# HG changeset patch
# User galaxyp
# Date 1521536976 14400
# Node ID f35bb9d0c93eab852b8196a1e6f8e2ccaa9002b7
# Parent  7963340ab569bcb0da4025ede6193df3d89b54f7
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb

diff -r 7963340ab569 -r f35bb9d0c93e peptide_shaker.xml
--- a/peptide_shaker.xml	Mon Mar 05 10:09:34 2018 -0500
+++ b/peptide_shaker.xml	Tue Mar 20 05:09:36 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="1.16.4">
+<tool id="peptide_shaker" name="Peptide Shaker" version="1.16.17">
     <description>
         Perform protein identification using various search engines based on results from SearchGUI
     </description>
@@ -6,7 +6,7 @@
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="1.16.4">peptide-shaker</requirement>
+        <requirement type="package" version="1.16.17">peptide-shaker</requirement>
     </requirements>
     <expand macro="stdio" />
     <command>
@@ -36,6 +36,20 @@
             -id_params \$cwd/SEARCHGUI_IdentificationParameters.par
             -out \$cwd/peptideshaker_output.cpsx
             -zip \$cwd/peptideshaker_output.zip
+            #set $cleaned_list = str($outputs).split(',')
+            #if 'cps' in $cleaned_list:
+                #silent $cleaned_list.remove('cps')
+            #end if
+            #if 'mzidentML' in $cleaned_list:
+                #silent $cleaned_list.remove('mzidentML')
+            #end if
+            #if 'zip' in $cleaned_list:
+                #silent $cleaned_list.remove('zip')
+            #end if
+            #if len($cleaned_list) > 0
+              ## Only numbers are left over. These corresponds to different reports.
+              -reports #echo ','.join($cleaned_list)#
+            #end if
 
             -threads "\${GALAXY_SLOTS:-12}"
 
@@ -107,12 +121,12 @@
                     -organization_email "galaxyp@umn.edu"
                     -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
                 #end if
-            2>> $temp_stderr) 
+            2>> $temp_stderr)
             &&
         #end if
 
         ## Generate Reports if the user has selected one of the 8 additional reports
-        ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker 
+        ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker
         ## and will not be passed to the command line
         #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ):
 
@@ -305,7 +319,7 @@
         <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
             <filter>'mzidentML' in outputs</filter>
         </data>
-        <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cps" label="${tool.name} on ${on_string}: CPS file">
+        <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cpsx" label="${tool.name} on ${on_string}: CPS file">
             <filter>'cps' in outputs</filter>
         </data>
         <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive">
@@ -406,6 +420,18 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
+            <param name="processing_options_selector" value="no"/>
+            <param name="filtering_options_selector" value="no"/>
+            <param name="outputs" value="3,cps"/>
+            <output name="output_cps" file="peptide_shaker_result1.cpsx" ftype="peptideshaker_archive" compare="sim_size" delta="3000"/>
+            <output name="output_psm">
+                <assert_contents>
+                    <has_text text="cds.comp41779_c0_seq1" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 **What it does**
diff -r 7963340ab569 -r f35bb9d0c93e searchgui.xml
--- a/searchgui.xml	Mon Mar 05 10:09:34 2018 -0500
+++ b/searchgui.xml	Tue Mar 20 05:09:36 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.3">
+<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.4">
     <description>
         Perform protein identification using various search engines and prepare results for input to Peptide Shaker
     </description>
@@ -200,9 +200,10 @@
             #end if
             *#
 
-            #* Not working in tests
             #if $advanced_options.tide.tide_advanced == "yes"
-                -tide_num_ptms ${advanced_options.tide.tide_num_ptms}
+                #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != '':
+                  -tide_num_ptms ${advanced_options.tide.tide_max_spectrum_mz}
+                #end if
                 -tide_num_ptms_per_type ${advanced_options.tide.tide_num_ptms_per_type}
                 -tide_min_pep_length ${advanced_options.tide.tide_min_pep_length}
                 -tide_max_pep_length ${advanced_options.tide.tide_max_pep_length}
@@ -210,8 +211,6 @@
                 -tide_max_prec_mass ${advanced_options.tide.tide_max_prec_mass}
                 -tide_decoy_format ${advanced_options.tide.tide_decoy_format}
                 -tide_keep_terminals ${advanced_options.tide.tide_keep_terminals}
-
-                -tide_output_folder ${advanced_options.tide.tide_output_folder}
                 -tide_print_peptides ${advanced_options.tide.tide_print_peptides}
                 -tide_verbosity ${advanced_options.tide.tide_verbosity}
                 -tide_monoisotopic ${advanced_options.tide.tide_monoisotopic}
@@ -221,7 +220,9 @@
                 -tide_max_psms ${advanced_options.tide.tide_max_psms}
                 -tide_compute_p ${advanced_options.tide.tide_compute_p}
                 -tide_min_spectrum_mz ${advanced_options.tide.tide_min_spectrum_mz}
-                -tide_max_spectrum_mz ${advanced_options.tide.tide_max_spectrum_mz}
+                #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != '':
+                  -tide_max_spectrum_mz ${advanced_options.tide.tide_max_spectrum_mz}
+                #end if
                 -tide_min_spectrum_peaks ${advanced_options.tide.tide_min_spectrum_peaks}
                 -tide_spectrum_charges ${advanced_options.tide.tide_spectrum_charges}
                 -tide_remove_prec ${advanced_options.tide.tide_remove_prec}
@@ -232,14 +233,21 @@
                 -tide_mz_bin_width ${advanced_options.tide.tide_mz_bin_width}
                 -tide_mz_bin_offset ${advanced_options.tide.tide_mz_bin_offset}
                 -tide_concat ${advanced_options.tide.tide_concat}
-                -tide_export_text ${advanced_options.tide.tide_export_text}
-                -tide_export_sqt ${advanced_options.tide.tide_export_sqt}
-                -tide_export_pepxml ${advanced_options.tide.tide_export_pepxml}
-                -tide_export_mzid ${advanced_options.tide.tide_export_mzid}
-                -tide_export_pin ${advanced_options.tide.tide_export_pin}
+
+                #set $formats = ["tide_export_text", "tide_export_sqt", "tide_export_pepxml", "tide_export_mzid", "tide_export_pin"]
+                #for $format in $formats:
+                    #if str($advanced_options.tide.tide_export).strip() == $format:
+                      -$format 1
+                    #else:
+                      -$format 0
+                    #end if
+
+                #end for
+
                 -tide_remove_temp ${advanced_options.tide.tide_remove_temp}
+
             #end if
-            *#
+
 
             #if $advanced_options.comet.comet_advanced == "yes"
 
@@ -439,7 +447,7 @@
             help="Select appropriate MGF dataset(s) from history" />
 
         <!-- Search Engine Selection -->
-        <section name="search_engines_options" expanded="false" title="Search Engine Options">
+        <section name="search_engines_options" expanded="true" title="Search Engine Options">
             <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
                 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help>
                 <option value="X!Tandem" selected="True">X!Tandem</option>
@@ -447,8 +455,6 @@
                 <option value="MSGF" selected="True">MS-GF+</option>
                 <option value="OMSSA" selected="True">OMSSA</option>
                 <option value="Comet">Comet</option>
-                <!-- Not working in tests
-                -->
                 <option value="Tide">Tide</option>
                 <!-- Not working in tests
                 -->
@@ -748,7 +754,6 @@
 
 
             <!-- TIDE ADVANCED PARAMETERS -->
-            <!-- Not working in tests
             <conditional name="tide">
                 <param name="tide_advanced" type="select" label="TIDE Options">
                     <option value="yes">Advanced</option>
@@ -756,7 +761,7 @@
                 </param>
                 <when value="no" />
                 <when value="yes">
-                    <param name="tide_num_ptms" type="integer" value="100"
+                    <param name="tide_num_ptms" type="integer" value="" optional="true"
                         label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/>
                     <param name="tide_num_ptms_per_type" type="integer" value="2"
                         label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/>
@@ -782,8 +787,6 @@
                     </param>
                     <param name="tide_decoy_seed" type="integer" value="1"
                         label="TIDE: Decoy Seed" help="Set the decoy seed"/>
-                    <param name="tide_output_folder" type="text" value="crux-output"
-                        label="TIDE: Output Folder" help="Set the results output folder (relative to the Tide working folder)"/>
                     <param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false"
                         label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/>
                     <param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress">
@@ -812,7 +815,7 @@
                         label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/>
                     <param name="tide_min_spectrum_mz" type="float" value="0.0"
                         label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/>
-                    <param name="tide_max_spectrum_mz" type="float" value="100000.0"
+                    <param name="tide_max_spectrum_mz" type="float" value="" optional="true"
                         label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/>
                     <param name="tide_min_spectrum_peaks" type="integer" value="20"
                         label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/>
@@ -838,21 +841,29 @@
                         label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/>
                     <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false"
                         label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/>
-                    <param name="tide_export_text" type="boolean" truevalue="1" falsevalue="0" checked="true"
-                        label="TIDE: Export Text" help="If true, a text-formatted output file is exported"/>
-                    <param name="tide_export_sqt" type="boolean" truevalue="1" falsevalue="0" checked="false"
-                        label="TIDE: Export SQT" help="If true, a sqt-formatted output file is exported"/>
-                    <param name="tide_export_pepxml" type="boolean" truevalue="1" falsevalue="0" checked="false"
-                        label="TIDE: Export Pepxml" help="If true, a pepxml output file is exported"/>
-                    <param name="tide_export_mzid" type="boolean" truevalue="1" falsevalue="0" checked="false"
-                        label="TIDE: Export Mzid" help="If true, a mzid output file is exported"/>
-                    <param name="tide_export_pin" type="boolean" truevalue="1" falsevalue="0" checked="false"
-                        label="TIDE: Export Percolator Input File" help="If true, a percolator input file is exported"/>
+
+                    <param name="tide_export" label="TIDE: Output Format" type="select" help="Choose the output format">
+                        <option value="tide_export_text" selected="True">Text</option>
+                        <option value="tide_export_sqt" >SQT</option>
+                        <option value="tide_export_pepxml" >pepxml</option>
+              <!--
+                        MZidentML and Percolator input file options generates files with the format (ie. if we use a spectrum file called ´qExactive01819´):
+                        galaxy/database/jobs_directory/000/88/working/bin/resources/Tide/linux/linux_64bit/crux-output/qExactive01819.tide-search.target.mzid
+                        instead of
+                        galaxy/database/jobs_directory/000/88/working/bin/resources/Tide/linux/linux_64bit/crux-output/qExactive01819.tide-search.mzid
+                        which is the expected one, so current searchgui version gives a "does not exist error".
+              -->
+              <!--
+                        <option value="tide_export_mzid" >MzIdentML</option
+                        <option value="tide_export_pin" >Percolator input file</option>
+              -->
+                    </param>
+
                     <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true"
                         label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/>
                 </when>
             </conditional>
-            -->
+
 
             <!-- MyriMatch ADVANCED PARAMETERS -->
             <!-- Not working in tests
diff -r 7963340ab569 -r f35bb9d0c93e test-data/peptide_shaker_result1.cpsx
Binary file test-data/peptide_shaker_result1.cpsx has changed