Mercurial > repos > dfornika > data_manager_build_kma_index

changeset 7:83d7739cca27 draft

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kma_index/ commit 11c754405bb15ea8734cd233cd1ddcc80b36faac-dirty
author dfornika
date Thu, 03 Oct 2019 15:31:35 -0400
parents 0fcad3adec23
children c44b52119169
files data_manager/kma_build_index.py data_manager/kma_build_index.xml
diffstat 2 files changed, 5 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/kma_build_index.py	Thu Oct 03 15:04:30 2019 -0400
+++ b/data_manager/kma_build_index.py	Thu Oct 03 15:31:35 2019 -0400
@@ -24,7 +24,7 @@
         '-ML', str(kma_index_args["ML"]),
         '-ht', str(kma_index_args["ht"]),
         '-hq', str(kma_index_args["hq"]),
-        '-o', os.path.join(UUID, index),
+        '-o', os.path.join(UUID, "index"),
         '-i', " ".join(kma_index_args["fasta"]),
     ]
 
@@ -36,7 +36,7 @@
                 {
                     "value": UUID,
                     "name": index_name,
-                    "path": UUID,
+                    "path": os.path.join(UUID, "index"),
                 }
             ]
         }
@@ -89,7 +89,7 @@
     parser.add_argument('--ML', dest='ML', type=int, default=16, help='')
     parser.add_argument('--ht', dest='ht', type=float, default=1.0, help='')
     parser.add_argument('--hq', dest='hq', type=float, default=1.0, help='')
-    parser.add_argument('--name', dest='index_name',help='')
+    parser.add_argument('--name', dest='index_name', help='')
     parser.add_argument('fasta', nargs='+', help='fasta file(s) to index')
     args = parser.parse_args()
     main(args)
--- a/data_manager/kma_build_index.xml	Thu Oct 03 15:04:30 2019 -0400
+++ b/data_manager/kma_build_index.xml	Thu Oct 03 15:31:35 2019 -0400
@@ -15,6 +15,7 @@
 	  --ML ${ML}
 	  --ht ${ht}
 	  --hq ${hq}
+          --name ${name}
 	  ${fasta}
     ]]>
     </command>
@@ -25,6 +26,7 @@
         <param name="ML" type="integer" value="16" label="Minimum length of templates" />
         <param name="ht" type="float" value="1.0" min="0.0" max="1.0" label="Homology template" />
         <param name="hq" type="float" value="1.0" min="0.0" max="1.0" label="Homology query" />
+	<param name="name" type="string" label="Name for index" />
 	<param name="fasta" type="data" format="fasta" label="Sequence to index (fasta)" />
     </inputs>
     <outputs>