# HG changeset patch
# User iuc
# Date 1594276750 14400
# Node ID ca9e70c0fef81f80a49274ce31ef7bf1eeeace35
# Parent  2af5541124184c1f0ee8f1d17aef0f89c19ac656
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit c2985b5c91a932e175cbfaf9b54a76e23beff9e9"

diff -r 2af554112418 -r ca9e70c0fef8 NanocomporeDB_process.py
--- a/NanocomporeDB_process.py	Wed Jun 17 13:28:53 2020 -0400
+++ b/NanocomporeDB_process.py	Thu Jul 09 02:39:10 2020 -0400
@@ -40,7 +40,7 @@
                         help='path to the annotations')
     parser.add_argument('--bedgraph', action="store_true",
                         help='write output in BEDGRAPH format instead of BED')
-    parser.add_argument('--pvalue-threshold', default=1.0,
+    parser.add_argument('--pvalue-threshold', type=float, default=1.0,
                         help='Maximum reported p-value.')
     parser.add_argument('--out-dir', default="./", type=is_valid_directory,
                         help='path the plotting output directory.')
@@ -52,9 +52,15 @@
     print(db)
     print("DB read ids:", db.ref_id_list)
 
+    if args.bedgraph:
+        file_ext = 'bedgraph'
+    else:
+        file_ext = 'bed'
+
     if args.annotation_bed:
         for pt in args.pvalue_types.split(','):
-            print("bedgraph output for p-value type:", pt)
-            db.save_to_bed(output_fn='{}/{}.bedgraph'.format(args.out_dir, pt),
+            out_path = '{}/{}.{}'.format(args.out_dir, pt, file_ext)
+            print("%s output for p-value type:" % out_path, pt)
+            db.save_to_bed(output_fn=out_path,
                            pvalue_field=pt, pvalue_thr=args.pvalue_threshold,
                            bedgraph=args.bedgraph)
diff -r 2af554112418 -r ca9e70c0fef8 nanocompore_db.xml
--- a/nanocompore_db.xml	Wed Jun 17 13:28:53 2020 -0400
+++ b/nanocompore_db.xml	Thu Jul 09 02:39:10 2020 -0400
@@ -1,61 +1,59 @@
-<tool id="nanocompore_db" name="NanoComporeDB" version="@TOOL_VERSION@+galaxy1">
+<tool id="nanocompore_db" name="NanoComporeDB" version="@TOOL_VERSION@+galaxy2">
     <description>Process SampComp results database</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
-mkdir results && 
-tar -xf $db --strip-components 1 -C results/ && 
+mkdir -p results plots && 
+tar -xf '$db' --strip-components 1 -C results/ &&
 python '$__tool_directory__/NanocomporeDB_process.py'
 --db-path 'results/out_SampComp.db'
 --ref-fasta '$reference'
 --annotation-bed '$annotation'
+--pvalue-types '$pvalue_types'
+--pvalue-threshold $pvalue_threshold
+--out-dir ./plots/
 $bedgraph
+
     ]]></command>
     <inputs>
         <param name="reference" type="data" format="fasta" label="The reference genome used for read alignment."/>
         <param name="annotation" format="bed" type="data" label="BED file containing the annotation of the transcriptome used as reference when mapping"/>
         <param name="db" type="data" format="tar" label="SampComp Database" />
-        <param argument="--bedgraph" type="boolean" truevalue="--bedgraph" falsevalue="" label="Write output in BEDGRAPH format instead of BED"/>
+        <param argument="--pvalue-types" type="text" value="GMM_logit_pvalue,KS_dwell_pvalue,KS_intensity_pvalue" label="pvalue field names" help="Comma-separated values.">
+            <validator type="regex" message="No valid pvalue field name list.">^(\w+(,\w+)*)?$</validator>
+        </param>
+        <param argument="pvalue-threshold" type="float" value="1.0" min="0.0" label="Maximum reported p-value"/>
+        <param argument="--bedgraph" type="boolean" truevalue="--bedgraph" falsevalue="" label="Write output in BedGraph format instead of BED"/>
     </inputs>
     <outputs>
-        <data name="GMM_logit" format="bed" from_work_dir="GMM_logit_pvalue.bedgraph" label="${tool.name} on ${on_string}: GMM_logit">
-            <change_format>
-                <when input="bedgraph" value="true" format="bedgraph"/>
-            </change_format>
-        </data>
-
-        <data name="KS_dwell" format="bed" from_work_dir="KS_dwell_pvalue.bedgraph" label="${tool.name} on ${on_string}: KS_dwell">
-            <change_format>
-                <when input="bedgraph" value="true" format="bedgraph"/>
-            </change_format>
-        </data>
-
-        <data name="KS_intensity" format="bed" from_work_dir="KS_intensity_pvalue.bedgraph" label="${tool.name} on ${on_string}: KS_intensity">
-            <change_format>
-                <when input="bedgraph" value="true" format="bedgraph"/>
-            </change_format>
-        </data>
+        <collection name="pvalue_output" type="list">
+            <discover_datasets pattern="__name_and_ext__" directory="plots" />
+        </collection>
     </outputs>
     <tests>
         <test>
             <param name="reference" value="reference.fa"/>
             <param name="annotation" value="annot.bed"/>
-            <param name="db" value="DB.tar"/>
-            <output name="GMM_logit" file="GMM_logit_pvalue.bed"/>
-            <output name="KS_dwell" file="KS_dwell_pvalue.bed"/>
-            <output name="KS_intensity" file="KS_intensity_pvalue.bed"/>
+            <param name="db" value="DB.tar" ftype="tar" />
+            <output_collection name="pvalue_output" type="list" count="3">
+                <element name="GMM_logit_pvalue" file="GMM_logit_pvalue.bed" ftype="bed"/>
+                <element name="KS_dwell_pvalue" file="KS_dwell_pvalue.bed" ftype="bed"/>
+                <element name="KS_intensity_pvalue" file="KS_intensity_pvalue.bed" ftype="bed"/>
+            </output_collection>
         </test>
         <test>
             <param name="reference" value="reference.fa"/>
             <param name="annotation" value="annot.bed"/>
-            <param name="db" value="DB.tar"/>
-            <param name="bedgraph" value="true"/>   
-            <output name="GMM_logit" file="GMM_logit_pvalue.bedgraph"/>
-            <output name="KS_dwell" file="KS_dwell_pvalue.bedgraph"/>
-            <output name="KS_intensity" file="KS_intensity_pvalue.bedgraph"/>
-        </test>        
+            <param name="db" value="DB.tar" ftype="tar" />
+            <param name="bedgraph" value="true"/>
+            <param name="pvalue_types" value="GMM_logit_pvalue,KS_dwell_pvalue"/>
+            <output_collection name="pvalue_output" type="list" count="2">
+                <element name="GMM_logit_pvalue" file="GMM_logit_pvalue.bedgraph" ftype="bedgraph"/>
+                <element name="KS_dwell_pvalue" file="KS_dwell_pvalue.bedgraph" ftype="bedgraph"/>
+            </output_collection>
+        </test>
     </tests>
     <help><![CDATA[
 Produces interval bed and bedgraph outputs from NanoCompore SampComp results as input using NaonComporeDB API. 
diff -r 2af554112418 -r ca9e70c0fef8 test-data/KS_intensity_pvalue.bedgraph
--- a/test-data/KS_intensity_pvalue.bedgraph	Wed Jun 17 13:28:53 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-chr	22104	22105	0.5940708247528699
-chr	22105	22106	0.5940708247528699