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comparison tophat2_wrapper.xml @ 8:758594ed0364 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 commit 1dbddfa19e12087e6e9fc177a088cdbf7ab9b414
author devteam
date Mon, 09 May 2016 10:33:50 -0400
parents 4eb3c3beb9c7
children 0849fa93eadb
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7:4eb3c3beb9c7 8:758594ed0364
1 <tool id="tophat2" name="TopHat" version="0.9"> 1 <tool id="tophat2" name="TopHat" version="2.1.0">
2 <!-- Wrapper compatible with Tophat version 2.0.0+ --> 2 <!-- Wrapper compatible with Tophat version 2.0.0+ -->
3 <description>Gapped-read mapper for RNA-seq data</description> 3 <description>Gapped-read mapper for RNA-seq data</description>
4 <version_command>tophat2 --version</version_command> 4 <macros>
5 <import>tophat_macros.xml</import>
6 <xml name="paired_parameters">
7 <param name="mate_inner_distance" type="integer" value="300" label="Mean Inner Distance between Mate Pairs" help="-r/--mate-inner-dist; This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. The default is 50bp."/>
8 <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs" help="--mate-std-dev; The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp."/>
9 <!-- Discordant pairs. -->
10 <param name="report_discordant_pairs" type="select" label="Report discordant pair alignments?" help="--no-discordant">
11 <option value="No">No</option>
12 <option selected="True" value="Yes">Yes</option>
13 </param>
14 </xml>
15 <macro name="dbKeyActions">
16 <actions>
17 <conditional name="refGenomeSource.genomeSource">
18 <when value="indexed">
19 <action type="metadata" name="dbkey">
20 <option type="from_data_table" name="tophat2_indexes" column="1" offset="0">
21 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
22 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
23 </option>
24 </action>
25 </when>
26 <when value="history">
27 <action type="metadata" name="dbkey">
28 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
29 </action>
30 </when>
31 </conditional>
32 </actions>
33 </macro>
34 </macros>
5 <requirements> 35 <requirements>
6 <requirement type="package" version="2.2.5">bowtie2</requirement> 36 <requirement type="package" version="2.2.5">bowtie2</requirement>
7 <requirement type="package" version="2.0.14">tophat</requirement> 37 <requirement type="package" version="2.1.0">tophat</requirement>
8 </requirements> 38 </requirements>
39 <stdio>
40 <regex match="Exception|Error" source="both" level="fatal" description="Tool execution failed"/>
41 <regex match=".*" source="both" level="log" description="tool progress"/>
42 </stdio>
43 <version_command>tophat2 --version</version_command>
9 44
10 <command> 45 <command>
11 ## 46 ##
12 ## Set path to index, building the reference if necessary. 47 ## Set path to index, building the reference if necessary.
13 ## 48 ##
73 108
74 #if $params.coverage_search.use_search == "Yes": 109 #if $params.coverage_search.use_search == "Yes":
75 --coverage-search 110 --coverage-search
76 --min-coverage-intron $params.coverage_search.min_coverage_intron 111 --min-coverage-intron $params.coverage_search.min_coverage_intron
77 --max-coverage-intron $params.coverage_search.max_coverage_intron 112 --max-coverage-intron $params.coverage_search.max_coverage_intron
78 #else: 113 #elif $params.coverage_search.use_search == "No"
79 --no-coverage-search 114 --no-coverage-search
80 #end if 115 #end if
81 116
82 #if str($params.microexon_search) == "Yes": 117 #if str($params.microexon_search) == "Yes":
83 --microexon-search 118 --microexon-search
191 <param name="output_unmapped" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output unmapped reads" help="If checked, a BAM with the unmapped reads will be added to the history" /> 226 <param name="output_unmapped" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output unmapped reads" help="If checked, a BAM with the unmapped reads will be added to the history" />
192 <!-- Options for supplying own junctions. --> 227 <!-- Options for supplying own junctions. -->
193 <expand macro="own_junctionsConditional" /> 228 <expand macro="own_junctionsConditional" />
194 <!-- Coverage search. --> 229 <!-- Coverage search. -->
195 <conditional name="coverage_search"> 230 <conditional name="coverage_search">
196 <param name="use_search" type="select" label="Use Coverage Search" help="Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity."> 231 <param name="use_search" type="select" label="Use coverage-based search for junctions" help="Select 'Auto' to let TopHat decide when to enable coverage search (e.g. disable it for reads 75bp or longer). Select 'Yes' to enforce maximum sensitivity and to specify minimum and maximum intron length">
197 <option selected="true" value="No">No</option> 232 <option selected="true" value="auto">Auto</option>
198 <option value="Yes">Yes</option> 233 <option value="No">No (--no-coverage-search)</option>
234 <option value="Yes">Yes (--coverage-search)</option>
199 </param> 235 </param>
236 <when value="auto" />
200 <when value="Yes"> 237 <when value="Yes">
201 <param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" help="--min-coverage-intron; The minimum intron length that may be found during coverage search. The default is 50."/> 238 <param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" help="--min-coverage-intron; The minimum intron length that may be found during coverage search. The default is 50."/>
202 <param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" help="--max-coverage-intron; The maximum intron length that may be found during coverage search. The default is 20000."/> 239 <param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" help="--max-coverage-intron; The maximum intron length that may be found during coverage search. The default is 20000."/>
203 </when> 240 </when>
204 <when value="No" /> 241 <when value="No" />
268 </when> 305 </when>
269 <when value="no" /> 306 <when value="no" />
270 </conditional> <!-- readGroup --> 307 </conditional> <!-- readGroup -->
271 </inputs> 308 </inputs>
272 309
273 <stdio>
274 <regex match="Exception|Error" source="both" level="fatal" description="Tool execution failed"/>
275 <regex match=".*" source="both" level="log" description="tool progress"/>
276 </stdio>
277
278 <outputs> 310 <outputs>
279 <data format="txt" name="align_summary" label="${tool.name} on ${on_string}: align_summary" from_work_dir="tophat_out/align_summary.txt"/> 311 <data format="txt" name="align_summary" label="${tool.name} on ${on_string}: align_summary" from_work_dir="tophat_out/align_summary.txt"/>
280 <data format="tabular" name="fusions" label="${tool.name} on ${on_string}: fusions" from_work_dir="tophat_out/fusions.out"> 312 <data format="tabular" name="fusions" label="${tool.name} on ${on_string}: fusions" from_work_dir="tophat_out/fusions.out">
281 <filter>(params['settingsType'] == 'full' and params['fusion_search']['do_search'] == 'Yes')</filter> 313 <filter>(params['settingsType'] == 'full' and params['fusion_search']['do_search'] == 'Yes')</filter>
282 </data> 314 </data>
296 <filter>(params['settingsType'] == 'full' and params['output_unmapped'])</filter> 328 <filter>(params['settingsType'] == 'full' and params['output_unmapped'])</filter>
297 <expand macro="dbKeyActions" /> 329 <expand macro="dbKeyActions" />
298 </data> 330 </data>
299 331
300 </outputs> 332 </outputs>
301
302 <macros>
303 <import>tophat_macros.xml</import>
304 <xml name="paired_parameters">
305 <param name="mate_inner_distance" type="integer" value="300" label="Mean Inner Distance between Mate Pairs" help="-r/--mate-inner-dist; This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. The default is 50bp."/>
306 <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs" help="--mate-std-dev; The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp."/>
307 <!-- Discordant pairs. -->
308 <param name="report_discordant_pairs" type="select" label="Report discordant pair alignments?" help="--no-discordant">
309 <option value="No">No</option>
310 <option selected="True" value="Yes">Yes</option>
311 </param>
312 </xml>
313 <macro name="dbKeyActions">
314 <actions>
315 <conditional name="refGenomeSource.genomeSource">
316 <when value="indexed">
317 <action type="metadata" name="dbkey">
318 <option type="from_data_table" name="tophat2_indexes" column="1" offset="0">
319 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
320 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
321 </option>
322 </action>
323 </when>
324 <when value="history">
325 <action type="metadata" name="dbkey">
326 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
327 </action>
328 </when>
329 </conditional>
330 </actions>
331 </macro>
332 </macros>
333 333
334 <tests> 334 <tests>
335 <!-- Test base-space single-end reads with pre-built index and preset parameters --> 335 <!-- Test base-space single-end reads with pre-built index and preset parameters -->
336 <test> 336 <test>
337 <!-- TopHat commands: 337 <!-- TopHat commands: