="true">No</option> 341 <option value="false" selected="true">No</option>
335 <option value="true">Yes</option> 342 <option value="true">Yes</option>
336 <help> 343 <help>
337 Use this option if you are a G-OnRamp developer 344 Use this option if you are a G-OnRamp developer
338 </help> 345 </help>
339 </param> 346 </param>
340 </when> 347 </when>
341 <when value="off"> 348 <when value="off">
342 <param name="debug_mode" type="hidden" 349 <param name="debug_mode" type="hidden" value="false" />
343 value="false"> 350 <param name="feature_tracks_type" type="hidden" value="CanvasFeatures" />
344 </param>
345 </when> 351 </when>
346 </conditional> 352 </conditional>
347 </inputs> 353 </inputs>
348 354
349 <outputs> 355 <outputs>
351 </outputs> 357 </outputs>
352 <tests> 358 <tests>
353 <test> 359 <test>
354 <param name="genome_name" value="Dbia3"/> 360 <param name="genome_name" value="Dbia3"/>
355 <param name="fasta_file" value="common/dbia3.fa"/> 361 <param name="fasta_file" value="common/dbia3.fa"/>
356 <output name="output" file="only_genome/only_genome.html"> 362 <output name="output" file="only_genome/${tool.name}.html">
357 <!-- Use macro to check the whole common structure without repeated code --> 363 <!-- Use macro to check the whole common structure without repeated code -->
358 <expand macro="verify_hub_structure_no_track" test="only_genome" /> 364 <expand macro="verify_hub_structure_no_track" test="only_genome" />
359 </output> 365 </output>
360 </test> 366 </test>
361 </tests> 367 </tests>
362 <help> 368 <help>
363 This Galaxy tool will create a jbrowse hub which including binary datasets and json datasets that can be used for 369 This Galaxy tool will prepare your files to be ready for visualization on JBrowse/Apollo.
364 JBrowse visualization.
365 </help> 370 </help>
366 <citations> 371 <citations>
367 </citations> 372 </citations>
368 </tool> 373 </tool>