diff data_manager/hisat2_index_builder.xml @ 2:b3d94db291c1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41

--- a/data_manager/hisat2_index_builder.xml	Fri Apr 25 21:34:28 2025 +0000
+++ b/data_manager/hisat2_index_builder.xml	Tue Jul 29 17:09:29 2025 +0000
@@ -2,7 +2,7 @@
     <description>builder</description>
     <macros>
         <token name="@WRAPPER_VERSION@">2.2.1</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@WRAPPER_VERSION@">hisat2</requirement>
@@ -26,10 +26,10 @@
 
         mkdir -p '${out_file.extra_files_path}' &&
         ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' &&
-        working=`pwd` &&
+        working=$(pwd)` &&
         cd '${out_file.extra_files_path}' &&
 
-        hisat2-build -p \${GALAXY_SLOTS:-1}
+        hisat2-build -p "\${GALAXY_SLOTS:-1}"
             #if $advanced.adv_param_select == 'yes':
                 --noauto
                 #if $advanced.snps:
@@ -46,6 +46,7 @@
                 --offrate $advanced.offrate
             #end if
             '${fasta_file_name}' '${value}' &&
+        rm '${out_file.extra_files_path}/${fasta_file_name}' &&
 
         cp '$dmjson' '$out_file'
         ]]>
@@ -62,7 +63,7 @@
         "value": "${value}",
         "dbkey": "${all_fasta_source.fields.dbkey}",
         "name": "${name}",
-        "path": "${fasta_file_name}"
+        "path": "${value}"
       }
     ]
   }
@@ -103,11 +104,11 @@
             <param name="all_fasta_source" value="phiX174"/>
             <param name="sequence_name" value="Galeocerdo cuvier"/>
             <param name="sequence_id" value="tigHai1"/>
-            <param name="adv_param_select" value="yes"/>
-            <param name="bmax" value="3"/>
-            <param name="bmaxdivn" value="3"/>
-            <param name="dcv" value="4"/>
-            <param name="offrate" value="5"/>
+            <param name="advanced|adv_param_select" value="yes"/>
+            <param name="advanced|bmax" value="3"/>
+            <param name="advanced|bmaxdivn" value="3"/>
+            <param name="advanced|dcv" value="4"/>
+            <param name="advanced|offrate" value="5"/>
             <output name="out_file" file="hisat2_data_manager.2.json"/>
         </test>
     </tests>