# HG changeset patch
# User dfornika
# Date 1562641828 14400
# Node ID 5542de6121ac4ef82fd3a33d0465450b8a1b3091
# Parent  4d65b79b638dce80e8d9daa0855d7a28e8ffc574
planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/cgview commit 423cf96266f6ac433052ff72edb1397502313010-dirty

diff -r 4d65b79b638d -r 5542de6121ac cgview.xml
--- a/cgview.xml	Mon Jul 08 22:34:01 2019 -0400
+++ b/cgview.xml	Mon Jul 08 23:10:28 2019 -0400
@@ -5,9 +5,8 @@
     </requirements>   
     <command detect_errors="exit_code">
         <![CDATA[
-          ln -s '${input}' input.xml &&
           cgview
-           -i 'input.xml'
+           -i '${input}'
            -o '${output}'
         ]]>  
     </command>
diff -r 4d65b79b638d -r 5542de6121ac reformat_blastn_output.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reformat_blastn_output.xml	Mon Jul 08 23:10:28 2019 -0400
@@ -0,0 +1,37 @@
+<tool id="reformat_blastn_output" name="reformat blastn output" version="1.0+galaxy0">
+    <description>Reformat blastn output for cgview_xml_builder</description>
+    <requirements>
+    </requirements>   
+    <command detect_errors="exit_code">
+        <![CDATA[
+          awk -F'\t' 'BEGIN {OFS = FS} $2 = $2 FS "match"' '${input}' |
+          sed '1iquery_id\tmatch_id\tmatch_description\t%_identity\talignment_length\tmismatches\tgap_openings\tq_start\tq_end\ts_start\ts_end\tevalue\tbit_score' '${input}'
+          > '${output}'
+        ]]>  
+    </command>
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Input" help=""/>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular"/> 
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @article{
+              stothard2004circular,
+              title={Circular genome visualization and exploration using CGView},
+              author={Stothard, Paul and Wishart, David S},
+              journal={Bioinformatics},
+              volume={21},
+              number={4},
+              pages={537--539},
+              year={2004},
+              publisher={Oxford University Press}
+            }
+    </citation>
+  </citations>
+</tool>
diff -r 4d65b79b638d -r 5542de6121ac test-data/blastn_output.save.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blastn_output.save.tsv	Mon Jul 08 23:10:28 2019 -0400
@@ -0,0 +1,8 @@
+LR595890.1_segment	LR595890.1	100.00	9180	0	0	1	9180	23821	33000	0.0	16556
+LR595890.1_segment	LR595890.1	75.25	198	49	0	7921	8118	31621	31818	8e-33	136
+LR595890.1_segment	LR595890.1	75.25	198	49	0	7801	7998	31741	31938	8e-33	136
+LR595890.1_segment	LR595890.1	89.61	77	6	1	1312	1388	56503	56577	6e-22	100
+LR595890.1_segment	LR595890.1	74.17	120	31	0	7915	8034	30388	30507	7e-15	77.0
+LR595890.1_segment	LR595890.1	74.17	120	31	0	6568	6687	31735	31854	7e-15	77.0
+LR595890.1_segment	LR595890.1	84.29	70	7	2	1326	1393	56585	56518	3e-13	71.6
+LR595890.1_segment	LR595890.1	79.76	84	8	5	1312	1389	89049	89129	5e-10	60.8
diff -r 4d65b79b638d -r 5542de6121ac test-data/blastn_output.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blastn_output.tsv	Mon Jul 08 23:10:28 2019 -0400
@@ -0,0 +1,8 @@
+LR595890.1_segment	LR595890.1	100.00	9180	0	0	1	9180	23821	33000	0.0	16556
+LR595890.1_segment	LR595890.1	75.25	198	49	0	7921	8118	31621	31818	8e-33	136
+LR595890.1_segment	LR595890.1	75.25	198	49	0	7801	7998	31741	31938	8e-33	136
+LR595890.1_segment	LR595890.1	89.61	77	6	1	1312	1388	56503	56577	6e-22	100
+LR595890.1_segment	LR595890.1	74.17	120	31	0	7915	8034	30388	30507	7e-15	77.0
+LR595890.1_segment	LR595890.1	74.17	120	31	0	6568	6687	31735	31854	7e-15	77.0
+LR595890.1_segment	LR595890.1	84.29	70	7	2	1326	1393	56585	56518	3e-13	71.6
+LR595890.1_segment	LR595890.1	79.76	84	8	5	1312	1389	89049	89129	5e-10	60.8