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comparison cravatp_submit.xml @ 3:a018c44dc18b draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatp_score_and_annotate commit d80e60ce74aabe64e131d560085af099d52b81cf-dirty
author galaxyp
date Fri, 07 Sep 2018 16:53:05 -0400
parents 2c7bcc1219fc
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2:f3027b8f28bd 3:a018c44dc18b
1 <tool id="cravatp_submit" name="CRAVAT-P Submit, Intersect, Check, and Retrieve" version="1.0.0"> 1 <tool id="cravatp_submit" name="CRAVAT-P Submit, Intersect, Check, and Retrieve" version="1.1.0">
2 <description>| Submits, intersects, checks for, and retrieves data for cancer annotation.</description> 2 <description>| Submits, intersects, checks for, and retrieves data for cancer annotation.</description>
3 <command detect_errors="aggressive"> 3 <command detect_errors="aggressive">
4 <![CDATA[ 4 <![CDATA[
5 #if $proteo.proteoInput == 'yes': 5 #if $proteo.proteoInput == 'yes':
6 #if '$analysis.type' == 'CHASM' or '$analysis.type' == 'CHASM+VEST': 6 #if '$analysis.type' == 'CHASM' or '$analysis.type' == 'CHASM+VEST':
7 python '$__tool_directory__/cravatp_submit.py' '$input' '$GRCh' '$variant' '$gene' '$noncoding' '$error' '$analysis.type' --classifier '$analysis.classifier' --proBED '$proBED' --intersectOnly '$proteo.intersectedVariants' --vcfOutput '$vcf_output' 7 python '$__tool_directory__/cravatp_submit.py' '$input' '$GRCh' '$variant' '$gene' '$noncoding' '$error' '$analysis.type' --classifier '$analysis.classifier' --proBED '$proBED' Do-allIntersect '$proteo.intersectedVariants' --vcfOutput '$vcf_output'
8 #else: 8 #else:
9 python '$__tool_directory__/cravatp_submit.py' '$input' '$GRCh' '$variant' '$gene' '$noncoding' '$error' '$analysis.type' --proBED '$proBED' --intersectOnly '$proteo.intersectedVariants' --vcfOutput '$vcf_output' 9 python '$__tool_directory__/cravatp_submit.py' '$input' '$GRCh' '$variant' '$gene' '$noncoding' '$error' '$analysis.type' --proBED '$proBED' --allIntersect '$proteo.intersectedVariants' --vcfOutput '$vcf_output'
10 #end if 10 #end if
11 #else: 11 #else:
12 #if $analysis.type == 'CHASM' or $analysis.type == 'CHASM+VEST': 12 #if $analysis.type == 'CHASM' or $analysis.type == 'CHASM+VEST':
13 python '$__tool_directory__/cravatp_submit.py' '$input' '$GRCh' '$variant' '$gene' '$noncoding' '$error' '$analysis.type' --classifier '$analysis.classifier' 13 python '$__tool_directory__/cravatp_submit.py' '$input' '$GRCh' '$variant' '$gene' '$noncoding' '$error' '$analysis.type' --classifier '$analysis.classifier'
14 #else: 14 #else:
18 ]]></command> 18 ]]></command>
19 19
20 <inputs> 20 <inputs>
21 <param format="vcf" name="input" type="data" label="Source file" help="Accepts transcriptomic or genomic inputs (e.g., tabular, VCF). Additional details can be found below."></param> 21 <param format="vcf" name="input" type="data" label="Source file" help="Accepts transcriptomic or genomic inputs (e.g., tabular, VCF). Additional details can be found below."></param>
22 <conditional name="proteo"> 22 <conditional name="proteo">
23 <param name="proteoInput" type="select" label="Intersect with proteogenomic input?" help="Source file (first input) must be in genomic input to enable intersection with this proteogenomic file."> 23 <param name="proteoInput" type="select" label="Intersect with proteogenomic input?" help="Source file (first input) must be in genomic input to enable intersection with this proteogenomic file. Only variants intersected between the genomic and proteogenomic files are annotated, unless specified otherwise below.">
24 <option value="yes">Yes</option> 24 <option value="yes">Yes</option>
25 <option value="no" selected="true">No</option> 25 <option value="no" selected="true">No</option>
26 </param> 26 </param>
27 <when value="yes"> 27 <when value="yes">
28 <param format="BED" name="proBED" type="data" label="Peptides with Genomic Coordinates (ProBED Format)"></param> 28 <param format="BED" name="proBED" type="data" label="Peptides with Genomic Coordinates (ProBED Format)"></param>
29 <param name="intersectedVariants" type="boolean" checked="false" label="Submit only intersected variants?" help="Submits the intersected portion of the genomic file to CRAVAT's server. Restricting analysis to only intersected variants takes less time but also provides less-comprehensive results."></param> 29 <param name="intersectedVariants" type="boolean" checked="false" label="Submit all variants?" help="Submits all variants, including non-intersected variants, to the CRAVAT server. This results in a complete genomic analysis at the expense of a longer runtime."></param>
30 <param name="output_vcf" type="boolean" checked="false" label="Output intersected genomic file?" help="The intersected genomic file (e.g., VCF) will be included as a result."></param> 30 <param name="output_vcf" type="boolean" checked="false" label="Output intersected genomic file?" help="The intersected genomic file (e.g., VCF) will be included as a result."></param>
31 </when> 31 </when>
32 <when value="no"> 32 <when value="no">
33 </when> 33 </when>
34 </conditional> 34 </conditional>
35 <conditional name="analysis"> 35 <conditional name="analysis">
36 <param format="tabular" name="type" type="select" label="Analysis Program" help="VEST and CHASM are machine learning methods for predicting the pathogenicity and functional significance of variants, respectively."> 36 <param format="tabular" name="type" type="select" label="Analysis Program" help="CHASM and VEST are machine learning methods for predicting the functional significance and pathogenicity of variants, respectively.">
37 <option value="None">None</option> 37 <option value="None">None</option>
38 <option value="CHASM">CHASM</option> 38 <option value="CHASM">CHASM</option>
39 <option value="VEST">VEST</option> 39 <option value="VEST">VEST</option>
40 <option value="CHASM+VEST">CHASM and VEST</option> 40 <option value="CHASM+VEST">CHASM and VEST</option>
41 </param> 41 </param>
108 <option value="GRCh38">GRCh38/hg38</option> 108 <option value="GRCh38">GRCh38/hg38</option>
109 <option value="GRCh37">GRCh37/hg19</option> 109 <option value="GRCh37">GRCh37/hg19</option>
110 </param> 110 </param>
111 </inputs> 111 </inputs>
112 <outputs> 112 <outputs>
113 <collection name="results" type="list" label="CRAVAT Results on ${on_string}"> 113 <collection name="results" type="list" label="CRAVAT-P Results on ${on_string}">
114 <data format="tabular" label="CRAVAT: Gene Level Annotation Report on ${on_string}" name="gene" /> 114 <data format="tabular" label="CRAVAT: gene Level Annotation Report on ${on_string}" name="gene" />
115 <data format="tabular" label="CRAVAT: Variant Report on ${on_string}" name="variant" /> 115 <data format="tabular" label="CRAVAT: Variant Report on ${on_string}" name="variant" />
116 <data format="tabular" label="CRAVAT: Non-coding Variant Report on ${on_string}" name="noncoding" /> 116 <data format="tabular" label="CRAVAT: Non-coding Variant Report on ${on_string}" name="noncoding" />
117 <data format="tabular" label="CRAVAT: Errors on ${on_string}" name="error" /> 117 <data format="tabular" label="CRAVAT: Errors on ${on_string}" name="error" />
118 </collection> 118 </collection>
119 <data format="vcf" label="Intersected VCF on ${on_string}" name="vcf_output"> 119 <data format="vcf" label="Intersected VCF on ${on_string}" name="vcf_output">
120 <filter>proteo['proteoInput'] == 'yes' and proteo['output_vcf']</filter> 120 <filter>proteo['proteoInput'] == 'yes' and proteo['output_vcf']</filter>
121 </data> 121 </data>
122 </outputs> 122 </outputs>
123 <tests> 123 <tests>
124 <!-- GRCh38/hg38 and no analysis test case -->
125 <test>
126 <param name="input" value="Freebayes_one-variant.vcf"/>
127 <param name="GRCh" value="GRCh38"/>
128 <param name="variant" value="variant.tsv"/>
129 <param name="gene" value="gene.tsv"/>
130 <param name="noncoding" value="noncoding.tsv"/>
131 <param name="error" value="error.tsv"/>
132 <param name="type" value="None"/>
133 <output_collection name="results" type="list">
134 <element name="variant">
135 <assert_contents>
136 <has_text text="#Variant Report" />
137 <has_text text="hg38"/>
138 <has_text text="UPF1" />
139 <not_has_text text="VEST" />
140 </assert_contents>
141 </element>
142 </output_collection>
143 </test>
144 <!-- GRCh38/hg38 and no analysis test case -->
145 <test>
146 <param name="input" value="Freebayes_one-variant.vcf"/>
147 <param name="GRCh" value="GRCh38"/>
148 <param name="variant" value="variant.tsv"/>
149 <param name="gene" value="gene.tsv"/>
150 <param name="noncoding" value="noncoding.tsv"/>
151 <param name="error" value="error.tsv"/>
152 <param name="type" value="None"/>
153 <output_collection name="results" type="list">
154 <element name="variant">
155 <assert_contents>
156 <has_text text="#Variant Report" />
157 <has_text text="hg38"/>
158 <has_text text="UPF1" />
159 <not_has_text text="VEST" />
160 </assert_contents>
161 </element>
162 </output_collection>
163 </test>
164 <!-- GRCh37/hg19 and no analysis test case -->
165 <test>
166 <param name="input" value="Freebayes_one-variant.vcf"/>
167 <param name="GRCh" value="GRCh37"/>
168 <param name="variant" value="variant.tsv"/>
169 <param name="gene" value="gene.tsv"/>
170 <param name="noncoding" value="noncoding.tsv"/>
171 <param name="error" value="error.tsv"/>
172 <param name="type" value="None"/>
173 <output_collection name="results" type="list">
174 <element name="variant">
175 <assert_contents>
176 <has_text text="#Variant Report" />
177 <has_text text="hg19"/>
178 <not_has_text text="VEST" />
179 </assert_contents>
180 </element>
181 </output_collection>
182 </test>
183 <!-- CHASM with "Breast" classifier test case -->
184 <test>
185 <param name="input" value="Freebayes_one-variant.vcf"/>
186 <param name="GRCh" value="GRCh38"/>
187 <param name="variant" value="variant.tsv"/>
188 <param name="gene" value="gene.tsv"/>
189 <param name="noncoding" value="noncoding.tsv"/>
190 <param name="error" value="error.tsv"/>
191 <param name="type" value="CHASM"/>
192 <param name="classifier" value="Breast"/>
193 <output_collection name="results" type="list">
194 <element name="variant">
195 <assert_contents>
196 <has_text text="hg38"/>
197 <has_text text="UPF1" />
198 <has_text text="Breast" />
199 <has_text text="#Variant Report" />
200 <not_has_text text="VEST" />
201 </assert_contents>
202 </element>
203 </output_collection>
204 </test>
205 <!-- Proteogenomic test case --> 124 <!-- Proteogenomic test case -->
206 <test> 125 <test>
207 <param name="input" value="Freebayes_one-variant.vcf"/> 126 <param name="input" value="Freebayes_one-variant.vcf"/>
208 <param name="GRCh" value="GRCh38"/> 127 <param name="GRCh" value="GRCh38"/>
209 <param name="variant" value="variant.tsv"/> 128 <param name="variant" value="variant.tsv"/>
215 <param name="proteoInput" value="yes" /> 134 <param name="proteoInput" value="yes" />
216 <param name="proBED" value="MCF7_proBed.bed"/> 135 <param name="proBED" value="MCF7_proBed.bed"/>
217 <output_collection name="results" type="list"> 136 <output_collection name="results" type="list">
218 <element name="variant"> 137 <element name="variant">
219 <assert_contents> 138 <assert_contents>
220 <has_text text="#Variant Report" /> 139 <has_text text="hg38"/>
221 <has_text text="hg38"/> 140 <has_text text="UPF1" />
222 <has_text text="UPF1" /> 141 <not_has_text text="CRABP2"/>
223 <has_text text="EAIDSPVSFLVLHNQIR" /> 142 </assert_contents>
224 </assert_contents> 143 </element>
225 </element> 144 </output_collection>
226 </output_collection> 145 </test>
227 </test> 146 <!-- GRCh38/hg38 and no analysis test case -->
147 <test>
148 <param name="input" value="Freebayes_one-variant.vcf"/>
149 <param name="GRCh" value="GRCh38"/>
150 <param name="variant" value="variant.tsv"/>
151 <param name="gene" value="gene.tsv"/>
152 <param name="noncoding" value="noncoding.tsv"/>
153 <param name="error" value="error.tsv"/>
154 <param name="type" value="None"/>
155 <output_collection name="results" type="list">
156 <element name="variant">
157 <assert_contents>
158 <has_text text="#Variant Report" />
159 <has_text text="hg38"/>
160 <has_text text="UPF1" />
161 <not_has_text text="VEST" />
162 </assert_contents>
163 </element>
164 </output_collection>
165 </test>
166 <!-- GRCh38/hg38 and no analysis test case -->
167 <test>
168 <param name="input" value="Freebayes_one-variant.vcf"/>
169 <param name="GRCh" value="GRCh38"/>
170 <param name="variant" value="variant.tsv"/>
171 <param name="gene" value="gene.tsv"/>
172 <param name="noncoding" value="noncoding.tsv"/>
173 <param name="error" value="error.tsv"/>
174 <param name="type" value="None"/>
175 <output_collection name="results" type="list">
176 <element name="variant">
177 <assert_contents>
178 <has_text text="#Variant Report" />
179 <has_text text="hg38"/>
180 <has_text text="UPF1" />
181 <not_has_text text="VEST" />
182 </assert_contents>
183 </element>
184 </output_collection>
185 </test>
186 <!-- GRCh37/hg19 and no analysis test case -->
187 <test>
188 <param name="input" value="Freebayes_one-variant.vcf"/>
189 <param name="GRCh" value="GRCh37"/>
190 <param name="variant" value="variant.tsv"/>
191 <param name="gene" value="gene.tsv"/>
192 <param name="noncoding" value="noncoding.tsv"/>
193 <param name="error" value="error.tsv"/>
194 <param name="type" value="None"/>
195 <output_collection name="results" type="list">
196 <element name="variant">
197 <assert_contents>
198 <has_text text="#Variant Report" />
199 <has_text text="hg19"/>
200 <not_has_text text="VEST" />
201 </assert_contents>
202 </element>
203 </output_collection>
204 </test>
205 <!-- CHASM with "Breast" classifier test case -->
206 <test>
207 <param name="input" value="Freebayes_one-variant.vcf"/>
208 <param name="GRCh" value="GRCh38"/>
209 <param name="variant" value="variant.tsv"/>
210 <param name="gene" value="gene.tsv"/>
211 <param name="noncoding" value="noncoding.tsv"/>
212 <param name="error" value="error.tsv"/>
213 <param name="type" value="CHASM"/>
214 <param name="classifier" value="Breast"/>
215 <output_collection name="results" type="list">
216 <element name="variant">
217 <assert_contents>
218 <has_text text="hg38"/>
219 <has_text text="UPF1" />
220 <has_text text="Breast" />
221 <has_text text="#Variant Report" />
222 <not_has_text text="VEST" />
223 </assert_contents>
224 </element>
225 </output_collection>
226 </test>
227
228 <!-- "Output intersected VCF" test case --> 228 <!-- "Output intersected VCF" test case -->
229 <test> 229 <test>
230 <param name="input" value="Freebayes_one-variant.vcf"/> 230 <param name="input" value="Freebayes_one-variant.vcf"/>
231 <param name="GRCh" value="GRCh38"/> 231 <param name="GRCh" value="GRCh38"/>
232 <param name="variant" value="variant.tsv"/> 232 <param name="variant" value="variant.tsv"/>
238 <param name="proteoInput" value="yes" /> 238 <param name="proteoInput" value="yes" />
239 <param name="proBED" value="MCF7_proBed.bed"/> 239 <param name="proBED" value="MCF7_proBed.bed"/>
240 <param name="output_vcf" value="true"/> 240 <param name="output_vcf" value="true"/>
241 <output name="vcf_output" file="results/intersected_vcf.vcf"/> 241 <output name="vcf_output" file="results/intersected_vcf.vcf"/>
242 </test> 242 </test>
243 <!-- "Only intersected proteogenomic variants submitted" test case--> 243 <!-- "All proteogenomic variants submitted" test case-->
244 <test> 244 <test>
245 <param name="input" value="Freebayes_two-variants.vcf"/> 245 <param name="input" value="Freebayes_two-variants.vcf"/>
246 <param name="GRCh" value="GRCh38"/> 246 <param name="GRCh" value="GRCh38"/>
247 <param name="variant" value="variant.tsv"/> 247 <param name="variant" value="variant.tsv"/>
248 <param name="gene" value="gene.tsv"/> 248 <param name="gene" value="gene.tsv"/>
256 <output_collection name="results" type="list"> 256 <output_collection name="results" type="list">
257 <element name="variant"> 257 <element name="variant">
258 <assert_contents> 258 <assert_contents>
259 <has_text text="hg38"/> 259 <has_text text="hg38"/>
260 <has_text text="UPF1" /> 260 <has_text text="UPF1" />
261 <not_has_text text="CRABP2"/> 261 <has_text text="CRABP2"/>
262 </assert_contents>
263 </element>
264 </output_collection>
265 </test>
266 <!-- "Only intersected proteogenomic variants submitted" test case-->
267 <test>
268 <param name="input" value="Freebayes_two-variants.vcf"/>
269 <param name="GRCh" value="GRCh38"/>
270 <param name="variant" value="variant.tsv"/>
271 <param name="gene" value="gene.tsv"/>
272 <param name="noncoding" value="noncoding.tsv"/>
273 <param name="error" value="error.tsv"/>
274 <param name="type" value="CHASM" />
275 <param name="classifier" value="Breast" />
276 <param name="proteoInput" value="yes" />
277 <param name="proBED" value="MCF7_proBed.bed"/>
278 <param name="intersectedVariants" value="true" />
279 <output_collection name="results" type="list">
280 <element name="variant">
281 <assert_contents>
282 <has_text text="#Variant Report" />
283 <has_text text="hg38"/>
284 <has_text text="UPF1" />
285 <has_text text="EAIDSPVSFLVLHNQIR" />
262 </assert_contents> 286 </assert_contents>
263 </element> 287 </element>
264 </output_collection> 288 </output_collection>
265 </test> 289 </test>
266 </tests> 290 </tests>
288 CSub1 chr2 39644095 \+ ATGCT GA TCGA-02-0252 312 CSub1 chr2 39644095 \+ ATGCT GA TCGA-02-0252
289 ===== ===== ========= ====== ========= ========= ==================== 313 ===== ===== ========= ====== ========= ========= ====================
290 ]]> 314 ]]>
291 </help> 315 </help>
292 <citations> 316 <citations>
317 <citation type="doi">10.1021/acs.jproteome.8b00404</citation>
293 <citation type="doi">10.1158/0008-5472.CAN-17-0338</citation> 318 <citation type="doi">10.1158/0008-5472.CAN-17-0338</citation>
294 <citation type="doi">10.1186/s13059-017-1377-x</citation> 319 <citation type="doi">10.1186/s13059-017-1377-x</citation>
295 </citations> 320 </citations>
296 </tool> 321 </tool>