# HG changeset patch
# User dfornika
# Date 1554744428 14400
# Node ID 892c6690a1e8343c82f851c781aa6ac5ecfca166
# Parent  20ad934c553615976e9ae929c1ac18bdd847d877
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty

diff -r 20ad934c5536 -r 892c6690a1e8 augur_align.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/augur_align.xml	Mon Apr 08 13:27:08 2019 -0400
@@ -0,0 +1,47 @@
+<tool id="augur_align" name="augur align" 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 align
+          --nthreads \${GALAXY_SLOTS:-1}
+          --sequences '$sequences'
+          --reference-sequence '$reference_sequence'
+          $fill_gaps
+          --output 'output'
+    ]]></command>
+    <inputs>
+        <param name="sequences" type="data" format="fasta" label="Sequences"/>
+        <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence"/>
+        <param name="fill_gaps" type="boolean" checked="false" truevalue="--fill-gaps" falsevalue="" label="Fill Gaps"/>
+    </inputs>
+    <outputs>
+        <data name="pre_aligner_output" format="fasta" >
+            <discover_datasets pattern="output.pre_aligner.fasta" format="fasta" visible="true" />
+        </data>
+        <data name="post_aligner_output" format="fasta" >
+            <discover_datasets pattern="output.post_aligner.fasta" format="fasta" visible="true" />
+        </data>
+        <data name="log" format="text" >
+            <discover_datasets pattern="*.log" format="text" visible="true" />
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="sequences" value="augur_align_test_0_sequences.input.fasta" />
+            <param name="reference_sequence" value="augur_align_test_0_reference_sequence.input.fasta" />
+	    <param name="fill_gaps" value="false" />
+            <output name="pre_aligner_output" file="augur_align_test_0_pre_aligner_output.output.fasta" />
+            <output name="post_aligner_output" file="augur_align_test_0_post_aligner_output.output.fasta" />
+        </test>
+    </tests>
+    <help><![CDATA[
+Align multiple sequences from FASTA or VCF.
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff -r 20ad934c5536 -r 892c6690a1e8 augur_filter.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/augur_filter.xml	Mon Apr 08 13:27:08 2019 -0400
@@ -0,0 +1,37 @@
+<tool id="augur_filter" name="augur filter" 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 filter
+          --sequences '$sequences'
+          --metadata '$metadata'
+          --exclude '$exclude'
+          --output '$output'
+    ]]></command>
+    <inputs>
+        <param name="sequences" type="data" format="fasta" label="Sequences"/>
+        <param name="metadata" type="data" format="tabular" label="Metadata"/>
+        <param name="exclude" type="data" format="tabular" label="Excluded Strains"/>
+    </inputs>
+    <outputs>
+      <data name="output" format="fasta" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="sequences" value="augur_filter_test_0_sequences.input.fasta" />
+            <param name="metadata" value="augur_filter_test_0_metadata.input.csv" />
+            <param name="exclude" value="augur_filter_test_0_excluded_strains.input.csv" />
+            <output name="output" file="augur_filter_test_0_output.output.fasta" />
+        </test>
+    </tests>
+    <help><![CDATA[
+Filter and subsample a sequence set.
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff -r 20ad934c5536 -r 892c6690a1e8 augur_parse.xml
--- a/augur_parse.xml	Fri Apr 05 13:45:27 2019 -0400
+++ b/augur_parse.xml	Mon Apr 08 13:27:08 2019 -0400
@@ -18,35 +18,30 @@
     <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"/>
+        <param name="separator" type="text" value="|" label="Separator in fasta header">
+            <sanitizer>
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+                <mapping initial="none">
+                </mapping>
+            </sanitizer>
+        </param>
     </inputs>
     <outputs>
-      <data name="output_sequences" format="fasta" />
-      <data name="output_metadata" format="tabular" />
+        <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" />
+            <param name="sequences" value="augur_parse_test_0_sequences.input.fasta" />
+            <param name="fields" value="strain country year" />
+            <output name="output_sequences" file="augur_parse_test_0_sequences.output.fasta" />
+            <output name="output_metadata" file="augur_parse_test_0_metadata.output.csv" />
         </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>
+    <expand macro="citations" />
 </tool>
diff -r 20ad934c5536 -r 892c6690a1e8 augur_tree.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/augur_tree.xml	Mon Apr 08 13:27:08 2019 -0400
@@ -0,0 +1,24 @@
+<tool id="augur_tree" name="augur tree" 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 tree
+    ]]></command>
+    <inputs>
+    </inputs>
+    <outputs>
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help><![CDATA[
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff -r 20ad934c5536 -r 892c6690a1e8 macros.xml
--- a/macros.xml	Fri Apr 05 13:45:27 2019 -0400
+++ b/macros.xml	Mon Apr 08 13:27:08 2019 -0400
@@ -1,3 +1,19 @@
 <macros>
     <token name="@TOOL_VERSION@">3.1.5</token>
+    <xml name="citations">
+        <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>
+    </xml>
 </macros>
diff -r 20ad934c5536 -r 892c6690a1e8 test-data/augur_align_test_0_output.output.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/augur_align_test_0_output.output.fasta	Mon Apr 08 13:27:08 2019 -0400
@@ -0,0 +1,10 @@
+>strain-01
+ATTCGATC
+>strain-02
+ATGCGATC
+>strain-03
+ATTCCATC
+>reference
+ATTGGATC
+>strain-04
+ATTCGTC-
diff -r 20ad934c5536 -r 892c6690a1e8 test-data/augur_align_test_0_post_aligner_output.output.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/augur_align_test_0_post_aligner_output.output.fasta	Mon Apr 08 13:27:08 2019 -0400
@@ -0,0 +1,10 @@
+>strain-01
+ATTCGATC
+>strain-02
+ATGCGATC
+>strain-03
+ATTCCATC
+>reference
+ATTGGATC
+>strain-04
+ATTCGTC-
diff -r 20ad934c5536 -r 892c6690a1e8 test-data/augur_align_test_0_pre_aligner_output.output.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/augur_align_test_0_pre_aligner_output.output.fasta	Mon Apr 08 13:27:08 2019 -0400
@@ -0,0 +1,10 @@
+>strain-01
+ATTCGATC
+>strain-02
+ATGCGATC
+>strain-03
+ATTCCATC
+>strain-04
+ATTCGTC
+>reference
+ATTGGATC
diff -r 20ad934c5536 -r 892c6690a1e8 test-data/augur_align_test_0_reference_sequence.input.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/augur_align_test_0_reference_sequence.input.fasta	Mon Apr 08 13:27:08 2019 -0400
@@ -0,0 +1,2 @@
+>reference
+ATTGGATC
diff -r 20ad934c5536 -r 892c6690a1e8 test-data/augur_align_test_0_sequences.input.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/augur_align_test_0_sequences.input.fasta	Mon Apr 08 13:27:08 2019 -0400
@@ -0,0 +1,8 @@
+>strain-01
+ATTCGATC
+>strain-02
+ATGCGATC
+>strain-03
+ATTCCATC
+>strain-04
+ATTCGTC
diff -r 20ad934c5536 -r 892c6690a1e8 test-data/augur_align_test_0_sequences.input.fasta.ref.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/augur_align_test_0_sequences.input.fasta.ref.fasta	Mon Apr 08 13:27:08 2019 -0400
@@ -0,0 +1,10 @@
+>strain-01
+ATTCGATC
+>strain-02
+ATGCGATC
+>strain-03
+ATTCCATC
+>strain-04
+ATTCGTC
+>reference
+ATTGGATC
diff -r 20ad934c5536 -r 892c6690a1e8 test-data/augur_filter_test_0_excluded_strains.input.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/augur_filter_test_0_excluded_strains.input.csv	Mon Apr 08 13:27:08 2019 -0400
@@ -0,0 +1,2 @@
+strain-02
+strain-03
diff -r 20ad934c5536 -r 892c6690a1e8 test-data/augur_filter_test_0_metadata.input.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/augur_filter_test_0_metadata.input.csv	Mon Apr 08 13:27:08 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
diff -r 20ad934c5536 -r 892c6690a1e8 test-data/augur_filter_test_0_output.output.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/augur_filter_test_0_output.output.fasta	Mon Apr 08 13:27:08 2019 -0400
@@ -0,0 +1,4 @@
+>strain-01
+ATTCGATC
+>strain-04
+ATTCGTC
diff -r 20ad934c5536 -r 892c6690a1e8 test-data/augur_filter_test_0_sequences.input.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/augur_filter_test_0_sequences.input.fasta	Mon Apr 08 13:27:08 2019 -0400
@@ -0,0 +1,8 @@
+>strain-01
+ATTCGATC
+>strain-02
+ATGCGATC
+>strain-03
+ATTCCATC
+>strain-04
+ATTCGTC
diff -r 20ad934c5536 -r 892c6690a1e8 test-data/augur_parse_test_0_metadata.output.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/augur_parse_test_0_metadata.output.csv	Mon Apr 08 13:27:08 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
diff -r 20ad934c5536 -r 892c6690a1e8 test-data/augur_parse_test_0_sequences.input.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/augur_parse_test_0_sequences.input.fasta	Mon Apr 08 13:27:08 2019 -0400
@@ -0,0 +1,8 @@
+>strain-01|France|2012
+ATTCGATC
+>strain-02|Germany|2008
+ATGCGATC
+>strain-03|China|2016
+ATTCCATC
+>strain-04|Canada|2008
+ATTCGTC
diff -r 20ad934c5536 -r 892c6690a1e8 test-data/augur_parse_test_0_sequences.output.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/augur_parse_test_0_sequences.output.fasta	Mon Apr 08 13:27:08 2019 -0400
@@ -0,0 +1,8 @@
+>strain-01
+ATTCGATC
+>strain-02
+ATGCGATC
+>strain-03
+ATTCCATC
+>strain-04
+ATTCGTC
diff -r 20ad934c5536 -r 892c6690a1e8 test-data/output
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output	Mon Apr 08 13:27:08 2019 -0400
@@ -0,0 +1,10 @@
+>strain-01
+ATTCGATC
+>strain-02
+ATGCGATC
+>strain-03
+ATTCCATC
+>reference
+ATTGGATC
+>strain-04
+ATTCGTC-
diff -r 20ad934c5536 -r 892c6690a1e8 test-data/output.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.log	Mon Apr 08 13:27:08 2019 -0400
@@ -0,0 +1,52 @@
+inputfile = orig
+5 x 8 - 7 d
+nthread = 1
+nthreadpair = 1
+nthreadtb = 1
+ppenalty_ex = 0
+stacksize: 8192 kb
+generating a scoring matrix for nucleotide (dist=200) ... done
+Gap Penalty = -1.53, +0.00, +0.00
+
+
+
+Making a distance matrix ..
+
    1 / 5 (thread    0)
+done.
+
+Constructing a UPGMA tree (efffree=0) ... 
+
    0 / 5
+done.
+
+Progressive alignment 1/2... 
+
STEP     1 / 4 (thread    0) f
STEP     2 / 4 (thread    0) d
STEP     3 / 4 (thread    0) d
STEP     4 / 4 (thread    0) d
+done.
+
+Making a distance matrix from msa.. 
+
    0 / 5 (thread    0)
+done.
+
+Constructing a UPGMA tree (efffree=1) ... 
+
    0 / 5
+done.
+
+Progressive alignment 2/2... 
+
STEP     1 / 4 (thread    0) f
STEP     2 / 4 (thread    0) d
STEP     3 / 4 (thread    0) d
STEP     4 / 4 (thread    0) d
+done.
+
+disttbfast (nuc) Version 7.407
+alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
+1 thread(s)
+
+
+Strategy:
+ FFT-NS-2 (Fast but rough)
+ Progressive method (guide trees were built 2 times.)
+
+If unsure which option to use, try 'mafft --auto input > output'.
+For more information, see 'mafft --help', 'mafft --man' and the mafft page.
+
+The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
+It tends to insert more gaps into gap-rich regions than previous versions.
+To disable this change, add the --leavegappyregion option.
+
diff -r 20ad934c5536 -r 892c6690a1e8 test-data/output.post_aligner.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.post_aligner.fasta	Mon Apr 08 13:27:08 2019 -0400
@@ -0,0 +1,10 @@
+>strain-01
+ATTCGATC
+>strain-02
+ATGCGATC
+>strain-03
+ATTCCATC
+>reference
+ATTGGATC
+>strain-04
+ATTCGTC-
diff -r 20ad934c5536 -r 892c6690a1e8 test-data/output.pre_aligner.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.pre_aligner.fasta	Mon Apr 08 13:27:08 2019 -0400
@@ -0,0 +1,10 @@
+>strain-01
+ATTCGATC
+>strain-02
+ATGCGATC
+>strain-03
+ATTCCATC
+>strain-04
+ATTCGTC
+>reference
+ATTGGATC
diff -r 20ad934c5536 -r 892c6690a1e8 test-data/test_00_metadata.output.tsv
--- a/test-data/test_00_metadata.output.tsv	Fri Apr 05 13:45:27 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-strain	country	year
-strain-01	France	2012
-strain-02	Germany	2008
-strain-03	China	2016
-strain-04	Canada	2008
diff -r 20ad934c5536 -r 892c6690a1e8 test-data/test_00_sequences.input.fasta
--- a/test-data/test_00_sequences.input.fasta	Fri Apr 05 13:45:27 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
->strain-01|France|2012
-ATTCGATC
->strain-02|Germany|2008
-TAGACGGA
->strain-03|China|2016
-AGGATTAC
->strain-04|Canada|2008
-TAATTAGG
diff -r 20ad934c5536 -r 892c6690a1e8 test-data/test_00_sequences.output.fasta
--- a/test-data/test_00_sequences.output.fasta	Fri Apr 05 13:45:27 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
->strain-01
-ATTCGATC
->strain-02
-TAGACGGA
->strain-03
-AGGATTAC
->strain-04
-TAATTAGG