# HG changeset patch
# User galaxyp
# Date 1666740901 0
# Node ID d8962e547c9c6c56e9bf00232a450fd44d4cf7f4
# Parent  3b2874c58bcd71404e53b91e0707a51ca525cb97
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d

diff -r 3b2874c58bcd -r d8962e547c9c pepquery2.xml
--- a/pepquery2.xml	Tue Oct 25 16:06:20 2022 +0000
+++ b/pepquery2.xml	Tue Oct 25 23:35:01 2022 +0000
@@ -178,7 +178,7 @@
                             <option value="single">Single peptide entered as text</option>
                         </param> 
                         <when value="multiple">
-                            <param name="input" argument="-i" type="data" format="txt" label="Peptide Sequences (.txt)">
+                            <param name="input" argument="-i" type="data" format="tabular" label="Peptide Sequences (.txt)">
                                 <help>Peptide sequence file containing peptides which you want to search (no column headers).
                                       First column is am peptide sequence. Optional second column is spectrum title.
                                 </help>
@@ -186,7 +186,7 @@
                         </when>
                         <when value="single">
                             <param name="input" argument="-i" type="text" label="Peptide Sequence" help="Peptide sequence(s) which you want to search">
-                                <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+(,[AC-IK-NP-TV-Yac-ik-np-tv-y]+)*$</validator>
+                                <validator type="regex" message="Must be AA letters, multiple peptides separated by commas">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+(,[AC-IK-NP-TV-Yac-ik-np-tv-y]+)*$</validator>
                             </param>
                         </when>
                     </conditional>
@@ -387,7 +387,7 @@
         <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>
     <outputs>
-        <data name="log" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log.txt">
+        <data name="log_txt" format="txt" from_work_dir="log.txt" label="${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">
         </data> 
@@ -462,7 +462,7 @@
                     <param name="input_type_selector" value="peptide"/>
                     <conditional name="multiple">
                         <param name="peptide_input_selector" value="single" />
-                        <param name="input" value="LVVVGADGVGK"/>
+                        <param name="input" value="LVVVGADGVGK,AHSSMVGVNLPQK"/>
                     </conditional>
                 </conditional>
                 <conditional name="db_type">
@@ -510,12 +510,87 @@
             <output name="psm_txt">
                 <assert_contents>
                     <has_text text="LVVVGADGVGK" />
+                    <not_has_text text="AHSSMVGVNLPQK" />
                     <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" />
                 </assert_contents>
             </output>
+            <output name="log_txt">
+                <assert_contents>
+                    <has_text text="Ignore peptide (reason: exist in reference database): AHSSMVGVNLPQK" />
+                </assert_contents>
+            </output>
         </test>
 
-        <!-- Test-2  MGF peptide Uniprot.fasta -->
+        <!-- Test-2  PepQueryDB peptide gencode:human pep.txt -->
+        <test>
+            <conditional name="validation">
+                <param name="task_type" value="novel"/>
+            </conditional>
+            <section name="req_inputs">
+                <conditional name="input_type">
+                    <param name="input_type_selector" value="peptide"/>
+                    <conditional name="multiple">
+                        <param name="peptide_input_selector" value="multiple" />
+                        <param name="input" ftype="tabular" value="pep.txt"/>
+                    </conditional>
+                </conditional>
+                <conditional name="db_type">
+                    <param name="db_type_selector" value="download" />
+                    <param name="db_id" value="gencode:human"/>
+                </conditional>
+                <conditional name="ms_dataset">
+                    <param name="ms_dataset_type" value="PepQueryDB"/>
+                    <param name="dataset" value="CPTAC_LUAD_Discovery_Study_Proteome_PDC000153" />
+                </conditional>
+                <param name="indexType" value="1"/>
+            </section>
+            <param name="parameter_set" value=""/>
+            <section name="modifications">
+                 <param name="fixed_mod" value="1"/>
+                 <param name="var_mod" value="2"/>
+                 <param name="max_mods" value="3"/>
+                 <param name="unmodified" value="True"/>
+                 <param name="aa" value="False"/>
+            </section>
+            <section name="digestion">
+                <param name="enzyme" value="1"/>
+                <param name="max_missed_cleavages" value="2"/>
+            </section>
+            <section name="ms_params">
+                <section name="tolerance_params">
+                    <param name="precursor_tolerance" value="10"/>
+                    <param name="precursor_unit" value="ppm"/>
+                    <param name="tolerance" value="0.6"/>
+                </section>
+                <section name="search">
+                    <param name="frag_method" value="1"/>
+                    <param name="scoring_method" value="1"/>
+                    <param name="extra_score_validation" value="False"/>
+                    <param name="min_charge" value="2"/>
+                    <param name="max_charge" value="3"/>
+                    <param name="min_peaks" value="10"/>
+                    <param name="isotope_error" value="0"/>
+                    <param name="min_score" value="12"/>
+                    <param name="min_length" value="7"/>
+                    <param name="max_length" value="45"/>
+                    <param name="num_random_peptides" value="1000"/>
+                </section>
+            </section>
+            <output name="psm_txt">
+                <assert_contents>
+                    <has_text text="LVVVGADGVGK" />
+                    <not_has_text text="AHSSMVGVNLPQK" />
+                    <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" />
+                </assert_contents>
+            </output>
+            <output name="log_txt">
+                <assert_contents>
+                    <has_text text="Ignore peptide (reason: exist in reference database): AHSSMVGVNLPQK" />
+                </assert_contents>
+            </output>
+        </test>
+
+        <!-- Test-3  MGF peptide Uniprot.fasta -->
         <test>
             <conditional name="validation">
                 <param name="task_type" value="novel"/>
@@ -586,6 +661,40 @@
             </output>
         </test>
 
+        <!-- Test-4  PepQueryDB known peptide gencode:human pep.txt -->
+        <test>
+            <conditional name="validation">
+                <param name="task_type" value="known"/>
+            </conditional>
+            <section name="req_inputs">
+                <conditional name="input_type">
+                    <param name="input_type_selector" value="peptide"/>
+                    <conditional name="multiple">
+                        <param name="peptide_input_selector" value="single" />
+                        <param name="input" value="AHSSMVGVNLPQK"/>
+                    </conditional>
+                </conditional>
+                <conditional name="db_type">
+                    <param name="db_type_selector" value="download" />
+                    <param name="db_id" value="gencode:human"/>
+                </conditional>
+                <conditional name="ms_dataset">
+                    <param name="ms_dataset_type" value="PepQueryDB"/>
+                    <param name="dataset" value="CPTAC_LUAD_Discovery_Study_Proteome_PDC000153" />
+                </conditional>
+                <param name="indexType" value="1"/>
+            </section>
+            <section name="modifications">
+                 <param name="unmodified" value="True"/>
+            </section>
+            <output name="psm_txt">
+                <assert_contents>
+                    <has_text text="AHSSMVGVNLPQK" />
+                    <has_text text="6CPTAC_LUAD_W_BI_20180718_KL_f12:20286:3" />
+                </assert_contents>
+            </output>
+        </test>
+
     </tests>
     <help><![CDATA[
 **PepQuery2**
diff -r 3b2874c58bcd -r d8962e547c9c test-data/pep.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pep.txt	Tue Oct 25 23:35:01 2022 +0000
@@ -0,0 +1,2 @@
+LVVVGADGVGK
+AHSSMVGVNLPQK