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changeset 0:20ad934c5536 draft

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
author dfornika
date Fri, 05 Apr 2019 13:45:27 -0400
parents
children 892c6690a1e8
files augur_parse.xml macros.xml test-data/test_00_metadata.output.tsv test-data/test_00_sequences.input.fasta test-data/test_00_sequences.output.fasta
diffstat 5 files changed, 76 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/augur_parse.xml	Fri Apr 05 13:45:27 2019 -0400
@@ -0,0 +1,52 @@
+<tool id="augur_parse" name="augur parse" version="@TOOL_VERSION@+galaxy0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">augur</requirement>
+    </requirements>
+    <version_command>augur --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        augur parse
+          --sequences '$sequences'
+          --fields $fields
+          --separator '$separator'
+          --output-sequences '$output_sequences'
+          --output-metadata '$output_metadata'
+    ]]></command>
+    <inputs>
+        <param name="sequences" type="data" format="fasta" label="Sequences"/>
+        <param name="fields" type="text" label="Fields in fasta header"/>
+	<param name="separator" type="text" value="|" label="Separator in fasta header"/>
+    </inputs>
+    <outputs>
+      <data name="output_sequences" format="fasta" />
+      <data name="output_metadata" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+          <param name="sequences" value="test_00_sequences.input.fasta" />
+	  <param name="fields" value="strain country year" />
+	  <output name="output_sequences" file="test_00_sequences.output.fasta" />
+	  <output name="output_metadata" file="test_00_metadata.output.fasta" />
+        </test>
+    </tests>
+    <help><![CDATA[
+Parse delimited fields from FASTA sequence names into a TSV and FASTA file.
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+	  @article{hadfield2018nextstrain,
+	    title={Nextstrain: real-time tracking of pathogen evolution},
+	    author={Hadfield, James and Megill, Colin and Bell, Sidney M and Huddleston, John and Potter, Barney and Callender, Charlton and Sagulenko, Pavel and Bedford, Trevor and Neher, Richard A},
+	    journal={Bioinformatics},
+	    volume={34},
+	    number={23},
+	    pages={4121--4123},
+	    year={2018},
+	    publisher={Oxford University Press}
+	  }
+	</citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Apr 05 13:45:27 2019 -0400
@@ -0,0 +1,3 @@
+<macros>
+    <token name="@TOOL_VERSION@">3.1.5</token>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_00_metadata.output.tsv	Fri Apr 05 13:45:27 2019 -0400
@@ -0,0 +1,5 @@
+strain	country	year
+strain-01	France	2012
+strain-02	Germany	2008
+strain-03	China	2016
+strain-04	Canada	2008
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_00_sequences.input.fasta	Fri Apr 05 13:45:27 2019 -0400
@@ -0,0 +1,8 @@
+>strain-01|France|2012
+ATTCGATC
+>strain-02|Germany|2008
+TAGACGGA
+>strain-03|China|2016
+AGGATTAC
+>strain-04|Canada|2008
+TAATTAGG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_00_sequences.output.fasta	Fri Apr 05 13:45:27 2019 -0400
@@ -0,0 +1,8 @@
+>strain-01
+ATTCGATC
+>strain-02
+TAGACGGA
+>strain-03
+AGGATTAC
+>strain-04
+TAATTAGG