# HG changeset patch
# User galaxyp
# Date 1667751785 0
# Node ID 01fd80b1505385664c44b967c6ce47965c23a9a4
# Parent  2045f3b6877356a554f982a3903b3181d68fbac8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597

diff -r 2045f3b68773 -r 01fd80b15053 pepquery2.tar.gz
Binary file pepquery2.tar.gz has changed
diff -r 2045f3b68773 -r 01fd80b15053 pepquery2.xml
--- a/pepquery2.xml	Mon Oct 31 14:41:50 2022 +0000
+++ b/pepquery2.xml	Sun Nov 06 16:23:05 2022 +0000
@@ -165,11 +165,7 @@
                     <option value="peptide">peptide</option>
                     <option value="protein">protein</option>
                     <option value="DNA">DNA (translate to protein sequences)</option>
-                    <!-- these are not working with pepquery version 1.6
-                    <option value="3">VCF (translate to protein sequences)</option>
-                    <option value="4">BED (translate to protein sequences)</option>
-                    <option value="5">GTF (translate to protein sequences)</option>
-                    -->
+                    <!-- VCF,BED,GTF input options have not been implemented in this tool -->
                 </param>
                 <when value="peptide">
                     <conditional name="multiple">
@@ -231,20 +227,6 @@
                         <option value="6">6</option>
                     </param>
                 </when>
-                <!-- these are not working with pepquery version 1.6
-                <when value="3">   
-                    <param name="input" type="data" format="vcf" label="VCF File" argument="-i" help="" />
-                    <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the VCF file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
-                </when>
-                <when value="4">   
-                    <param name="input" type="data" format="bed" label="BED File" argument="-i" help="" />
-                    <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the BED file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
-                </when>
-                <when value="5">   
-                    <param name="input" type="data" format="gtf" label="GTF File" argument="-i" help="" />
-                    <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the GTF file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
-                </when>
-                -->
             </conditional>
             <conditional name="db_type">
                 <param name="db_type_selector" type="select" label="Protein Reference Database from" help="" >
@@ -454,7 +436,7 @@
     </outputs>
     <tests>
         <!-- Test-1  PepQueryDB peptide gencode:human -->
-        <test>
+        <test expect_num_outputs="2">
             <conditional name="validation">
                 <param name="task_type" value="novel"/>
             </conditional>
@@ -513,6 +495,7 @@
                     <has_text text="LVVVGADGVGK" />
                     <not_has_text text="AHSSMVGVNLPQK" />
                     <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" />
+                    <has_n_columns n="22" />
                 </assert_contents>
             </output>
             <output name="log_txt">
@@ -523,7 +506,7 @@
         </test>
 
         <!-- Test-2  PepQueryDB peptide gencode:human pep.txt -->
-        <test>
+        <test expect_num_outputs="2">
             <conditional name="validation">
                 <param name="task_type" value="novel"/>
             </conditional>
@@ -582,6 +565,7 @@
                     <has_text text="LVVVGADGVGK" />
                     <not_has_text text="AHSSMVGVNLPQK" />
                     <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" />
+                    <has_n_columns n="22" />
                 </assert_contents>
             </output>
             <output name="log_txt">
@@ -592,7 +576,7 @@
         </test>
 
         <!-- Test-3  MGF peptide Uniprot.fasta -->
-        <test>
+        <test expect_num_outputs="2">
             <conditional name="validation">
                 <param name="task_type" value="novel"/>
             </conditional>
@@ -652,18 +636,14 @@
             <output name="psm_rank_txt">
                 <assert_contents>
                     <has_text text="ELGSSDLTAR" />
-                </assert_contents>
-            </output>
-            <output name="psm_rank_txt">
-                <assert_contents>
-                    <has_text text="ELGSSDLTAR" />
                     <has_line_matching expression="ELGSSDLTAR\tiTRAQ 4-plex of peptide N-term@0\[144.1\d+\]\t2\tiTRAQ_f4:3:2\t2\t1191.62\d+\t-3.04\d+\t-0.003\d+\t0.0\t1191.6\d+\t596.8\d+\t24.1\d+\t0\t0\t1\t995\t0.002\d+\t1\t0\tYes\t24.1\d+\t24.1\d+"/>
+                    <has_n_columns n="22" />
                 </assert_contents>
             </output>
         </test>
 
         <!-- Test-4  PepQueryDB known peptide gencode:human pep.txt -->
-        <test>
+        <test expect_num_outputs="2">
             <conditional name="validation">
                 <param name="task_type" value="known"/>
             </conditional>
@@ -692,6 +672,7 @@
                 <assert_contents>
                     <has_text text="AHSSMVGVNLPQK" />
                     <has_text text="6CPTAC_LUAD_W_BI_20180718_KL_f12:20286:3" />
+                    <has_n_columns n="22" />
                 </assert_contents>
             </output>
         </test>