diff nanocompore_db.xml @ 0:b6eeea872fd2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nanocompore_db.xml	Mon Jun 08 14:41:41 2020 -0400
@@ -0,0 +1,43 @@
+<tool id="nanocompore_db" name="NanoComporeDB" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
+    <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 $db --strip-components 1 -C results/ && 
+ python '$__tool_directory__/NanocomporeDB_process.py'
+ --db-path 'results/out_SampComp.db'
+ --ref-fasta '$reference'
+--annotation-bed '$annotation'
+    ]]></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" />
+    </inputs>
+    <outputs>
+        <data name="GMM_logit" format="bedgraph" from_work_dir="GMM_logit_pvalue.bedgraph" />
+        <data name="KS_dwell" format="bedgraph" from_work_dir="KS_dwell_pvalue.bedgraph" />
+        <data name="KS_intensity" format="bedgraph" from_work_dir="KS_intensity_pvalue.bedgraph" />
+    </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.bedgraph"/>
+            <output name="KS_dwell" file="KS_dwell_pvalue.bedgraph"/>
+            <output name="KS_intensity" file="KS_intensity_pvalue.bedgraph"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Produces interval bed and bedgraph outputs from NanoCompore SampComp results as input using NaonComporeDB API. 
+
+**References**
+
+@REFERENCES@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>