Mercurial > repos > dfornika > ncbi_acc_download

changeset 3:9f5ae4f003c0 draft

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"planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/ncbi_acc_download commit 32f001f49f6e6fb64422a46907bd7293988d0832-dirty"
author dfornika
date Tue, 05 Nov 2019 15:55:50 -0500
parents ed222c86e08d
children a7492cf1549b
files ncbi_acc_download.xml
diffstat 1 files changed, 12 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/ncbi_acc_download.xml	Tue Nov 05 15:12:46 2019 -0500
+++ b/ncbi_acc_download.xml	Tue Nov 05 15:55:50 2019 -0500
@@ -11,8 +11,8 @@
         ncbi-acc-download
             --molecule '${molecule}'
             --format '${format}'
-            '${accession}'
-        done; < '${accessions}'
+            \${accession};
+        done < '${accessions}'
     ]]></command>
     <inputs>
         <param name="molecule" type="select" label="Molecule Type">
@@ -28,8 +28,13 @@
         <param name="accessions" type="data" format="tabular" />
     </inputs>
     <outputs>
-        <collection name="output" type="list" format="fasta,genbank,feattable,gff3" label="Output files">
-            <discover_datasets pattern="__name__" format="fasta,genbank,feattable,gff3" directory="." />
+        <collection name="output_fasta" type="list" label="Output files">
+	    <filter>options['fasta']</filter>
+            <discover_datasets pattern="__name__" directory="." format="fasta"/>
+        </collection>
+        <collection name="output_genbank" type="list" label="Output files">
+	    <filter>options['genbank']</filter>
+            <discover_datasets pattern="__name__" directory="." format="genbank"/>
         </collection>
     </outputs>
     <tests>
@@ -37,9 +42,9 @@
             <param name="molecule" value="nucleotide"/>
 	    <param name="format" value="fasta"/>
             <param name="accessions" value="accessions_1.tsv"/>
-            <output_collection name="output" type="list">
-              <element file="CP011064.fa" ftype="fasta" />
-	      <element file="CP021680.fa" ftype="fasta" />
+            <output_collection name="output_fasta" type="list">
+              <element name="CP011064.fa" file="CP011064.fa" ftype="fasta" />
+	      <element name="CP021680.fa" file="CP021680.fa" ftype="fasta" />
             </output_collection>
         </test>
     </tests>