Mercurial > repos > galaxyp > msconvert

comparison msconvert_macros.xml @ 13:9337a492ebab draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 73cce4134ad971568ac8e557df97bab93ff24d4d
author galaxyp
date Fri, 25 Apr 2025 10:03:13 +0000
parents 5e94d5403baf
children
comparison
equal deleted inserted replaced
12:5e94d5403baf 13:9337a492ebab
1 <macros> 1 <macros>
2 <token name="@VERSION@">3.0.20287</token> 2 <token name="@VERSION@">3.0.20287</token>
3 <token name="@FULL_VERSION@">@VERSION@-769529fa4</token> 3 <token name="@FULL_VERSION@">@VERSION@-769529fa4</token>
4 <token name="@PROFILE_VERSION@">24.2</token> 4 <token name="@PROFILE_VERSION@">23.2</token>
5 <xml name="msconvertCommand"> 5 <xml name="msconvertCommand">
6 <command detect_errors="exit_code"> 6 <command detect_errors="exit_code">
7 <![CDATA[ 7 <![CDATA[
8 #import re 8 #import re
9 #set $ext = $input.ext 9 #set $ext = $input.ext
37 #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext)) 37 #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext))
38 #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv' 38 #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv'
39 ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' && 39 ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' &&
40 #end if 40 #end if
41 41
42 CAN_SUDO=\$(sudo -n -l > /dev/null 2> /dev/null; echo $?) && 42 ## CAN_SUDO is "" if successful and "1" otherwise
43 if [ "\$CAN_SUDO" -eq "0" ]; then 43 CAN_SUDO=\$(sudo -n -l > /dev/null 2> /dev/null || echo \$?) &&
44 echo "CAN SUDO \$CAN_SUDO" &&
45 if [ -z "\$CAN_SUDO" ]; then
44 uid=`id -u` && 46 uid=`id -u` &&
45 gid=`id -g` && 47 gid=`id -g` &&
46 WINE="wine64_anyuser"; 48 WINE="wine64_anyuser";
47 else 49 else
48 WINE="wine64" && 50 WINE="wine64" &&
49 ## create a writable copy of wine prefix (since copying fails for some html 51 ## create a writable copy of wine prefix (since copying fails for some html
50 ## stderr and exit code is swallowed) 52 ## stderr and exit code is swallowed)
213 215
214 #if $general_options.multi_run_output.do_multi_run_output == 'false': 216 #if $general_options.multi_run_output.do_multi_run_output == 'false':
215 --outfile '${os.path.splitext($basename)[0]}' 217 --outfile '${os.path.splitext($basename)[0]}'
216 #end if 218 #end if
217 && 219 &&
218 if [ "\$CAN_SUDO" -eq "0" ]; then 220 if [ -z "\$CAN_SUDO" ]; then
219 sudo chown -R \$uid:\$gid './'; 221 sudo chown -R \$uid:\$gid './';
220 fi 222 fi
221 #if $general_options.multi_run_output.do_multi_run_output == 'false': 223 #if $general_options.multi_run_output.do_multi_run_output == 'false':
222 && mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}' 224 && mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}'
223 #else 225 #else
224 ## make mzML and mzXML extensions lower case (the Galaxy data type is ) otherwise detetion of the file 226 ## make mzML and mzXML extensions lower case (the Galaxy data type is ) otherwise detetion of the file
225 ## this won't be necessay from Galaxy 21.01 https://github.com/galaxyproject/galaxy/pull/10803 227 ## this won't be necessay from Galaxy 25.0 https://github.com/galaxyproject/galaxy/pull/19954
226 #if $output_type == 'mzML' or $output_type == 'mzXML' 228 #if $output_type == 'mzML' or $output_type == 'mzXML'
227 && find outputs/ -name "*.$output_type" | xargs -I "FILE" sh -c 'mv FILE outputs/\$(basename FILE .$output_type).#echo str($output_type).lower() 229 && find outputs/ -name "*.$output_type" | xargs -I "FILE" sh -c 'mv FILE outputs/\$(basename FILE .$output_type).#echo str($output_type).lower()
228 ## a newline is needed after `#echo ...` therefore the `;'` on the next line 230 ## a newline is needed after `#echo ...` therefore the `;'` on the next line
229 ;' 231 ;'
230 #end if 232 #end if
427 </when> 429 </when>
428 <when value="false" /> 430 <when value="false" />
429 </conditional> 431 </conditional>
430 432
431 </section> 433 </section>
432
433 434
434 <section name="filtering" title="Scan Inclusion/Exclusion Filters"> 435 <section name="filtering" title="Scan Inclusion/Exclusion Filters">
435 436
436 <param name="activation" type="select" label="Filter by Activation"> 437 <param name="activation" type="select" label="Filter by Activation">
437 <option value="false" selected="true">no</option> 438 <option value="false" selected="true">no</option>
563 <data format="tsv" name="output_refinement" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.mzRefinement.tsv"> 564 <data format="tsv" name="output_refinement" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.mzRefinement.tsv">
564 <filter>data_processing['precursor_refinement']['use_mzrefinement'] == "true"</filter> 565 <filter>data_processing['precursor_refinement']['use_mzrefinement'] == "true"</filter>
565 </data> 566 </data>
566 <collection name="multi_run_output_list" type="list" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type} collection"> 567 <collection name="multi_run_output_list" type="list" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type} collection">
567 <filter>general_options['multi_run_output']['do_multi_run_output'] == "true"</filter> 568 <filter>general_options['multi_run_output']['do_multi_run_output'] == "true"</filter>
568 <discover_datasets pattern="__name_and_ext__" directory="outputs" /> 569 <discover_datasets pattern="__name_and_ext__" directory="outputs" sort_by="designation" />
569 </collection> 570 </collection>
570 </outputs> 571 </outputs>
571 </xml> 572 </xml>
572 573
573 574