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comparison tophat2_wrapper.xml @ 4:d1009ebd6f15 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 commit d930385294c447acf3d18e3a8efbe5dbea524b5d
author devteam
date Sun, 01 Jan 2017 06:51:19 -0500
parents 7f44f7ee7ab3
children 8d4074c9c2d8
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3:1449cb926fce 4:d1009ebd6f15
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 ##
58 --no-novel-indels 93 --no-novel-indels
59 #end if 94 #end if
60 95
61 ## Supplying junctions parameters. 96 ## Supplying junctions parameters.
62 #if $params.own_junctions.use_junctions == "Yes": 97 #if $params.own_junctions.use_junctions == "Yes":
63 #if $params.own_junctions.gene_model_ann.use_annotations == "Yes": 98 #if $params.own_junctions.gene_model_ann.use_annotations == "indexed"
99 -G $params.own_junctions.gene_model_ann.gene_annotation_model.fields.path
100 #elif $params.own_junctions.gene_model_ann.use_annotations == "history"
64 -G $params.own_junctions.gene_model_ann.gene_annotation_model 101 -G $params.own_junctions.gene_model_ann.gene_annotation_model
65 #end if 102 #end if
66 #if $params.own_junctions.raw_juncs.use_juncs == "Yes": 103 #if $params.own_junctions.raw_juncs.use_juncs == "Yes":
67 -j $params.own_junctions.raw_juncs.raw_juncs 104 -j $params.own_junctions.raw_juncs.raw_juncs
68 #end if 105 #end if
73 110
74 #if $params.coverage_search.use_search == "Yes": 111 #if $params.coverage_search.use_search == "Yes":
75 --coverage-search 112 --coverage-search
76 --min-coverage-intron $params.coverage_search.min_coverage_intron 113 --min-coverage-intron $params.coverage_search.min_coverage_intron
77 --max-coverage-intron $params.coverage_search.max_coverage_intron 114 --max-coverage-intron $params.coverage_search.max_coverage_intron
78 #else: 115 #elif $params.coverage_search.use_search == "No"
79 --no-coverage-search 116 --no-coverage-search
80 #end if 117 #end if
81 118
82 #if str($params.microexon_search) == "Yes": 119 #if str($params.microexon_search) == "Yes":
83 --microexon-search 120 --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" /> 228 <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. --> 229 <!-- Options for supplying own junctions. -->
193 <expand macro="own_junctionsConditional" /> 230 <expand macro="own_junctionsConditional" />
194 <!-- Coverage search. --> 231 <!-- Coverage search. -->
195 <conditional name="coverage_search"> 232 <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."> 233 <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> 234 <option selected="true" value="auto">Auto</option>
198 <option value="Yes">Yes</option> 235 <option value="No">No (--no-coverage-search)</option>
236 <option value="Yes">Yes (--coverage-search)</option>
199 </param> 237 </param>
238 <when value="auto" />
200 <when value="Yes"> 239 <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."/> 240 <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."/> 241 <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> 242 </when>
204 <when value="No" /> 243 <when value="No" />
268 </when> 307 </when>
269 <when value="no" /> 308 <when value="no" />
270 </conditional> <!-- readGroup --> 309 </conditional> <!-- readGroup -->
271 </inputs> 310 </inputs>
272 311
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> 312 <outputs>
279 <data format="txt" name="align_summary" label="${tool.name} on ${on_string}: align_summary" from_work_dir="tophat_out/align_summary.txt"/> 313 <data format="txt" name="align_summary" label="${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 ${on_string}: fusions" from_work_dir="tophat_out/fusions.out"> 314 <data format="tabular" name="fusions" label="${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> 315 <filter>(params['settingsType'] == 'full' and params['fusion_search']['do_search'] == 'Yes')</filter>
282 </data> 316 </data>
296 <filter>(params['settingsType'] == 'full' and params['output_unmapped'])</filter> 330 <filter>(params['settingsType'] == 'full' and params['output_unmapped'])</filter>
297 <expand macro="dbKeyActions" /> 331 <expand macro="dbKeyActions" />
298 </data> 332 </data>
299 333
300 </outputs> 334 </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>
333 335
334 <tests> 336 <tests>
335 <!-- Test base-space single-end reads with pre-built index and preset parameters --> 337 <!-- Test base-space single-end reads with pre-built index and preset parameters -->
336 <test> 338 <test>
337 <!-- TopHat commands: 339 <!-- TopHat commands: