--- a/bio2srr.xml	Wed Oct 27 05:00:45 2021 -0400
+++ b/bio2srr.xml	Fri May 03 01:17:43 2024 -0400
@@ -1,35 +1,31 @@
-<tool id="bio2srr" name="Bioproject to SRR" version="1.0.0">
-	<description>Retrieve SRR accessions and sample metadata from BioProject or BioSample.</description>
+<tool id="bio2srr" name="Bioproject to SRR" version="3.0.0">
+	<description>Retrieve SRR accessions and sample metadata from BioProject. Recursively follows links to subprojects.</description>
     <requirements>
-        <requirement type="package" version="3.8">python</requirement>
-    	<requirement type="package" version="2.24.0">requests</requirement>
+        <requirement type="package" version="3.12">python</requirement>
+    	<requirement type="package" version="2.31.0">requests</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        #if $src_metadata
-        $__tool_directory__/bio2srr.py "$input1" $src_metadata > "$output"
-        #else
-        $__tool_directory__/bio2srr.py "$input1" > "$output"
-        #end if
+        python $__tool_directory__/bio2srr.py "$input1"
     ]]></command>
     <inputs>
-        <param type="text" name="input1" label="BioProject or BioSample" />
-        <param type="data" format="tabular" name="src_metadata" label="Table of your own metadata" optional="true" help="Optional metadata table to be folded in." />
+        <param type="text" name="input1" label="BioProject" />
     </inputs>
     <outputs>
-    	<data format="txt" name="output" label="SRR Accession List" />
+    	<data format="txt" name="output" from_work_dir="accessions.txt" label="SRR Accession List" />
         <data format="tabular" name="metadata" from_work_dir="metadata.tsv" label="Sample Metadata Table" />
     </outputs>
     <tests>
     	<test>
-    		<param name="input1" value="NOTHING" />
-    		<output name="output" file="test.txt" />
+    		<param name="input1" value="PRJNA681235" />
+    		<output name="output" file="accessions.txt" />
             <output name="metadata" file="metadata.tsv" />
     	</test>
+        <test expect_failure="1">
+            <param name="input1" value="NOTHING" />
+        </test>
     </tests>
     <help><![CDATA[
-        Retrieve SRR accessions and metadata from a BioProject.
-
-        If you have metadata for your own samples (that aren't from the BioProject) you can provide a TSV table with it and they'll be folded together. (It's a union, not a join.) Put sample ID's under the header 'sample'.
+        Retrieve SRR accessions and sample metadata from a BioProject, including subprojects. It's a JOIN, so if a sample is associated with multiple SRA runs, then each run has a copy of the sample's metadata.
     ]]></help>
     <citations>
     </citations>