diff data_manager/funannotate.xml @ 5:d2eb758a1d7d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4

--- a/data_manager/funannotate.xml	Fri Mar 07 22:28:23 2025 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-<tool id="data_manager_funannotate" name="Funannotate data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
-    <macros>
-        <token name="@TOOL_VERSION@">1.8.15</token>
-        <token name="@VERSION_SUFFIX@">0</token>
-    </macros>
-    <requirements>
-        <requirement type="package" version="@TOOL_VERSION@">funannotate</requirement>
-    </requirements>
-    <version_command>funannotate check --show-versions</version_command>
-    <command detect_errors="exit_code"><![CDATA[
-        #if $wget:
-            ## Asked for wget, we assume there's a certificate problem on (at least) one
-            ## of the many requested servers, force disable of all checks
-            echo "check_certificate = off" > \$HOME/.wgetrc &&
-        #end if
-
-        funannotate setup
-            -d '$output_file.extra_files_path'
-        #if $partial_data
-            -i merops -b eukaryota
-        #else
-            -b all
-        #end if
-            $wget
-        &&
-        cp '$dmjson' '$output_file'
-    ]]></command>
-    <configfiles>
-        <configfile name="dmjson"><![CDATA[
-#from datetime import datetime
-#set version_id=datetime.now().strftime("%Y-%m-%d-%H%M%S")
-    {
-      "data_tables":{
-        "funannotate":[
-          {
-            "value":"$version_id",
-            "description":"Funannotate database $version_id",
-            "format_version":"1.0",
-            "path":"$output_file.extra_files_path"
-          }
-        ]
-      }
-    }]]></configfile>
-    </configfiles>
-    <inputs>
-        <param name="partial_data" type="hidden" value="" help="Used for testing"/>
-        <param name="wget" type="boolean" truevalue="--wget" falsevalue="" checked="False" label="Download using wget" help="Try this if you get certificate errors"/>
-    </inputs>
-    <outputs>
-        <data name="output_file" format="data_manager_json"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="partial_data" value="--partial"/>
-            <output name="output_file">
-                <assert_contents>
-                    <has_text text="Funannotate database "/>
-                    <has_text text='"format_version":"1.0"'/>
-                </assert_contents>
-            </output>
-        </test>
-        <test>
-            <param name="partial_data" value="--partial"/>
-            <param name="wget" value="True"/>
-            <output name="output_file">
-                <assert_contents>
-                    <has_text text="Funannotate database "/>
-                    <has_text text='"format_version":"1.0"'/>
-                </assert_contents>
-            </output>
-        </test>
-    </tests>
-    <help><![CDATA[
-        This data managers fetches data from various databases for the funannotate
-        annotation tool and updates the funannotate data table.
-
-        .. _funannotate: https://funannotate.readthedocs.io
-    ]]></help>
-    <citations>
-        <citation type="doi">10.5281/zenodo.4054262</citation>
-    </citations>
-</tool>