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changeset 6:8c6526a46319 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api commit 69cdfd826c760c5b091703919ddaee9c9f90d530
author iuc
date Sun, 23 Nov 2025 16:19:36 +0000
parents 1911ec100221
children
files iedb_api.xml
diffstat 1 files changed, 35 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/iedb_api.xml	Fri Nov 07 18:26:22 2025 +0000
+++ b/iedb_api.xml	Sun Nov 23 16:19:36 2025 +0000
@@ -2,7 +2,7 @@
     <description>MHC Binding prediction</description>
     <macros>
         <token name="@TOOL_VERSION@">2.15.3</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
         <token name="@PROFILE@">24.2</token>
         <xml name="alleles" token_hla_regex="" token_hla_examples="" token_hlalen_examples=""> 
             <conditional name="alleles">
@@ -108,7 +108,7 @@
                     <option value="netmhccons">netmhccons</option>
                     <option value="pickpocket">pickpocket</option>
                 </param>
-                <expand macro="alleles" hla_regex="(HLA-[A-CEG]\*[0-8][[0-9]:[0-9][0-9][0-9]*|BoLA-.+|Gogo-.+|H-2-[DKL][bdk]|Mamu-.+|Patr-.+|RT.+|SLA-.+)(,([8-9]|1[0-5]))*" hla_examples="HLA-A*03:01  HLA-B*07:02" hlalen_examples="HLA-A*03:01,8,9,10  HLA-B*07:02,9"/>
+                <expand macro="alleles" hla_regex="(HLA-[A-CEG]\*[0-8][0-9]:[0-9][0-9][0-9]*|BoLA-.+|Gogo-.+|H-2-[DKL][bdk]|Mamu-.+|Patr-.+|RT.+|SLA-.+)(,([8-9]|1[0-5]))*" hla_examples="HLA-A*03:01  HLA-B*07:02" hlalen_examples="HLA-A*03:01,8,9,10  HLA-B*07:02,9"/>
                 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
                     <help>Used for any alleles which don't include specified lengths</help>
                     <option value="8" selected="true">8</option>
@@ -172,7 +172,7 @@
                     <option value="immuno">immuno</option>
                     <option value="constitutive">constitutive</option>
                 </param>
-                <expand macro="alleles" hla_regex="(HLA-[A-CE]\*[0-8][[0-9]:[0-9][0-9]|BoLA-.+|Gogo-.+|H-2-[DKL][bdk]|Mamu-.+|Patr-.+|RT.+|SLA-.+)(,([8-9]|1[0-4]))*" hla_examples="HLA-A*03:01  HLA-B*07:02" hlalen_examples="HLA-A*03:01,8,9,10  HLA-B*07:02,9"/> 
+                <expand macro="alleles" hla_regex="(HLA-[A-CE]\*[0-8][0-9]:[0-9][0-9]|BoLA-.+|Gogo-.+|H-2-[DKL][bdk]|Mamu-.+|Patr-.+|RT.+|SLA-.+)(,([8-9]|1[0-4]))*" hla_examples="HLA-A*03:01  HLA-B*07:02" hlalen_examples="HLA-A*03:01,8,9,10  HLA-B*07:02,9"/> 
                 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
                     <help>Used for any alleles which don't include specified lengths</help>
                     <option value="8" selected="true">8</option>
@@ -236,12 +236,12 @@
         -->
         <data name="output" format="tabular" label="IEDB ${prediction.tool} ${prediction.method}"/>
         <data name="output2" format="tabular" label="IEDB ${prediction.tool} ${prediction.method} residue scores" from_work_dir="iedb_results2">
-            <filter>prediction['method'].startswith('Bepipred')</filter>
+            <filter>prediction['method'] == 'Bepipred'</filter>
         </data> 
     </outputs>
     <tests>
         <!-- test1 -->
-        <test> 
+        <test expect_num_outputs="1"> 
             <conditional name="prediction">
                 <param name="tool" value="mhci"/>
                 <param name="method" value="recommended"/>
@@ -261,7 +261,7 @@
             </output>
         </test>
         <!-- test2 -->
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="prediction">
                 <param name="tool" value="mhci"/>
                 <param name="method" value="recommended"/>
@@ -282,7 +282,7 @@
             </output>
         </test>
         <!-- test3 -->
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="prediction">
                 <param name="tool" value="mhci"/>
                 <param name="method" value="recommended"/>
@@ -306,7 +306,7 @@
             </output>
         </test>
         <!-- test4 -->
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="prediction">
                 <param name="tool" value="mhcii"/>
                 <param name="method" value="recommended"/>
@@ -327,7 +327,7 @@
             </output>
         </test>
         <!-- test5 -->
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="prediction">
                 <param name="tool" value="processing"/>
                 <param name="method" value="recommended"/>
@@ -348,7 +348,7 @@
             </output>
         </test>
         <!-- test6 -->
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="prediction">
                 <param name="tool" value="mhcnp"/>
                 <param name="method" value="mhcnp"/>
@@ -368,7 +368,7 @@
             </output>
         </test>
         <!-- test7 -->
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="prediction">
                 <param name="tool" value="bcell"/>
                 <param name="method" value="Emini"/>
@@ -384,7 +384,7 @@
             </output>
         </test>
         <!-- test8 -->
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="prediction">
                 <param name="tool" value="bcell"/>
                 <param name="method" value="Kolaskar-Tongaonkar"/>
@@ -400,6 +400,29 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- test9 test 2nd output for Bepipred, no idea if its possible to have output non-empty -->
+        <test expect_num_outputs="2">
+            <conditional name="prediction">
+                <param name="tool" value="bcell"/>
+                <param name="method" value="Bepipred"/>
+                <param name="window_size" value="9"/>
+            </conditional>
+            <conditional name="sequence">
+                <param name="seqsrc" value="fasta"/>
+                <param name="seq_fasta" ftype="fasta" value="bcell.fa"/>
+            </conditional>
+            <output name="output">
+                <assert_contents>
+                    <has_n_lines n="0" />
+                </assert_contents>
+            </output>
+            <output name="output2">
+                <assert_contents>
+                    <has_n_lines n="106"/>
+                    <has_n_columns n="5"/>
+                </assert_contents>
+            </output>
+        </test>
 
     </tests>
     <help><![CDATA[