# HG changeset patch
# User iuc
# Date 1755354919 0
# Node ID 6754002631cde14c674f7c7838f6abcece9baf5e
# Parent  39865c64a4e126d5d2e9383d2e7274e9a1e047aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit e5971e34b23280f7c3d6291a03325b6dd47e3fdd

diff -r 39865c64a4e1 -r 6754002631cd data_manager/bowtie2_index_builder.xml
--- a/data_manager/bowtie2_index_builder.xml	Thu Dec 05 06:48:52 2024 +0000
+++ b/data_manager/bowtie2_index_builder.xml	Sat Aug 16 14:35:19 2025 +0000
@@ -2,7 +2,7 @@
     <description>builder</description>
     <macros>
         <token name="@WRAPPER_VERSION@">2.5.4</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@WRAPPER_VERSION@">bowtie2</requirement>
@@ -14,6 +14,7 @@
         ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' &&
         cd '${out_file.extra_files_path}' &&
         bowtie2-build --threads \${GALAXY_SLOTS:-1} '${out_file.extra_files_path}/${fasta_file_name}' '${value}' &&
+        rm '${out_file.extra_files_path}/${fasta_file_name}' &&
         cp '$dmjson' '$out_file'
     ]]></command>
     <configfiles>
@@ -28,7 +29,7 @@
         "value": "${value}",
         "dbkey": "${all_fasta_source.fields.dbkey}",
         "name": "${name}",
-        "path": "${fasta_file_name}"
+        "path": "${value}"
       }
 #if $tophat2:
     ],
@@ -37,7 +38,7 @@
         "value": "${value}",
         "dbkey": "${all_fasta_source.fields.dbkey}",
         "name": "${name}",
-        "path": "${fasta_file_name}"
+        "path": "${value}"
       }
 #end if
     ]
diff -r 39865c64a4e1 -r 6754002631cd data_manager_conf.xml
--- a/data_manager_conf.xml	Thu Dec 05 06:48:52 2024 +0000
+++ b/data_manager_conf.xml	Sat Aug 16 14:35:19 2025 +0000
@@ -11,7 +11,7 @@
                         <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base -->
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">genomes/${dbkey}/bowtie_index/v2/${value}</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomes/${dbkey}/bowtie_index/v2/${value}/${path}</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomes/${dbkey}/bowtie_index/v2/${value}/${value}</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
@@ -24,7 +24,7 @@
                 <column name="name" />
                 <column name="path" output_ref="out_file" >
                     <!-- no move, always happens as part of bowtie2 and uses that path -->
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomes/${dbkey}/bowtie_index/v2/${value}/${path}</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomes/${dbkey}/bowtie_index/v2/${value}/${value}</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
diff -r 39865c64a4e1 -r 6754002631cd test-data/bowtie2_data_manager.1.json
--- a/test-data/bowtie2_data_manager.1.json	Thu Dec 05 06:48:52 2024 +0000
+++ b/test-data/bowtie2_data_manager.1.json	Sat Aug 16 14:35:19 2025 +0000
@@ -5,7 +5,7 @@
         "value": "phiX174",
         "dbkey": "phiX174",
         "name": "phiX 174",
-        "path": "phiX174.fasta"
+        "path": "phiX174"
       }
     ],
     "tophat2_indexes":[
@@ -13,7 +13,7 @@
         "value": "phiX174",
         "dbkey": "phiX174",
         "name": "phiX 174",
-        "path": "phiX174.fasta"
+        "path": "phiX174"
       }
     ]
   }
diff -r 39865c64a4e1 -r 6754002631cd test-data/bowtie2_data_manager.2.json
--- a/test-data/bowtie2_data_manager.2.json	Thu Dec 05 06:48:52 2024 +0000
+++ b/test-data/bowtie2_data_manager.2.json	Sat Aug 16 14:35:19 2025 +0000
@@ -5,7 +5,7 @@
         "value": "tigHai1",
         "dbkey": "phiX174",
         "name": "Galeocerdo cuvier",
-        "path": "phiX174.fasta"
+        "path": "tigHai1"
       }
     ]
   }