# HG changeset patch
# User bgruening
# Date 1710754517 0
# Node ID a896b8b7d26455bd66927d0baf74ffdb2d47efc7
# Parent  dba18bf7528f3f0dd5b26c3192b71a8565e198c0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a

diff -r dba18bf7528f -r a896b8b7d264 macros.xml
--- a/macros.xml	Fri Jun 23 17:02:59 2023 +0000
+++ b/macros.xml	Mon Mar 18 09:35:17 2024 +0000
@@ -1,8 +1,13 @@
 <macros>
     <token name="@TOOL_VERSION@">1.10.1</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@IDX_VERSION@">q7</token>
     <token name="@PROFILE_VERSION@">20.01</token>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">salmon</xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">salmon</requirement>
@@ -121,9 +126,10 @@
         label="Discard orphan quasi"
         help="Discard orphan mappings in quasi-mapping mode. If this flag is passed then only paired mappings will be considered toward quantification estimates.  The default behavior is to consider orphan mappings if no valid paired mappings exist."/>
         <conditional name="validmap">
-            <param name="validateMappings" type="boolean" truevalue="--validateMappings" falsevalue="" checked="False"
-            label="Validate mappings"
-            help="Validate mappings using alignment-based verifcation. If this flag is passed, quasi-mappings will be validated to ensure that they could give rise to a reasonable alignment before they are further used for quantification."/>
+            <param name="validateMappings" type="select" label="Validate mappings" help="Validate mappings using alignment-based verifcation. If this flag is passed, quasi-mappings will be validated to ensure that they could give rise to a reasonable alignment before they are further used for quantification.">
+                <option value="--validateMappings">True</option>
+                <option value="" selected="true">False</option>
+            </param>
             <when value="--validateMappings">
                 <param name="minScoreFraction" type="float" value="0.65" min="0.0" max="0.99"
                 label="Min Score Fraction"
@@ -390,7 +396,7 @@
             #end if
             ln -s '${quant_type.input.single_or_paired.input_1.forward}' ./mate1.$ext &&
             ln -s '${quant_type.input.single_or_paired.input_1.reverse}' ./mate2.$ext &&
-        #else if '$quant_type.input.single_or_paired.single_or_paired_opts' == 'paired_interleaved':
+        #else if $quant_type.input.single_or_paired.single_or_paired_opts == 'paired_interleaved':
             #if $quant_type.input.single_or_paired.input_1.ext == 'fasta':
                 #set $ext = 'fasta'
             #else:
diff -r dba18bf7528f -r a896b8b7d264 salmonquantmerge.xml
--- a/salmonquantmerge.xml	Fri Jun 23 17:02:59 2023 +0000
+++ b/salmonquantmerge.xml	Mon Mar 18 09:35:17 2024 +0000
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         @qmerge@