changeset 25:a77f693df58c draft

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 42691bb143bd1ff7a13b0307d96ccb0fbf3747ca

--- a/macros.xml	Wed Jan 08 19:34:42 2025 +0000
+++ b/macros.xml	Thu Jan 16 17:35:49 2025 +0000
@@ -4,8 +4,8 @@
             <container type="docker">quay.io/galaxy/egapx:@TOOL_VERSION@</container>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">0.3.2-alpha</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">0.2-alpha</token>
+    <token name="@VERSION_SUFFIX@">9</token>
     <token name="@PROFILE@">23.0</token>
     <xml name="edam_ontology">
         <edam_operations>

--- a/ncbi_egapx.xml	Wed Jan 08 19:34:42 2025 +0000
+++ b/ncbi_egapx.xml	Thu Jan 16 17:35:49 2025 +0000
@@ -6,8 +6,6 @@
     <expand macro="edam_ontology"/>
     <expand macro="requirements"/>
     <command detect_errors="aggressive"><![CDATA[
-    export NXF_DEBUG=3 &&
-    echo \${PWD} &&
     #if $cond_input_style.input_style == "fillform"
         #set yamlconfig = $egapx_config
         ## The EGAPx pipeline code determines that a file is gzipped if it has a '.gz' extension.
@@ -53,8 +51,13 @@
     ## use the augmented container EGAPx config
     ln -s /galaxy/egapx/egapx_config &&
     ## run EGAPx
-    python3 /galaxy/egapx/ui/egapx.py '$yamlconfig' -e galaxy -o 'egapx_out'
+    python3 /galaxy/egapx/ui/egapx.py '$yamlconfig' -e galaxy -o 'egapx_out' &&
+    ## hack to support 0.2-alpha
+    if [ -e egapx_out/accept.gff ]; then ln -s accept.gff egapx_out/complete.genomic.gff; fi
     ]]></command>
+    <environment_variables>
+         <environment_variable name="NXF_DEBUG">3</environment_variable>
+    </environment_variables>
     <configfiles>
         <configfile name="reads_config"><![CDATA[
         #if $cond_input_style.input_style == "fillform" and $cond_input_style.cond_rnaseq_style.rnaseq_style == "history"
@@ -176,12 +179,12 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="output" format="gff" label="EGAPx annotation for ${on_string}" from_work_dir="egapx_out/accept.gff"/>
+        <data name="output" format="gff" label="EGAPx annotation for ${on_string}" from_work_dir="egapx_out/complete.genomic.gff"/>
         <collection name="nextflow_stats" type="list" label="EGAPx nextflow stats for ${on_string}">
+            <data name="nf_report" format="html" label="Nextflow execution report" from_work_dir="egapx_out/run.report.html"/>
+            <data name="nf_timeline" format="html" label="Nextflow execution timeline" from_work_dir="egapx_out/run.timeline.html"/>
             <data name="nf_log" format="txt" label="Nextflow execution log" from_work_dir="egapx_out/nextflow.log"/>
-            <data name="nf_report" format="html" label="Nextflow execution report" from_work_dir="egapx_out/run.report.html"/>
             <data name="nf_trace" format="tabular" label="Nextflow trace file" from_work_dir="egapx_out/run.trace.txt"/>
-            <data name="nf_timeline" format="html" label="Nextflow execution timeline" from_work_dir="egapx_out/run.timeline.html"/>
             <data name="nf_params" format="yaml" label="Nextflow run parameters" from_work_dir="egapx_out/run_params.yaml"/>
         </collection>
     </outputs>
@@ -384,11 +387,11 @@
 Output
 =======
 
-EGAPx output will appear as a collection in the user history. The main annotation file is called *accept.gff*.
+EGAPx output will appear as a collection in the user history. The main annotation file is called *complete.genomic.gff*.
 
 ::
 
- accept.gff
+ complete.genomic.gff
  annot_builder_output
  nextflow.log
  run.report.html