Mercurial > repos > iuc > fastq_dl

diff fastq_dl.xml @ 2:0095a278a085 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 3253434cee1e88dcab77c1cc99264900c78eadb9
author iuc
date Thu, 13 Nov 2025 13:33:35 +0000
parents f1a958f3e3f6
children
line wrap: on
line diff
--- a/fastq_dl.xml	Tue Apr 29 06:04:25 2025 +0000
+++ b/fastq_dl.xml	Thu Nov 13 13:33:35 2025 +0000
@@ -57,8 +57,10 @@
     <tests>
         <!-- #1 Testing single end and paired end using accessions file -->
         <test expect_num_outputs="3">
-            <param name="select_input_type" value="accessions_list" />
-            <param name="accessions_file" value="accessions.txt" />
+            <conditional name="input_type">
+                <param name="select_input_type" value="accessions_list" />
+                <param name="accessions_file" value="accessions.txt" />
+            </conditional>
             <output_collection name="metadata" type="list" count="4">
                 <element name="DRR011117" file="Metadata_files/DRR011117.tsv" />
                 <element name="ERR2651925" file="Metadata_files/ERR2651925.tsv" />
@@ -112,8 +114,10 @@
         </test>
         <!-- #2 Testing single end and paired end using accessions as text input -->
         <test expect_num_outputs="3">
-            <param name="select_input_type" value="accession_ids" />
-            <param name="accessions" value="ERR4319712 DRR011117 ERR2651925 SRR9678965" />
+            <conditional name="input_type">
+                <param name="select_input_type" value="accession_ids" />
+                <param name="accessions" value="ERR4319712 DRR011117 ERR2651925 SRR9678965" />
+            </conditional>
             <output_collection name="metadata" type="list" count="4">
                 <element name="DRR011117" file="Metadata_files/DRR011117.tsv" />
                 <element name="ERR2651925" file="Metadata_files/ERR2651925.tsv" />
@@ -161,9 +165,11 @@
         </test>
         <!-- #3 Testing only download metadata -->
         <test expect_num_outputs="1">
-            <param name="select_input_type" value="accessions_list" />
-            <param name="accessions_file" value="accessions.txt" />
-            <param name="only_download_metadata" value="--only-download-metadata" />
+            <conditional name="input_type">
+                <param name="select_input_type" value="accessions_list" />
+                <param name="accessions_file" value="accessions.txt" />
+            </conditional>
+            <param name="only_download_metadata" value="true" />
             <output_collection name="metadata" type="list" count="4">
                 <element name="DRR011117" file="Metadata_files/DRR011117.tsv" />
                 <element name="ERR2651925" file="Metadata_files/ERR2651925.tsv" />
@@ -173,9 +179,11 @@
         </test>
         <!-- #4 Testing group by experiment -->
         <test expect_num_outputs="3">
-            <param name="select_input_type" value="accessions_list" />
-            <param name="accessions_file" value="accessions.txt" />
-            <param name="group_by_experiment" value="--group-by-experiment" />
+            <conditional name="input_type">
+                <param name="select_input_type" value="accessions_list" />
+                <param name="accessions_file" value="accessions.txt" />
+            </conditional>
+            <param name="group_by_experiment" value="true" />
             <output_collection name="metadata" type="list" count="4">
                 <element name="DRR011117" file="Metadata_files/DRR011117.tsv" />
                 <element name="ERR2651925" file="Metadata_files/ERR2651925.tsv" />
@@ -223,9 +231,11 @@
         </test>
         <!-- #5 Testing group by sample -->
         <test expect_num_outputs="3">
-            <param name="select_input_type" value="accessions_list" />
-            <param name="accessions_file" value="accessions.txt" />
-            <param name="group_by_sample" value="--group-by-sample" />
+            <conditional name="input_type">
+                <param name="select_input_type" value="accessions_list" />
+                <param name="accessions_file" value="accessions.txt" />
+            </conditional>
+            <param name="group_by_sample" value="true" />
             <output_collection name="metadata" type="list" count="4">
                 <element name="DRR011117" file="Metadata_files/DRR011117.tsv" />
                 <element name="ERR2651925" file="Metadata_files/ERR2651925.tsv" />
@@ -271,6 +281,16 @@
                 </element>
             </output_collection>
         </test>
+        <!-- #6 Testing exit code capture in the for loop  -->
+        <test expect_exit_code="1" expect_failure="true">
+            <conditional name="input_type">
+                <param name="select_input_type" value="accession_ids" />
+                <param name="accessions" value="DRR0117 ERR2651925" />
+            </conditional>
+            <assert_stderr>
+                <has_text text="fastq-dl failed for accession: DRR0117" />
+            </assert_stderr>
+        </test>
     </tests>
     <help><![CDATA[