Mercurial > repos > dfornika > cgview_reformat_blastn_output

diff reformat_blastn_output.xml @ 0:90ac002b2098 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
author dfornika
date Thu, 12 Dec 2019 19:44:51 +0000
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reformat_blastn_output.xml	Thu Dec 12 19:44:51 2019 +0000
@@ -0,0 +1,36 @@
+<tool id="cgview_reformat_blastn_output" name="reformat blastn output for cgview XML builder" version="1.0+galaxy0">
+    <description>Reformat blastn output for cgview_xml_builder</description>
+    <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' |
+	  sed '1i#PROGRAM=blastn'
+          > '${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>