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comparison moff.xml @ 1:8f0e76ad46ef draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41
author galaxyp
date Thu, 18 Jan 2018 00:51:56 -0500
parents b4098353ee73
children 28b65ce1a091
comparison
equal deleted inserted replaced
0:b4098353ee73 1:8f0e76ad46ef
1 <tool id="proteomics_moff" name="moFF" version="@VERSION@"> 1 <tool id="proteomics_moff" name="moFF" version="@VERSION@">
2 <description>extracts MS1 intensities from spectrum files</description> 2 <description>extracts MS1 intensities from spectrum files</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">1.2</token> 4 <token name="@VERSION@">1.2.1</token>
5 <!-- xml macros, used for shared Galaxy parameter inputs --> 5 <!-- xml macros, used for shared Galaxy parameter inputs -->
6 <xml name="ident_input_macro" token_allow_multiple="true" token_input_type="data"> 6 <xml name="ident_input_macro" token_allow_multiple="true" token_input_type="data">
7 <!-- this is exactly the same across all three, except for allowing multiple in MBR and all but not in moff --> 7 <!-- this is exactly the same across all three, except for allowing multiple in MBR and all but not in moff -->
8 <conditional name="ident_input"> 8 <conditional name="ident_input">
9 <param name="input_type_selector" type="select" label="Choose the format for the identification file:"> 9 <param name="input_type_selector" type="select" label="Choose the format for the identification file:">
174 --tol $task.tol 174 --tol $task.tol
175 --rt_w $task.rt_w 175 --rt_w $task.rt_w
176 --rt_p $task.rt_p 176 --rt_p $task.rt_p
177 --rt_p_match $task.rt_p_match 177 --rt_p_match $task.rt_p_match
178 --output_folder ./out 178 --output_folder ./out
179 --ext txt
180 #if $task.peptide_summary: 179 #if $task.peptide_summary:
181 --peptide_summary 1 180 --peptide_summary 1
182 #end if 181 #end if
183 && 182 &&
184 #if $task.peptide_summary: 183 #if $task.peptide_summary:
185 mv ./out/peptide_summary_intensity_moFF_run.tab '$output_peptide_summary' && 184 mv ./out/peptide_summary_intensity_moFF_run.tab '$output_peptide_summary'
186 #end if 185 #end if
187 echo -ne
188 #end if 186 #end if
189 ]]></command> 187 ]]></command>
190 <inputs> 188 <inputs>
191 <conditional name="task"> 189 <conditional name="task">
192 <param name="task_selector" type="select" label="Choose which module to run"> 190 <param name="task_selector" type="select" label="Choose which module to run">
248 </outputs> 246 </outputs>
249 <tests> 247 <tests>
250 <!-- test moff_all --> 248 <!-- test moff_all -->
251 <test> 249 <test>
252 <param name="task_selector" value="all"/> 250 <param name="task_selector" value="all"/>
253 <param name="input_type_selector" value="ps"/> 251 <param name="ident_input|input_type_selector" value="ps"/>
254 <param name="ident_input_file"> 252 <param name="ident_input_file">
255 <collection type="list"> 253 <collection type="list">
256 <element name="mbr_test1" value="input/mbr_test1.tabular"/> 254 <element name="mbr_test1" value="input/mbr_test1.tabular"/>
257 <element name="mbr_test2" value="input/mbr_test2.tabular"/> 255 <element name="mbr_test2" value="input/mbr_test2.tabular"/>
258 </collection> 256 </collection>
259 </param> 257 </param>
258 <param name="msms_input|input_type_selector" value="mzml"/>
260 <param name="inputraw"> 259 <param name="inputraw">
261 <collection type="list"> 260 <collection type="list">
262 <element name="mbr_test1" value="input/mbr_test1.mzml"/> 261 <element name="mbr_test1" value="input/mbr_test1.mzml"/>
263 <element name="mbr_test2" value="input/mbr_test2.mzml"/> 262 <element name="mbr_test2" value="input/mbr_test2.mzml"/>
264 </collection> 263 </collection>
269 <has_text text="sumIntensity_mbr_test1"/> 268 <has_text text="sumIntensity_mbr_test1"/>
270 <has_text text="sumIntensity_mbr_test2"/> 269 <has_text text="sumIntensity_mbr_test2"/>
271 </assert_contents> 270 </assert_contents>
272 </output> 271 </output>
273 <output_collection name="ident_output" type="list"> 272 <output_collection name="ident_output" type="list">
274 <element name="mbr_test1_match_moff_result" value="output1/mbr_test1_match_moff_result.txt"/> 273 <element name="mbr_test1_match_moff_result">
275 <element name="mbr_test2_match_moff_result" value="output1/mbr_test2_match_moff_result.txt"/> 274 <assert_contents>
275 <has_text text="NH2-QVEEAVQSDDK-COOH"/>
276 </assert_contents>
277 </element>
278 <element name="mbr_test2_match_moff_result">
279 <assert_contents>
280 <has_text text="NH2-RDVGINNTVK-COOH"/>
281 </assert_contents>
282 </element>
276 </output_collection> 283 </output_collection>
277 <output_collection name="log_output" type="list"> 284 <output_collection name="log_output" type="list">
278 <element name="mbr_test1_match__moff"> 285 <element name="mbr_test1_match__moff">
279 <assert_contents> 286 <assert_contents>
280 <has_line line="peptide at line 200 --> MZ: 783.4200 RT: 134.6997 matched (yes=1/no=0): 0"/> 287 <has_line line="peptide at line 200 --> MZ: 783.4200 RT: 134.6997 matched (yes=1/no=0): 0"/>
288 </output_collection> 295 </output_collection>
289 </test> 296 </test>
290 <!-- test moff alone --> 297 <!-- test moff alone -->
291 <test> 298 <test>
292 <param name="task_selector" value="moff"/> 299 <param name="task_selector" value="moff"/>
293 <param name="input_type_selector" value="ps"/> 300 <param name="ident_input|input_type_selector" value="ps"/>
294 <param name="ident_input_file" value="input/test.tabular" ftype="tabular"/> 301 <param name="ident_input_file" value="input/test.tabular" ftype="tabular"/>
295 <param name="msms_input" value="mzml"/> 302 <param name="msms_input|input_type_selector" value="mzml"/>
296 <param name="inputraw" value="input/test.mzml" ftype="mzml"/> 303 <param name="inputraw" value="input/test.mzml" ftype="mzml"/>
297 <param name="peptide_summary" value="true"/> 304 <param name="peptide_summary" value="true"/>
298 <output name="output_peptide_summary" ftype="tabular" file="output2/moff_test_pepsum.tab"/> 305 <output name="output_peptide_summary" ftype="tabular" file="output2/moff_test_pepsum.tab"/>
299 <output name="output_logs"> 306 <output name="output_logs">
300 <assert_contents> 307 <assert_contents>
303 </output> 310 </output>
304 </test> 311 </test>
305 <!-- test the generic input --> 312 <!-- test the generic input -->
306 <test> 313 <test>
307 <param name="task_selector" value="moff"/> 314 <param name="task_selector" value="moff"/>
308 <param name="input_type_selector" value="generic"/> 315 <param name="ident_input|input_type_selector" value="generic"/>
309 <param name="ident_input_file" value="input/test.tabular" ftype="tabular"/> 316 <param name="ident_input_file" value="input/test.tabular" ftype="tabular"/>
310 <param name="remove_header" value="true"/> 317 <param name="remove_header" value="true"/>
311 <param name="msms_input" value="mzml"/> 318 <param name="msms_input|input_type_selector" value="mzml"/>
312 <param name="inputraw" value="input/test.mzml" ftype="mzml"/> 319 <param name="inputraw" value="input/test.mzml" ftype="mzml"/>
313 <param name="peptide" value="3"/> 320 <param name="peptide" value="3"/>
314 <param name="prot" value="2"/> 321 <param name="prot" value="2"/>
315 <param name="mod_peptide" value="7"/> 322 <param name="mod_peptide" value="7"/>
316 <param name="rt" value="13"/> 323 <param name="rt" value="13"/>
326 </output> 333 </output>
327 </test> 334 </test>
328 <!-- test mbr --> 335 <!-- test mbr -->
329 <test> 336 <test>
330 <param name="task_selector" value="mbr"/> 337 <param name="task_selector" value="mbr"/>
331 <param name="input_type_selector" value="ps"/> 338 <param name="ident_input|input_type_selector" value="ps"/>
332 <param name="ident_input_file"> 339 <param name="ident_input_file">
333 <collection type="list"> 340 <collection type="list">
334 <element name="mbr_test1" value="input/mbr_test1.tabular"/> 341 <element name="mbr_test1" value="input/mbr_test1.tabular"/>
335 <element name="mbr_test2" value="input/mbr_test2.tabular"/> 342 <element name="mbr_test2" value="input/mbr_test2.tabular"/>
336 </collection> 343 </collection>
337 </param> 344 </param>
338 <param name="ext" value="tabular"/> 345 <param name="ext" value="tabular"/>
339 <output_collection name="ident_output" type="list" count="2"> 346 <output_collection name="ident_output" type="list" count="2">
340 <element name="mbr_test1_match" file="input/mbr_output/mbr_test1_match.txt"/> 347 <element name="mbr_test1_match">
341 <element name="mbr_test2_match" file="input/mbr_output/mbr_test2_match.txt"/> 348 <assert_contents>
349 <has_text text="NH2-QVEEAVQSDDK-COOH"/>
350 </assert_contents>
351 </element>
352 <element name="mbr_test2_match">
353 <assert_contents>
354 <has_text text="NH2-RDVGINNTVK-COOH"/>
355 </assert_contents>
356 </element>
342 </output_collection> 357 </output_collection>
343 </test> 358 </test>
344 </tests> 359 </tests>
345 <help> 360 <help>
346 <![CDATA[ 361 <![CDATA[