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comparison peptide_shaker.xml @ 57:da885ca16cb2 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
author galaxyp
date Tue, 16 Mar 2021 15:12:03 +0000
parents bb0130ff73ce
children 07ff622ec007
comparison
equal deleted inserted replaced
56:1beff3ddce58 57:da885ca16cb2
1 <tool id="peptide_shaker" name="Peptide Shaker" version="@PEPTIDESHAKER_VERSION@+galaxy@PEPTIDESHAKER_VERSION_SUFFIX@"> 1 <tool id="peptide_shaker"
2 name="Peptide Shaker"
3 version="@PEPTIDESHAKER_VERSION@+galaxy@PEPTIDESHAKER_VERSION_SUFFIX@"
4 profile="20.01"
5 >
6
2 <description> 7 <description>
3 Perform protein identification using various search engines based on results from SearchGUI 8 Perform protein identification using various search engines based on results from SearchGUI
4 </description> 9 </description>
5 <macros> 10 <macros>
6 <import>macros_basic.xml</import> 11 <import>macros_basic.xml</import>
9 <requirements> 14 <requirements>
10 <requirement type="package" version="@PEPTIDESHAKER_VERSION@">peptide-shaker</requirement> 15 <requirement type="package" version="@PEPTIDESHAKER_VERSION@">peptide-shaker</requirement>
11 <requirement type="package">unzip</requirement> 16 <requirement type="package">unzip</requirement>
12 </requirements> 17 </requirements>
13 <expand macro="stdio" /> 18 <expand macro="stdio" />
14 19 <!-- TODO: check trap comment.
15 <command><![CDATA[ 20 <command use_shared_home="false">
16 ## When supporting more advanced Galaxy versions: command use_shared_home="false" 21 -->
22 <command>
23 <![CDATA[
17 #from datetime import datetime 24 #from datetime import datetime
18 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s") 25 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
19 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s") 26 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
20 #set $temp_stderr = "peptideshaker_stderr"
21 #set $bin_dir = "bin" 27 #set $bin_dir = "bin"
22 #set $exporting_followup_boolean = False 28 #set $exporting_followup_boolean = False
29 ## TODO: Re-enable again when solving writing paths.txt to user-related folders and non-existing exportFactory.json file.
30 ## trap ">&2 cat resources/*.log" EXIT;
23 31
24 mkdir output_reports && 32 mkdir output_reports &&
25 cwd=`pwd` && 33 cwd=`pwd` &&
26 export HOME=\$cwd && 34 export HOME=\$cwd &&
27
28 echo "" > $temp_stderr &&
29 35
30 ln -s '$searchgui_input' searchgui_input.zip && 36 ln -s '$searchgui_input' searchgui_input.zip &&
31 37
32 ## OPTIONAL MAIN PARAMETERS 38 ## OPTIONAL MAIN PARAMETERS
33 ## If we have a specific Identification Parameters file to use, we will use it instead of the one provided in the search_gui file 39 ## If we have a specific Identification Parameters file to use, we will use it instead of the one provided in the search_gui file
62 #end if 68 #end if
63 69
64 ###################### 70 ######################
65 ## PeptideShakerCLI ## 71 ## PeptideShakerCLI ##
66 ###################### 72 ######################
67 (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI 73 peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI
68 -gui 0 74 -gui 0
69 -temp_folder \$cwd/PeptideShakerCLI 75 -temp_folder \$cwd/PeptideShakerCLI
70 -log \$cwd/resources 76 -log \$cwd/resources
71 -reference '$exp_str' 77 -reference '$exp_str'
72 -identification_files \$cwd/searchgui_input.zip 78 -identification_files \$cwd/searchgui_input.zip
180 -inclusion_list_rt_window $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_rt_window 186 -inclusion_list_rt_window $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_rt_window
181 #end if 187 #end if
182 #end if 188 #end if
183 #end if 189 #end if
184 190
185 2>> $temp_stderr)
186
187 ## If the user chose to zip the results but also export reports out of the zip, we have to unzip them 191 ## If the user chose to zip the results but also export reports out of the zip, we have to unzip them
188 #if $exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip and (len(output_reports_list)>0 or $exporting_followup_boolean): 192 #if $exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip and (len(output_reports_list)>0 or $exporting_followup_boolean):
189 ## This unzipping command creates a reports folder into the current folder! 193 ## This unzipping command creates a reports folder into the current folder!
190 && unzip \$cwd/peptideshaker_output.zip "reports/*" -d \$cwd 194 && unzip \$cwd/peptideshaker_output.zip "reports/*" -d \$cwd
191 && mv reports/* output_reports 195 && mv reports/* output_reports
236 && find \$cwd/output_reports -name '*Default_Protein_Report_with_non-validated_matches.txt' -exec bash -c 'mv "$0" "proteins_nonvalidated.txt"' {} \; 240 && find \$cwd/output_reports -name '*Default_Protein_Report_with_non-validated_matches.txt' -exec bash -c 'mv "$0" "proteins_nonvalidated.txt"' {} \;
237 #end if 241 #end if
238 #if '11' in $output_reports_list: 242 #if '11' in $output_reports_list:
239 && find \$cwd/output_reports -name '*Extended_PSM_Report.txt' -exec bash -c 'mv "$0" "psmx.txt"' {} \; 243 && find \$cwd/output_reports -name '*Extended_PSM_Report.txt' -exec bash -c 'mv "$0" "psmx.txt"' {} \;
240 #end if 244 #end if
245 ## the last ; is removed from the generated command line
246 ## thus we need to make sure that the above `find ... -exec ... \;`
247 ## is not the last command
248 && true
241 #end if 249 #end if
242 250
243 ## Moving followup analysis to the root folder (it is necessary if zip option was not chosen, or it was chosen but also exporting out of the zip) 251 ## Moving followup analysis to the root folder (it is necessary if zip option was not chosen, or it was chosen but also exporting out of the zip)
244 #if $exporting_options.followup_conditional.followup_conditional_selector == "yes" and ($exporting_options.zip_conditional.zip_output_boolean != 'zip' or ($exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip)): 252 #if $exporting_options.followup_conditional.followup_conditional_selector == "yes" and ($exporting_options.zip_conditional.zip_output_boolean != 'zip' or ($exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip)):
245 ## Spectrum analysis are already expected to be into the output_reports folder itself 253 ## Spectrum analysis are already expected to be into the output_reports folder itself
257 #end if 265 #end if
258 #if $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_selector != "off" 266 #if $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_selector != "off"
259 && mv \$cwd/output_reports/inclusion_list.txt \$cwd/inclusion_list.txt 267 && mv \$cwd/output_reports/inclusion_list.txt \$cwd/inclusion_list.txt
260 #end if 268 #end if
261 #end if 269 #end if
262 && cat $temp_stderr 2>&1;
263 ]]> 270 ]]>
264 </command> 271 </command>
265 <inputs> 272 <inputs>
266 <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results" 273 <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results"
267 help="SearchGUI Results from History"> 274 help="SearchGUI Results from History">
624 <assert_contents> 631 <assert_contents>
625 <has_line_matching expression="236.0470428 11.674492836"/> 632 <has_line_matching expression="236.0470428 11.674492836"/>
626 <has_line_matching expression="520.9862671 4666.4399414063"/> 633 <has_line_matching expression="520.9862671 4666.4399414063"/>
627 <has_line_matching expression="267.4349976 50.7710571289"/> 634 <has_line_matching expression="267.4349976 50.7710571289"/>
628 <has_line_matching expression="665.7418213 3.8165459633"/> 635 <has_line_matching expression="665.7418213 3.8165459633"/>
629 <has_line_matching expression="672.2329102 146.2656707764"/>
630 <has_line_matching expression="634.7792969 2367.6374511719"/> 636 <has_line_matching expression="634.7792969 2367.6374511719"/>
631 </assert_contents> 637 </assert_contents>
632 </element> 638 </element>
633 </output_collection> 639 </output_collection>
634 <output name="output_proteins_accessions" ftype="txt"> 640 <output name="output_proteins_accessions" ftype="txt">