changeset 4:f7810488bd92 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2063bc1f8f9cb97de147b86dbe9189fc496b206a"

--- a/hyphy_annotate.xml	Wed Jun 09 06:59:09 2021 +0000
+++ b/hyphy_annotate.xml	Wed Jun 09 17:25:00 2021 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hyphy_annotate" name="Annotate" version="@VERSION@">
+<tool id="hyphy_annotate" name="Annotate" version="@VERSION@+galaxy0">
     <description>a newick tree with HyPhy</description>
     <macros>
         <import>macros.xml</import>
@@ -10,7 +10,7 @@
         cp '$compressed_msa' input.$compressed_msa.extension &&
         cp '$__tool_directory__/scripts/annotator.bf' annotator.bf &&
         hyphy annotator.bf
-            input.nhx '$root' input.$compressed_msa.extension '$label' labeled_tree.
+            input.nhx '$root' input.$compressed_msa.extension '$label' labeled_tree_
         @ERRORS@
         ]]></command>
     <inputs>
@@ -20,9 +20,10 @@
         <param name="label" type="text" optional="false" value="Tree" label="Label for tree" />
     </inputs>
     <outputs>
-        <data name="labeled_tree_int" format="nhx" from_work_dir="labeled_tree.int.nwk" label="Labeled tree (int)" />
-        <data name="labeled_tree_clade" format="nhx" from_work_dir="labeled_tree.clade.nwk" label="Labeled tree (clade)" />
-        <data name="labeled_tree_full" format="nhx" from_work_dir="labeled_tree.full.nwk" label="Labeled tree (full)" />
+        <data name="labeled_tree_int" format="nhx" from_work_dir="labeled_tree_int.nwk" label="${tool.name} on ${on_string} Labeled tree (int)" />
+        <data name="labeled_tree_clade" format="nhx" from_work_dir="labeled_tree_clade.nwk" label="${tool.name} on ${on_string} Labeled tree (clade)" />
+        <data name="labeled_tree_full" format="nhx" from_work_dir="labeled_tree_full.nwk" label="${tool.name} on ${on_string} Labeled tree (full)" />
+        <data name="labeled_tree_json" format="hyphy_results.json" from_work_dir="labeled_tree_labels.json" label="${tool.name} on ${on_string} Labels" />
     </outputs>
     <tests>
         <test>
@@ -34,6 +35,7 @@
             <output name="labeled_tree_int" file="annotate-out1-int.nhx" />
             <output name="labeled_tree_full" file="annotate-out1-full.nhx" />
             <output name="labeled_tree_clade" file="annotate-out1-clade.nhx" />
+            <output name="labeled_tree_json" file="annotate-out1.json" />
         </test>
     </tests>
     <help><![CDATA[

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotate-out1.json	Wed Jun 09 17:25:00 2021 +0000
@@ -0,0 +1,10 @@
+{
+ "REFERENCE":"Annotated",
+ "epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021":"Annotated",
+ "epi_isl_1041406/hCoV-19/USA/NY-PRL-2021_02_08_05H12/2021":"Annotated",
+ "gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC63_2020_Segment_null_3":"Annotated",
+ "gb_MW467454_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_46_2020_Segment_null_1":"Annotated",
+ "gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1":"Annotated",
+ "gb_MW525081_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_0000025_G03_2021_Segment_null_1":"Annotated",
+ "gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_null_4":"Annotated"
+}
\ No newline at end of file