Mercurial > repos > dfornika > ncbi_acc_download

changeset 6:4872034b5ee6 draft

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"planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/ncbi_acc_download commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
author dfornika
date Tue, 05 Nov 2019 16:08:52 -0500
parents de54e4604a4a
children 12b7eaf50f00
files ncbi_acc_download.xml
diffstat 1 files changed, 4 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/ncbi_acc_download.xml	Tue Nov 05 16:05:20 2019 -0500
+++ b/ncbi_acc_download.xml	Tue Nov 05 16:08:52 2019 -0500
@@ -7,6 +7,8 @@
       <requirement type="package" version="@TOOL_VERSION@">ncbi-acc-download</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+        mkdir outdir &&
+        cd outdir &&
         while read accession; do
         ncbi-acc-download
             --molecule '${molecule}'
@@ -30,11 +32,11 @@
     <outputs>
         <collection name="output_fasta" type="list" label="FASTA Output">
 	    <filter>options['fasta']</filter>
-            <discover_datasets pattern="__name__and__ext__" directory="." format="fasta"/>
+            <discover_datasets pattern="__name__" directory="outdir" format="fasta"/>
         </collection>
         <collection name="output_genbank" type="list" label="GenBank Output">
 	    <filter>options['genbank']</filter>
-            <discover_datasets pattern="__name__and__ext__" directory="." format="genbank"/>
+            <discover_datasets pattern="__name__" directory="outdir" format="genbank"/>
         </collection>
     </outputs>
     <tests>