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comparison cravatp_submit.xml @ 1:2c7bcc1219fc draft

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Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL.
author galaxyp
date Thu, 16 Aug 2018 12:27:35 -0400
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children a018c44dc18b
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0:83181dabeb90 1:2c7bcc1219fc
1 <tool id="cravatp_submit" name="CRAVAT-P Submit, Intersect, Check, and Retrieve" version="1.0.0">
2 <description>| Submits, intersects, checks for, and retrieves data for cancer annotation.</description>
3 <command detect_errors="aggressive">
4 <![CDATA[
5 #if $proteo.proteoInput == 'yes':
6 #if '$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 '$vcf_output'
8 #else:
9 python '$__tool_directory__/cravatp_submit.py' '$input' '$GRCh' '$variant' '$gene' '$noncoding' '$error' '$analysis.type' --proBED '$proBED' --intersectOnly '$proteo.intersectedVariants' --vcfOutput '$vcf_output'
10 #end if
11 #else:
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'
14 #else:
15 python '$__tool_directory__/cravatp_submit.py' '$input' '$GRCh' '$variant' '$gene' '$noncoding' '$error' '$analysis.type'
16 #end if
17 #end if
18 ]]></command>
19
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>
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.">
24 <option value="yes">Yes</option>
25 <option value="no" selected="true">No</option>
26 </param>
27 <when value="yes">
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>
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>
32 <when value="no">
33 </when>
34 </conditional>
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.">
37 <option value="None">None</option>
38 <option value="CHASM">CHASM</option>
39 <option value="VEST">VEST</option>
40 <option value="CHASM+VEST">CHASM and VEST</option>
41 </param>
42 <when value="None"/>
43 <when value="VEST"/>
44 <when value="CHASM">
45 <param format="tabular" name="classifier" type="select" label="CHASM Classifier">
46 <option value="Bladder">Bladder</option>
47 <option value="Blood-Lymphocyte">Blood-Lymphocyte</option>
48 <option value="Blood-Myeloid">Blood-Myeloid</option>
49 <option value="Brain-Glioblastoma-Multiforme">Brain-Glioblastoma-Multiforme</option>
50 <option value="Brain-Lower-Grade-Glioma">Brain-Lower-Grade-Glioma</option>
51 <option value="Breast">Breast</option>
52 <option value="Cervix">Cervix</option>
53 <option value="Colon">Colon</option>
54 <option value="GID">GID</option>
55 <option value="Head-and-Neck">Head-and-Neck</option>
56 <option value="Kidney-Chromophobe">Kidney-Chromophobe</option>
57 <option value="Kidney-Clear-Cell">Kidney-Clear-Cell</option>
58 <option value="Kidney-Papillary-Cell">Kidney-Papillary-Cell</option>
59 <option value="Liver-Nonviral">Liver-Nonviral</option>
60 <option value="Liver-Viral">Liver-Viral</option>
61 <option value="Lung-Adenocarcinoma">Lung-Adenocarcinoma</option>
62 <option value="Lung-Squamous-Cell">Lung-Squamous-Cell</option>
63 <option value="Other">Other</option>
64 <option value="Ovary">Ovary</option>
65 <option value="Pancreas">Pancreas</option>
66 <option value="Prostate-Adenocarcinoma">Prostate-Adenocarcinoma</option>
67 <option value="Rectum">Rectum</option>
68 <option value="Skin">Skin</option>
69 <option value="Stomach">Stomach</option>
70 <option value="Thyroid">Thyroid</option>
71 <option value="Uterus">Uterus</option>
72 </param>
73 </when>
74 <when value="CHASM+VEST">
75 <param format="tabular" name="classifier" type="select" label="CHASM Classifier">
76 <option value="Bladder">Bladder</option>
77 <option value="Blood-Lymphocyte">Blood-Lymphocyte</option>
78 <option value="Blood-Myeloid">Blood-Myeloid</option>
79 <option value="Brain-Glioblastoma-Multiforme">Brain-Glioblastoma-Multiforme</option>
80 <option value="Brain-Lower-Grade-Glioma">Brain-Lower-Grade-Glioma</option>
81 <option value="Breast">Breast</option>
82 <option value="Cervix">Cervix</option>
83 <option value="Colon">Colon</option>
84 <option value="GID">GID</option>
85 <option value="Head-and-Neck">Head-and-Neck</option>
86 <option value="Kidney-Chromophobe">Kidney-Chromophobe</option>
87 <option value="Kidney-Clear-Cell">Kidney-Clear-Cell</option>
88 <option value="Kidney-Papillary-Cell">Kidney-Papillary-Cell</option>
89 <option value="Liver-Nonviral">Liver-Nonviral</option>
90 <option value="Liver-Viral">Liver-Viral</option>
91 <option value="Lung-Adenocarcinoma">Lung-Adenocarcinoma</option>
92 <option value="Lung-Squamous-Cell">Lung-Squamous-Cell</option>
93 <option value="Other">Other</option>
94 <option value="Ovary">Ovary</option>
95 <option value="Pancreas">Pancreas</option>
96 <option value="Prostate-Adenocarcinoma">Prostate-Adenocarcinoma</option>
97 <option value="Rectum">Rectum</option>
98 <option value="Skin">Skin</option>
99 <option value="Stomach">Stomach</option>
100 <option value="Thyroid">Thyroid</option>
101 <option value="Uterus">Uterus</option>
102 </param>
103 </when>
104 </conditional>
105 <!-- TODO: programatically retrieve the GRCh from a dataset rather than manually selecting it.-->
106 <param format="tabular" name="GRCh" type="select" label="Genome Reference Consortium Human Build (GRCh)"
107 help="The default human reference genome used for annotation is GRCh38, released on December 24th, 2013 from the Genome Reference Consortium.">
108 <option value="GRCh38">GRCh38/hg38</option>
109 <option value="GRCh37">GRCh37/hg19</option>
110 </param>
111 </inputs>
112 <outputs>
113 <collection name="results" type="list" label="CRAVAT Results on ${on_string}">
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" />
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" />
118 </collection>
119 <data format="vcf" label="Intersected VCF on ${on_string}" name="vcf_output">
120 <filter>proteo['proteoInput'] == 'yes' and proteo['output_vcf']</filter>
121 </data>
122 </outputs>
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 -->
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 <param name="proteoInput" value="yes" />
216 <param name="proBED" value="MCF7_proBed.bed"/>
217 <output_collection name="results" type="list">
218 <element name="variant">
219 <assert_contents>
220 <has_text text="#Variant Report" />
221 <has_text text="hg38"/>
222 <has_text text="UPF1" />
223 <has_text text="EAIDSPVSFLVLHNQIR" />
224 </assert_contents>
225 </element>
226 </output_collection>
227 </test>
228 <!-- "Output intersected VCF" test case -->
229 <test>
230 <param name="input" value="Freebayes_one-variant.vcf"/>
231 <param name="GRCh" value="GRCh38"/>
232 <param name="variant" value="variant.tsv"/>
233 <param name="gene" value="gene.tsv"/>
234 <param name="noncoding" value="noncoding.tsv"/>
235 <param name="error" value="error.tsv"/>
236 <param name="type" value="CHASM" />
237 <param name="classifier" value="Breast" />
238 <param name="proteoInput" value="yes" />
239 <param name="proBED" value="MCF7_proBed.bed"/>
240 <param name="output_vcf" value="true"/>
241 <output name="vcf_output" file="results/intersected_vcf.vcf"/>
242 </test>
243 <!-- "Only intersected proteogenomic variants submitted" test case-->
244 <test>
245 <param name="input" value="Freebayes_two-variants.vcf"/>
246 <param name="GRCh" value="GRCh38"/>
247 <param name="variant" value="variant.tsv"/>
248 <param name="gene" value="gene.tsv"/>
249 <param name="noncoding" value="noncoding.tsv"/>
250 <param name="error" value="error.tsv"/>
251 <param name="type" value="CHASM" />
252 <param name="classifier" value="Breast" />
253 <param name="proteoInput" value="yes" />
254 <param name="proBED" value="MCF7_proBed.bed"/>
255 <param name="intersectedVariants" value="true" />
256 <output_collection name="results" type="list">
257 <element name="variant">
258 <assert_contents>
259 <has_text text="hg38"/>
260 <has_text text="UPF1" />
261 <not_has_text text="CRABP2"/>
262 </assert_contents>
263 </element>
264 </output_collection>
265 </test>
266 </tests>
267 <help><![CDATA[
268 This tool submits, checks for, and retrieves data for cancer annotation from the CRAVAT platform at https://www.cravat.us.
269 For additional details on input format, visit this link: http://cravat.us/CRAVAT/help.jsp.
270
271 -----
272
273 **Input Type Example:**
274
275 CRAVAT Format (*Genomic-coordinate format*)
276
277 ===== ===== ========= ====== ========= ========= ====================
278 UID Chr. Position Strand Ref. base Alt. base Sample ID (optional)
279 ===== ===== ========= ====== ========= ========= ====================
280 TR1 chr17 7674188 \- G T TCGA-02-0231
281 TR2 chr10 121520166 \- G A TCGA-02-3512
282 TR3 chr13 48459831 \+ C A TCGA-02-3532
283 TR4 chr7 116777451 \+ G T TCGA-02-1523
284 TR5 chr7 140753336 \- T A TCGA-02-0023
285 TR6 chr17 39724745 \+ G T TCGA-02-0252
286 Ins1 chr17 39724745 \+ \- T TCGA-02-0252
287 Del1 chr17 39724745 \+ A \- TCGA-02-0252
288 CSub1 chr2 39644095 \+ ATGCT GA TCGA-02-0252
289 ===== ===== ========= ====== ========= ========= ====================
290 ]]>
291 </help>
292 <citations>
293 <citation type="doi">10.1158/0008-5472.CAN-17-0338</citation>
294 <citation type="doi">10.1186/s13059-017-1377-x</citation>
295 </citations>
296 </tool>