Mercurial > repos > bgruening > uniprot_rest_interface

diff uniprot.xml @ 10:5e57b0a0e8d0 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit daea630529977907a5fcfec24baeb920e41a4dd2
author bgruening
date Thu, 31 Jul 2025 17:11:00 +0000
parents f31d8d59ffb6
children
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--- a/uniprot.xml	Tue Aug 06 14:49:34 2024 +0000
+++ b/uniprot.xml	Thu Jul 31 17:11:00 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="uniprot" name="UniProt" version="0.6" profile="23.1">
+<tool id="uniprot" name="UniProt" version="0.7" profile="23.1">
     <description>ID mapping and retrieval</description>
     <requirements>
         <requirement type="package" version="2.25.1">requests</requirement>
@@ -826,7 +826,7 @@
                 <param name="format" type="select" label="Choose format of output file" help="">
                     <option value="fasta">fasta</option>
                     <option value="gff">gff</option>
-                    <option value="txt">Text</option>
+                    <option value="txt">embl</option>
                 </param>
             </when>
         </conditional>
@@ -842,8 +842,8 @@
                 <filter>tool['tool_choice'] == 'retrieve'</filter>
                 <filter>tool['format'] == 'gff'</filter>
             </data>
-            <data name="outfile_retrieve_txt" format="txt" from_work_dir="./output"
-                label="${tool.name} on ${on_string}: txt">
+            <data name="outfile_retrieve_txt" format="embl" from_work_dir="./output"
+                label="${tool.name} on ${on_string}: embl">
                	<filter>tool['tool_choice'] == 'retrieve'</filter>
                 <filter>tool['format'] == 'txt'</filter>
             </data>
@@ -853,18 +853,28 @@
             </data>
     </outputs>
     <tests>
+        <!-- test fasta output: atm 7 sequences, so we test for 10+-5 header lines, since its multi line fasta we assume at least 5 lines of sequence-->
         <test expect_num_outputs="1">
             <param name="infile" value="id_uniprot.tab" ftype="tabular"/>
-            <param name="id_column" value="c1"/>
-            <param name="format" value="fasta"/>
-            <param name="tool_choice" value="retrieve"/>
-            <output name="outfile_retrieve_fasta" file="test1_retrieve.fasta" ftype="fasta" compare="sim_size" />
+            <param name="id_column" value="1"/>
+            <conditional name="tool">
+                <param name="format" value="fasta"/>
+                <param name="tool_choice" value="retrieve"/>
+            </conditional>
+            <output name="outfile_retrieve_fasta" ftype="fasta">
+                <assert_contents>
+                    <has_line_matching expression="^>.+$" n="10" delta="5"/>
+                    <has_line_matching expression="^[A-Z]+$" min="5"/>
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="1">
             <param name="infile" value="id_uniprot.tab" ftype="tabular"/>
-            <param name="id_column" value="c1"/>
-            <param name="format" value="gff"/>
-            <param name="tool_choice" value="retrieve"/>
+            <param name="id_column" value="1"/>
+            <conditional name="tool">
+                <param name="format" value="gff"/>
+                <param name="tool_choice" value="retrieve"/>
+            </conditional>
             <output name="outfile_retrieve_gff" ftype="gff">
                 <assert_contents>
                     <has_n_lines min="80"/>
@@ -874,18 +884,30 @@
         </test>
         <test expect_num_outputs="1">
             <param name="infile" value="id_uniprot.tab" ftype="tabular"/>
-            <param name="id_column" value="c1"/>
-            <param name="tool_choice" value="map"/>
-            <param name="from" value="UniProtKB_AC-ID"/>
-            <param name="to" value="Gene_Name"/>
-            <output name="outfile_map" file="test1_map.tab" ftype="tabular" sort="true"/>
+            <param name="id_column" value="1"/>
+            <conditional name="tool">
+                <param name="format" value="txt"/>
+                <param name="tool_choice" value="retrieve"/>
+            </conditional>
+            <output name="outfile_retrieve_gff" ftype="embl">
+                <assert_contents>
+                    <has_n_lines min="80"/>
+                    <has_text text="UniProtKB"/>
+                    <has_line_matching expression="^ID .*"/>
+                    <has_line line="//"/>
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="1">
             <param name="infile" value="id_map_refseq.txt" ftype="tabular"/>
-            <param name="id_column" value="c1"/>
-            <param name="tool_choice" value="map"/>
-            <param name="from" value="RefSeq_Nucleotide"/>
-            <param name="to" value="UniProtKB"/>
+            <param name="id_column" value="1"/>
+            <conditional name="tool">
+                <param name="tool_choice" value="map"/>
+                <conditional name="from_cond">
+                    <param name="from" value="RefSeq_Nucleotide"/>
+                    <param name="to" value="UniProtKB"/>
+                </conditional>
+            </conditional>
             <output name="outfile_map" file="test2_map.tab" ftype="tabular" sort="true"/>
         </test>
     </tests>