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changeset 32:fb723c531be5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit ac10fe34f1b2d5e8109dcaaf42b7870bee57827b
author iuc
date Wed, 25 Oct 2023 07:10:06 +0000
parents 734abc7ac21d
children 6591f049cf7e
files fastq_dump.xml macros.xml
diffstat 2 files changed, 21 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/fastq_dump.xml	Thu Sep 14 07:38:02 2023 +0000
+++ b/fastq_dump.xml	Wed Oct 25 07:10:06 2023 +0000
@@ -12,7 +12,7 @@
     @SET_ACCESSIONS@
 
     #if $input.input_select == "sra_file":
-        fastq-dump --log-level fatal --accession '${input.file.name}'
+        fastq-dump --log-level fatal --accession "\$acc"
     #else:
         ## Do not use prefetch if region is specified, to avoid downloading
         ## the complete sra file.
@@ -20,8 +20,8 @@
             prefetch -X 200000000 "\$acc" &&
         #end if
         fastq-dump --accession "\$acc"
-        --split-files
     #end if
+    --split-files
     --defline-seq '$adv.defline_seq'
     --defline-qual '+'
 
@@ -269,6 +269,21 @@
                 </element>
             </output_collection>
         </test>
+        <test expect_num_outputs="2">
+            <param name="input_select" value="sra_file"/>
+            <param name="sra_file" value="SRR522874.sra"/>
+            <param name="split" value="True"/>
+            <param name="skip_technical" value="True"/>
+            <section name="adv">
+                <param name="defline_seq" value="@$sn/$ri"/>
+            </section>
+            <output_collection name="list_paired" type="list:paired" count="1">
+                <element name="SRR522874.sra">
+                    <element name="forward" file="SRR522874.sra_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
+                    <element name="reverse" file="SRR522874.sra_4.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
+                </element>
+            </output_collection>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does?**
--- a/macros.xml	Thu Sep 14 07:38:02 2023 +0000
+++ b/macros.xml	Wed Oct 25 07:10:06 2023 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">3.0.5</token>
-    <token name="@VERSION_SUFFIX@">3</token>
+    <token name="@TOOL_VERSION@">3.0.8</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">22.01</token>
     <xml name="edam_ontology">
         <edam_topics>
@@ -15,8 +15,8 @@
     <macro name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">sra-tools</requirement>
-            <requirement type="package" version="2.6">pigz</requirement>
-            <requirement type="package" version="1.17">samtools</requirement>
+            <requirement type="package" version="2.8">pigz</requirement>
+            <requirement type="package" version="1.18">samtools</requirement>
             <yield/>
         </requirements>
     </macro>