diff tools/blastxml_to_top_descr/blastxml_to_top_descr.xml @ 13:8dc4ba7eba5d draft default tip

v0.1.2 with Python 3.9 declaration

--- a/tools/blastxml_to_top_descr/blastxml_to_top_descr.xml	Wed Jul 30 05:36:52 2014 -0400
+++ b/tools/blastxml_to_top_descr/blastxml_to_top_descr.xml	Sun Sep 17 13:01:56 2023 +0000
@@ -1,27 +1,27 @@
-<tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.1.1">
+<tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.1.2" profile="16.10">
     <description>Make a table from BLAST output</description>
-    <version_command interpreter="python">blastxml_to_top_descr.py --version</version_command>
-    <command interpreter="python">
-blastxml_to_top_descr.py
--f "$input.in_format"
+    <requirements>
+        <requirement type="package" version="3.9">python</requirement>
+    </requirements>
+    <version_command>
+python $__tool_directory__/blastxml_to_top_descr.py --version
+    </version_command>
+    <command detect_errors="aggressive">
+python $__tool_directory__/blastxml_to_top_descr.py
+-f '$input.in_format'
 #if $input.in_format == "tabular":
     --qseqid $input.qseqid
     --sseqid $input.sseqid
     --salltitles $input.salltitles
 #end if
--o "${tabular_file}"
+-o '${tabular_file}'
 -t ${topN}
-"${in_file}"
+'${in_file}'
     </command>
-    <stdio>
-        <!-- Assume anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
     <inputs>
         <conditional name="input">
             <param name="in_format" type="select" label="Input format">
-                <option value="blastxml" select="True">BLAST XML</option>
+                <option value="blastxml" selected="true">BLAST XML</option>
                 <option value="tabular">Tabular</option>
             </param>
             <when value="blastxml">
@@ -30,17 +30,17 @@
             <when value="tabular">
                 <param name="in_file" type="data" format="tabular" label="BLAST results as tabular"/>
                 <param name="qseqid" type="data_column" data_ref="in_file"
-		       multiple="False" numerical="False" default_value="1" value="1"
-		       label="Column containing query ID (qseqid)"
-		       help="This is column 1 in standard BLAST tabular output" />
-		<param name="sseqid" type="data_column" data_ref="in_file"
-		       multiple="False" numerical="False" default_value="2" value="2"
-		       label="Column containing match ID (sseqid)"
-		       help="This is column 2 in standard BLAST tabular output"/>
+                       multiple="false" numerical="false" default_value="1" value="1"
+                       label="Column containing query ID (qseqid)"
+                       help="This is column 1 in standard BLAST tabular output" />
+                <param name="sseqid" type="data_column" data_ref="in_file"
+                       multiple="false" numerical="false" default_value="2" value="2"
+                       label="Column containing match ID (sseqid)"
+                       help="This is column 2 in standard BLAST tabular output"/>
                 <param name="salltitles" type="data_column" data_ref="in_file"
-		       multiple="False" numerical="False" default_value="25" value="25"
+                       multiple="false" numerical="false" default_value="25" value="25"
                        label="Column containing containing descriptions (salltitles)"
-		       help="This is column 25 in the default extended BLAST tabular output"/>
+                       help="This is column 25 in the default extended BLAST tabular output"/>
             </when>
         </conditional>
         <param name="topN" type="integer" min="1" max="100" optional="false" label="Number of descriptions" value="3"/>
@@ -48,8 +48,6 @@
     <outputs>
         <data name="tabular_file" format="tabular" label="Top $topN descriptions from $input.in_file.name" />
     </outputs>
-    <requirements>
-    </requirements>
     <tests>
         <test>
             <param name="in_format" value="blastxml" />
@@ -102,7 +100,7 @@
 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
 Galaxy tools and workflows for sequence analysis with applications
 in molecular plant pathology. PeerJ 1:e167
-http://dx.doi.org/10.7717/peerj.167
+https://doi.org/10.7717/peerj.167
 
 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr