Mercurial > repos > iuc > sra_tools

changeset 25:69ebb7f46e45 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit a464017f4a599697101dbd26cf5eb902588359b5"
author iuc
date Tue, 27 Apr 2021 08:55:34 +0000
parents e08a7ad4378b
children 83c7d564b128
files fasterq_dump.xml sra_macros.xml test-data/SRR522874.sra_1.fastq.gz test-data/SRR522874.sra_2.fastq.gz test-data/SRR522874.sra_3.fastq.gz test-data/SRR522874.sra_4.fastq.gz
diffstat 6 files changed, 21 insertions(+), 35 deletions(-) [+]
line wrap: on
line diff
--- a/fasterq_dump.xml	Mon Feb 01 20:03:42 2021 +0000
+++ b/fasterq_dump.xml	Tue Apr 27 08:55:34 2021 +0000
@@ -106,10 +106,10 @@
         </collection>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="4">
             <param name="input_select" value="accession_number"/>
             <param name="accession" value="ERR086330"/>
-            <output_collection name="list_paired" type="list:paired">
+            <output_collection name="list_paired" type="list:paired" count="1">
                 <element name="ERR086330">
                     <element name="forward" file="ERR086330_1.fastq.gz" decompress="True">
                     </element>
@@ -118,22 +118,22 @@
                 </element>
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="4">
             <param name="input_select" value="accession_number"/>
             <param name="accession" value="SRR002702"/>
             <param name="split" value="--split-files"/>
             <param name="skip_technical" value="False"/>
-            <output_collection name="output_collection_other" type="list">
+            <output_collection name="output_collection_other" type="list" count="2">
                 <element name="SRR002702_1" file="SRR002702_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
                 <element name="SRR002702_2" file="SRR002702_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="4">
             <param name="input_select" value="file"/>
             <param name="file" value="SRR522874.sra"/>
             <param name="split" value="--split-files"/>
             <param name="skip_technical" value="True"/>
-            <output_collection name="list_paired" type="list:paired">
+            <output_collection name="list_paired" type="list:paired" count="1">
                 <element name="SRR522874.sra">
                     <element name="forward" file="SRR522874.sra_2.fastq.gz" decompress="True">
                     </element>
@@ -142,64 +142,50 @@
                 </element>
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="4">
             <param name="input_select" value="file"/>
             <param name="file" value="SRR522874.sra"/>
             <param name="split" value="--split-files"/>
             <param name="skip_technical" value="False"/>
-            <output_collection name="output_collection_other" type="list">
-                <element name="SRR522874.sra_1" file="SRR522874.sra_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
-                <element name="SRR522874.sra_2" file="SRR522874.sra_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
-                <element name="SRR522874.sra_3" file="SRR522874.sra_3.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
-                <element name="SRR522874.sra_4" file="SRR522874.sra_4.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
+            <output_collection name="output_collection_other" type="list" count="4">
+                <element name="SRR522874_1" file="SRR522874.sra_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
+                <element name="SRR522874_2" file="SRR522874.sra_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
+                <element name="SRR522874_3" file="SRR522874.sra_3.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
+                <element name="SRR522874_4" file="SRR522874.sra_4.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="4">
             <param name="input_select" value="file_list"/>
             <param name="file_list" value="list_sra"/>
             <param name="minlen" value="21"/>
             <output_collection name="output_collection_other" type="list">
                 <element name="SRR522874__single" file="SRR522874.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
             </output_collection>
-            <output_collection name="list_paired" type="list:paired">
+            <output_collection name="list_paired" type="list:paired" count="1">
                 <element name="SRR522874">
-                    <element name="forward" file="SRR522874_1.fastq.gz" decompress="True">
-                    </element>
-                    <element name="reverse" file="SRR522874_2.fastq.gz" decompress="True">
-                    </element>
+                    <element name="forward" file="SRR522874_1.fastq.gz" decompress="True"/>
+                    <element name="reverse" file="SRR522874_2.fastq.gz" decompress="True"/>
                 </element>
             </output_collection>
             <output_collection name="output_collection" type="list">
                 <element name="SRR002702" file="SRR002702_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="4">
             <param name="input_select" value="file_list"/>
             <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/>
-            <output_collection name="list_paired" type="list:paired">
-                <element name="SRR11857975">
-                    <element name="forward" file="SRR11857975_1.fastq.gz" decompress="True">
-                    </element>
-                    <element name="reverse" file="SRR11857975_2.fastq.gz" decompress="True">
-                    </element>
-                </element>
-            </output_collection>
-        </test>
-        <test>
-            <param name="input_select" value="file_list"/>
-            <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/>
-            <output_collection name="list_paired" type="list:paired">
+            <output_collection name="list_paired" type="list:paired" count="1">
                 <element name="SRR11953971">
                     <element name="forward" file="SRR11953971_1.fastq.gz" decompress="True"/>
                     <element name="reverse" file="SRR11953971_2.fastq.gz" decompress="True"/>
                 </element>
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="4">
              <!-- test accession downloaded from public bucket -->
             <param name="input_select" value="accession_number"/>
             <param name="accession" value="SRR11859153"/>
-            <output_collection name="output_collection" type="list">
+            <output_collection name="output_collection" type="list" count="1">
                 <element name="SRR11859153" file="SRR11859153.fastq.gz" decompress="True"/>
             </output_collection>
             <output name="log">
--- a/sra_macros.xml	Mon Feb 01 20:03:42 2021 +0000
+++ b/sra_macros.xml	Tue Apr 27 08:55:34 2021 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@VERSION@">2.10.9</token>
+    <token name="@VERSION@">2.11.0</token>
     <token name="@ACCESSIONS_FROM_FILE@">
         grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$'
     </token>
Binary file test-data/SRR522874.sra_1.fastq.gz has changed
Binary file test-data/SRR522874.sra_2.fastq.gz has changed
Binary file test-data/SRR522874.sra_3.fastq.gz has changed
Binary file test-data/SRR522874.sra_4.fastq.gz has changed