changeset 1:dbcb26e2a1db draft

Updated tool version

--- a/genap2_kb_python/kb_count.xml	Fri Apr 16 18:18:21 2021 +0000
+++ b/genap2_kb_python/kb_count.xml	Mon Apr 19 18:33:14 2021 +0000
@@ -1,11 +1,8 @@
-<tool id="kb_python" name="kb_python" version="@VERSION@+galaxy0">
+<tool id="kb_python" name="kb_python" version="@VERSION@+galaxy1">
 	<description>performs gene and feature quantification on single-cell sequencing data.</description>
 	<macros>
         	<import>macros.xml</import>
     </macros>
-	<requirements>
-		<requirement type="package" version="0.25.1">kb-python</requirement>
-	</requirements>
 	<stdio>
 		<exit_code range="1:" />
 		<exit_code range=":-1" />
@@ -55,9 +52,8 @@
         #if $whitelist:
             --whitelist '${optional.whitelist}'
         #end if
-		#if $optional.multimap:
-			--mm
-		#end if
+		${optional.multimap}
+		${optional.report}
 		--workflow $workflow
 		#if $extra_dtype != "none":
 			$extra_dtype
@@ -100,7 +96,8 @@
 		<section name="optional" title="Optional commands" expanded="false">
 			<param name="whitelist" type="data" format="tsv,tabular" optional="true" label="Whitelist file" help="Whitelisted barcodes to correct to. If not provided and bustools supports the technology, a pre-packaged whitelist is used. If not, the bustools
 			whitelist command is used."/>
-			<param name="multimap" type="boolean" optional="true" label="Include multi pseudoaligned reads?" help="Do you want to include reads that pseudoalign to multiple genes?"/>
+			<param name="multimap" type="boolean" optional="true" truevalue="--mm" falsevalue="" label="Include multi pseudoaligned reads?" help="Do you want to include reads that pseudoalign to multiple genes?"/>
+			<param name="report" type="boolean" optional="true"  truevalue="--report" falsevalue=""  label="Create an html report?"  help="If true, will create an html report with mapping statistics and cell" checked="false"/>
 		</section>
 	</inputs>
     <outputs>
@@ -110,12 +107,18 @@
 		<data name="inspect" label="inspect_report" format="json" from_work_dir="kb_outs/inspect.json"/>
 		<data name="runinfo" label="run info" format="json" from_work_dir="kb_outs/run_info.json"/>
 		<data name="kbinfo" label="kb info" format="json" from_work_dir="kb_outs/kb_info.json"/>
-		<data name="kb_ref" label="kb_ref.idx" format="kallisto.idx" from_work_dir="index/kb_ref.idx"/>
-		<data name="t2g" label="t2g.txt" format="txt" from_work_dir="index/t2g.txt"/>
+		<data name="kb_ref" label="kb_ref.idx" format="kallisto.idx" from_work_dir="index/kb_ref.idx">
+			<filter>refTranscriptSource['TranscriptSource'] == "built"</filter>
+		</data>
+		<data name="t2g" label="t2g.txt" format="txt" from_work_dir="index/t2g.txt">
+			<filter>refTranscriptSource['TranscriptSource'] == "built"</filter>
+		</data>
 		<data name="cdna_t2c" label="-c1 cdna_t2c.txt" format="txt" from_work_dir="index/cdna_t2c.txt">
+			<filter>refTranscriptSource['TranscriptSource'] == "built"</filter>
 			<filter>workflow == "lamanno"</filter>
 		</data>
 		<data name="intron_t2c" label="-c2 intron_t2c.txt" format="txt" from_work_dir="index/intron_t2c.txt">
+			<filter>refTranscriptSource['TranscriptSource'] == "built"</filter>
 			<filter>workflow == "lamanno"</filter>
 		</data>	
 		<data name="adata" label="adata.h5ad" format="h5ad" from_work_dir="kb_outs/counts_unfiltered/adata.h5ad">
@@ -124,6 +127,9 @@
 		<data name="adata" label="adata.loom" format="loom" from_work_dir="kb_outs/counts_unfiltered/adata.loom">
 			<filter>extra_dtype == "--loom"</filter>
 		</data>
+		<data name="report" label="report.html" format="html" from_work_dir="kb_outs/report.html">
+			<filter>optional["report"]</filter>
+		</data>
 	</outputs>
 	<tests>
 		<expand macro="tests"/>

--- a/genap2_kb_python/macros.xml	Fri Apr 16 18:18:21 2021 +0000
+++ b/genap2_kb_python/macros.xml	Mon Apr 19 18:33:14 2021 +0000
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@VERSION@">0.1.0</token>
-    <token name="@IDX_VERSION@">q1</token>
+    <token name="@VERSION@">0.26.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@VERSION@">kb-python</requirement>
+			<requirement type="package" version="@VERSION@"	>kb-python</requirement>
+			<requirement type="package" version="1.0.0">jupyter</requirement>
         </requirements>
     </xml>
     <xml name="citations">
@@ -38,7 +38,7 @@
         </conditional>
     </xml>
     <xml name="tests">
-    		<!-- Test1: Test with pre-built index provided by user -->
+    		<!-- Test1: Test with pre-built index provided by user and generating report -->
 		<test>
 			<conditional name="refTranscriptSource">
                 <param name="TranscriptSource" value="history"/>