# HG changeset patch
# User galaxyp
# Date 1667223374 0
# Node ID 29e6417b913c0097648a79fc7f7ec7924a33be69
# Parent  d8962e547c9c6c56e9bf00232a450fd44d4cf7f4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202

diff -r d8962e547c9c -r 29e6417b913c pepquery2.xml
--- a/pepquery2.xml	Tue Oct 25 23:35:01 2022 +0000
+++ b/pepquery2.xml	Mon Oct 31 13:36:14 2022 +0000
@@ -374,15 +374,15 @@
         </section>
 
         <param name="outputs_selected" type="select" multiple="true" optional="false" label="Select outputs">
-            <option value="psm.txt" selected="true">psm.txt</option>
+            <option value="psm.txt">psm.txt</option>
             <option value="psm_rank.txt" selected="true">psm_rank.txt</option>
-            <option value="psm_rank.mgf" selected="true">psm_rank.mgf</option>
-            <option value="psm_annotation.txt" selected="true">psm_annotation.txt</option>
-            <option value="psm_type.txt" selected="false">psm_type.txt</option>
-            <option value="detail.txt" selected="true">detail.txt</option>
-            <option value="ptm.txt" selected="true">ptm.txt</option>
-            <option value="ptm_detail.txt" selected="true">ptm_detail.txt</option>
-            <option value="ms_index" selected="true">MS/MS Index</option>
+            <option value="psm_rank.mgf">psm_rank.mgf</option>
+            <option value="psm_annotation.txt">psm_annotation.txt</option>
+            <option value="psm_type.txt">psm_type.txt</option>
+            <option value="detail.txt">detail.txt</option>
+            <option value="ptm.txt">ptm.txt</option>
+            <option value="ptm_detail.txt">ptm_detail.txt</option>
+            <option value="ms_index">MS/MS Index</option>
         </param>
         <param name="fast" argument="-fast" type="boolean" truevalue="-fast" falsevalue="" checked="false" label="Use fast mode for searching" help="In fast mode, only one better match from reference peptide-based competitive filtering steps will be returned. A peptide identified or not is not affected by this setting. For most applications, fast mode will speed up the analysis." />
     </inputs>
@@ -390,6 +390,7 @@
         <data name="log_txt" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log.txt">
         </data> 
         <data name="parameter_txt" format="txt" from_work_dir="pepquery_output/parameter.txt" label="${tool.name} on ${on_string}: parameter.txt">
+            <filter>'parameter.txt' in outputs_selected and req_inputs['ms_dataset']['ms_dataset_type'] == 'history'</filter>
         </data> 
         <data name="ms_index" format="txt" label="${tool.name} on ${on_string}: index summary.txt" from_work_dir="index_dir/summary.txt">
             <filter>'ms_index' in outputs_selected and req_inputs['ms_dataset']['ms_dataset_type'] == 'history'</filter>
@@ -757,6 +758,17 @@
       The **PepQuery2 Show Sets** tool *PepQuery Modifications* lists all available modifications.
 
 **Outputs**
+    - Log.txt: 
+
+      - Logging output from PepQuery2
+      - When searching for *novel* peptides ignored peptide have a log message similar to: 
+
+        - Ignore peptide (reason: exist in reference database): *PEPTIDE*
+
+      - When searching for *known* proteins, ignored protein have a log message similar to:
+
+        - Target protein is not present in database *DATABASE_NAME*: *PROTEIN_NAME*, ignored!
+
     - Parameters: 
       
       - parameters used in the search
@@ -767,7 +779,7 @@
 
     - PSM Rank - tabular with columns: 
       
-      - peptide modification n spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue rank *n_ptm*
+      - peptide mo/dification n spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue rank n_ptm
 
     - An MGF with the best matching spectrums
 
@@ -789,8 +801,7 @@
 
     - An Indexed MS/MS dataset *when MS/MS data is MGF, mzML, or mzXML history datasets*
 
-    The *n_ptm* field is added when using unrestricted modification searching (-um).
-    
+
 .. _PepQuery: http://pepquery.org/document.html
 
     ]]></help>