diff arriba_download_reference.xml @ 2:7420753b0671 draft

"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"

--- a/arriba_download_reference.xml	Fri Oct 08 11:16:21 2021 +0000
+++ b/arriba_download_reference.xml	Fri Oct 08 19:23:48 2021 +0000
@@ -1,17 +1,18 @@
-<tool id="arriba_download_reference" name="Arriba Download Reference" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
-    <description></description>
+<tool id="arriba_download_reference" name="Arriba Reference" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
+    <description>Download to history</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
-    echo $arriba_reference_name > '$arriba_reference'
-    mkdir -p '$arriba_reference.files_path' &&
-    cd '$arriba_reference.files_path' &&
-    BASE_DIR=$(dirname $(dirname `which arriba`)) &&
-    REF_SCRIPT=`find $BASE_DIR -name 'download_references.sh'` &&
-    $REF_SCRIPT '$arriba_reference_name'
+    echo $arriba_reference_name > '$star_index' &&
+    BASE_DIR=\$(dirname \$(dirname `which arriba`)) &&
+    REF_SCRIPT=`find \$BASE_DIR -name 'download_references.sh'` &&
+    \$REF_SCRIPT '$arriba_reference_name' &&
+    cp *.fa* > '$genome_fasta' &&
+    cp *.gtf* > '$genome_gtf' &&
+    mv STAR*/* '$star_index.extra_files_path'
     ]]></command>
     <inputs>
         <param name="arriba_reference_name" type="select" label="Select reference">
@@ -56,7 +57,9 @@
         </param>
     </inputs>
     <outputs>
-        <data name="arriba_reference" format="txt" label="$arriba_reference_name"/>
+        <data name="genome_fasta" format="fasta" label="${tool.name} ${arriba_reference_name} fasta"/>
+        <data name="genome_gtf" format="gtf" label="${tool.name} ${arriba_reference_name} GTF"/>
+        <data name="star_index" format="txt" label="${tool.name} ${arriba_reference_name} STAR index"/>
     </outputs>
     <help><![CDATA[
 ** Arriba **