Mercurial > repos > sanbi-uwc > assess_poliovirus_alignment

changeset 12:ee98dcd9aad4 draft

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planemo upload for repository https://github.com/pvanheus/polio_report commit aa90f911e6269aba792c9814c98a659e631400b2-dirty
author sanbi-uwc
date Tue, 27 Sep 2022 18:56:28 +0000
parents fff48fa8a22b
children bf0bebcb6bb1
files assess_alignment.py assess_poliovirus_alignment.xml
diffstat 2 files changed, 3 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/assess_alignment.py	Tue Sep 27 09:18:56 2022 +0000
+++ b/assess_alignment.py	Tue Sep 27 18:56:28 2022 +0000
@@ -165,7 +165,6 @@
         "--dataset_names", type=comma_split, help="Comma separated names for datasets"
     )
     parser.add_argument("--datasets", nargs="+")
-    parser.add_argument("--consensi", nargs="+")
     args = parser.parse_args()
 
     offsets = {
--- a/assess_poliovirus_alignment.xml	Tue Sep 27 09:18:56 2022 +0000
+++ b/assess_poliovirus_alignment.xml	Tue Sep 27 18:56:28 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="assess_poliovirus_alignment" name="Assess poliovirus alignment" version="0.10.0+galaxy0" profile="21.05">
+<tool id="assess_poliovirus_alignment" name="Assess poliovirus alignment" version="0.11.0+galaxy0" profile="21.05">
     <requirements>
         <requirement type="package" version="3.9">python</requirement>
     </requirements>
@@ -13,16 +13,11 @@
         #for $dataset in $tracy_results
              '$dataset' 
         #end for
-            --consensi
-        #for $consensus in $tracy_consensus_results
-            '$consensus'
-        #end for
 
     ]]></command>
     <inputs>
         <!-- input is list of reports for poliovirus sabin 1, 2 and 3 -->
         <param name="tracy_results" format="json" type="data_collection" collection_type="list" label="Tracy JSON reports" help="Input is a list of tracy assemble JSON reports for assembly guided by there reference sequences for poliovirus sabin 1, 2 and 3" />
-        <param name="tracy_consensus_results" format="FASTA" type="data_collection" collection_type="list" label="Tracy Consensus sequences" help="Input is a list of tracy assemble consensus sequences for assembly guided by there reference sequences for poliovirus sabin 1, 2 and 3" />
     </inputs>
     <outputs>
         <data name="output1" format="json" label="Poliovirus alignment assessment on ${on_string}" />
@@ -53,7 +48,8 @@
         </test>
     </tests>
     <help><![CDATA[
-        Given the output of the poliovirus pipeline, make a JSON summarising the comparison against the three poliovirus Sabin reference genomes.
+        Given the output of the poliovirus pipeline, make a JSON summarising the comparison against the three poliovirus Sabin
+        reference genomes and output the best-matching consensus sequence.
     ]]></help>
     <citations>
         <citation type="bibtex"><![CDATA[