Merge pull request bgruening#1405 from bgruening/reago-biotools

Add bio.tools for reago
planemo-autoupdate · Apr 27, 2024 · f5be73e · f5be73e
2 parents 66411f2 + f180dba
commit f5be73e
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Showing 2 changed files with 21 additions and 26 deletions.
diff --git a/tools/rna_tools/reago/.shed.yml b/tools/rna_tools/reago/.shed.yml
@@ -7,3 +7,4 @@ homepage_url: https://github.com/chengyuan/reago-1.1
 name: reago
 owner: rnateam 
 remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago
+long_description: Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.
diff --git a/tools/rna_tools/reago/reago.xml b/tools/rna_tools/reago/reago.xml
@@ -1,37 +1,39 @@
-<tool id="reago" name="Reago" version="1.1">
+<tool id="reago" name="Reago" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <description> to assemble rRNA</description>
-
+    <macros>
+        <token name="@TOOL_VERSION@">1.1</token>
+        <token name="@VERSION_SUFFIX@">1</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">reago</xref>
+    </xrefs>
     <requirements>
-        <requirement type="package" version="1.1">reago</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">reago</requirement>
+        <requirement type="package" version="1.11">networkx</requirement>
     </requirements>
-
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
-
-    <command>
-<![CDATA[
+    <command detect_errors="exit_code">
+    <![CDATA[
         #set $r1_output=$os.path.splitext($os.path.basename(str($r1_file)))[0]
         #set $r2_output=$os.path.splitext($os.path.basename(str($r2_file)))[0]
 
-        python $__tool_directory__/format_reago_input_files.py 
-            --r1_input "$r1_file"
-            --r2_input "$r2_file"
-            --r1_output $r1_output
-            --r2_output $r2_output
+        python '$__tool_directory__/format_reago_input_files.py' 
+            --r1_input '$r1_file'
+            --r2_input '$r2_file'
+            --r1_output '$r1_output'
+            --r2_output '$r2_output'
 
         &&  
         filter_input.py 
-            $r1_output
-            $r2_output
+            '$r1_output'
+            '$r2_output'
             .
             \$(dirname \$(which reago.py))/cm/ 
             $cm_to_use
             "\${GALAXY_SLOTS:-4}"
 
         && 
         reago.py 
-            "filtered.fasta"
+            'filtered.fasta'
             .
             -l $read_length
             -o $overlap
@@ -64,9 +66,7 @@
             <option value="a">Archea only</option>
             <option value="ab">Bacteria and archea</option>
         </param>
-
     </inputs>
-
     <outputs>
         <data format="fasta" name="full_genes" 
             from_work_dir="full_genes.fasta"
@@ -75,24 +75,19 @@
             from_work_dir="fragments.fasta"
             label="Fragment genes of ${on_string} (Framebot)" />
     </outputs>
-
     <tests>
         <test>
             <param name="r1_file" value="reago_sample_1.fasta"/>
             <param name="r2_file" value="reago_sample_2.fasta"/>
             <param name="read_length" value="101" />
             <param name="overlap" value="0.8" />
-            <param name="error_correction" value="0.05" />
             <param name="tip_size" value="30" />
             <param name="path_finding_parameter" value="10"/>
             <param name="cm_to_use" value="ab" />
-            <param name="cpu_nb" value="4" />
-
             <output name="full_genes" file="reago_full_genes.fasta"/>
             <output name="fragments" file="reago_fragments.fasta"/>
         </test>
     </tests>
-
     <help>
 <![CDATA[
 
@@ -129,7 +124,6 @@ Reago produces two output files:
 
     ]]>
     </help>
-
     <citations>
         <citation type="doi">10.1093/bioinformatics/btv231</citation>
     </citations>