# HG changeset patch
# User iuc
# Date 1589231005 14400
# Node ID 9f4a66e22580c6b876a8b6db3528a16fdf245026

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"

diff -r 000000000000 -r 9f4a66e22580 rapidnj.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapidnj.xml	Mon May 11 17:03:25 2020 -0400
@@ -0,0 +1,79 @@
+<?xml version="1.0"?>
+<tool id="rapidnj" name="Join neighbors" version="@VERSION@">
+    <description>rapidly with RapidNJ</description>
+    <macros>
+        <token name="@VERSION@">2.3.2</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="v@VERSION@">rapidnj</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $alignments.is_of_type('fasta'):
+            #set $input_format = 'fa'
+        #else if $alignments.is_of_type('stockholm'):
+            #set $input_format = 'sth'
+        #else:
+            #set $input_format = 'pd'
+        #end if
+        ln -s '$alignments' input_file.$input_format &&
+        rapidnj '$alignments'
+            --input-format $input_format
+            --output-format $output_format
+            --evolution-model $evolution_model
+            --cores \${GALAXY_SLOTS:-1}
+            #if $bootstrap:
+                --bootstrap $bootstrap
+            #end if
+            --alignment-type $alignment_type
+            $no_negative_length
+            > '$distances'
+        ]]>
+    </command>
+    <inputs>
+        <param name="alignments" type="data" format="phylip,fasta,stockholm" label="Input to construct or reconstruct trees" />
+        <param argument="--output-format" name="output_format" type="select" label="Output format">
+            <option value="t">Phylogenetic tree in newick format</option>
+            <option value="m">Distance matrix</option>
+        </param>
+        <param argument="--evolution-model" name="evolution_model" type="select" label="Evolution model" help="Specifies which sequence evolution method to use when computing distance estimates from multiple alignments, using Kimura's model by default.">
+            <option value="kim">Kimura</option>
+            <option value="jc">Jukes-Cantor</option>
+        </param>
+        <param argument="--bootstrap" type="integer" optional="true" label="Samples to use for computing bootstrap" help="The output tree will be annotated with bootstrap values" />
+        <param argument="--alignment-type" name="alignment_type" type="select" label="Input alignment type">
+            <option value="p">Protein</option>
+            <option value="d">DNA</option>
+        </param>
+        <param argument="--no-negative-length" name="no_negative_length" type="boolean" truevalue="--no-negative-length" falsevalue="" label="Adjust for negative branch lengths." />
+    </inputs>
+    <outputs>
+        <data name="distances" format="nhx" label="${tool.name} on ${on_string}: Calculated distances">
+            <change_format>
+                <when input="output_format" value="m" format="tabular" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="alignments" value="rapidnj-in1.fa" />
+            <param name="output_format" value="t" />
+            <output name="distances" ftype="nhx" value="rapidnj-out1.nhx" />
+        </test>
+        <test>
+            <param name="alignments" value="rapidnj-in2.fa" />
+            <param name="output_format" value="t" />
+            <output name="distances" ftype="nhx" value="rapidnj-out2.nhx" />
+        </test>
+    </tests>
+    <help><![CDATA[
+============
+RapidNJ
+============
+
+Especially useful for large datasets where maximum-likelihood based phylogenetic inference becomes intractable, RapidNJ reduces the computing time of canonical neighbour-joining for phylogenetic tree inference. RapidNJ accepts either matrices in phylip format or alignments in stockholm or FASTA format. 
+        ]]>
+    </help>
+    <citations>
+        <citation type="doi">doi:10.1007/978-3-540-87361-7_10</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 9f4a66e22580 test-data/rapidnj-in1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rapidnj-in1.fa	Mon May 11 17:03:25 2020 -0400
@@ -0,0 +1,120 @@
+>BRO1_1
+ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG
+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC
+ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC
+CACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCC
+CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT
+CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC
+CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA
+GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T
+CAGAT-AGGGGTCCCTTGACCACCATCC
+>BRO2
+ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG
+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC
+ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC
+CACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCC
+CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT
+CAACTGCAACCCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC
+CTACCCACCC-TTAACAGTACATAGTGCATAAAGCCATTTACCGTACATA
+GCACATTATA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T
+CAGAT-AGGGGTCCCTTGACCACCATCC
+>BRO3_1
+ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG
+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC
+ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC
+CACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCC
+CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT
+CAGCTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC
+CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA
+GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T
+CAGAT-AGGGGTCCCTTGACCACCATCC
+>BRO4
+ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG
+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC
+ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC
+CACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCC
+CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCATACAT
+CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC
+CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA
+GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T
+CAGAT-AGGGGTCCCTTGACCACCATCC
+>BRO5
+ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG
+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC
+ATTAC-TGCCAGCCACCATGAATATTGTACAGTACCATAAA-TACTTGAC
+CACCTGTAGTACATAAAAACCC-AATCC--ACACCAAAA----CCCCCCC
+CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT
+CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC
+CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA
+GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T
+CAGAT-AGGGGTCCCTTGACCACCATCC
+>BRO6
+ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG
+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC
+ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC
+CACCTGTAATACATAAAAACCC-AATTC--ACACCAAAA----CCCCCCC
+CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT
+CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC
+CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA
+GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T
+CAGAT-AGGGGTCCCTTGACCACCATCC
+>BRO7_1
+ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG
+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC
+ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC
+CACCTGTAGTACATAAAAACCC-AATCC--ACACCAAAA----CCCCCCC
+CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT
+CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC
+CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA
+GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T
+CAGAT-AGGGGTCCCTTGACCACCATCC
+>BRO8
+ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG
+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC
+ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC
+CACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCC
+CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT
+CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGAATACCAACAAAC
+CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA
+GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T
+CAGAT-AGGGGTCCCTTGACCACCATCC
+>BRO9
+ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG
+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC
+ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC
+CACCTGTAGTACATAAAAACCC-AACCC--ACATCAAAA----CCCCCCC
+CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT
+CAATTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC
+CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA
+GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T
+CAGAT-AGGGGTCCCTTGACCACCATCC
+>BRO10
+ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG
+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC
+ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC
+CACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCC
+CC-CATGCTTACAAGCAAGTACAGCAATCAACCTTCAA-CTATCACACAT
+CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC
+CTACCCACCC-TTAACAGTACATAGCACATAAAGCCATTTATCGTACATA
+GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T
+CAGAT-AGGGGTCCCTTGACCACCATCC
+>BRO11_1
+ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG
+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC
+ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC
+TACCTGTAGTACATAAAAACCC-AACCC--ACATCAAAA----CCCTGCC
+CC-CATGCTTACAAGCAAGTACAGCAATCAACCTTCAA-CTGTCACACAT
+CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC
+CTACCCACCC-TTAACAGTACATAGCACATAAAGTCATTTACCGTACATA
+GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T
+CAGAT-AGGGGTCCCTTGACCACCATCC
+>BRO12
+ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG
+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC
+ATTAC-TGCCAGCCACCATGAATATTGTACAGTACCATAAA-TACTTGAC
+TACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCTC
+CC-CATGCTTACAAGCAAGTACAGCAATCAACCTTCAA-CTATCACACAT
+CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC
+CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA
+GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T
+CAGAT-AGGGGTCCCTTGACCACCATCC
\ No newline at end of file
diff -r 000000000000 -r 9f4a66e22580 test-data/rapidnj-in2.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rapidnj-in2.fa	Mon May 11 17:03:25 2020 -0400
@@ -0,0 +1,20 @@
+>Cow
+ATGGCATATCCCATACAACTAGGATTCCAAGATGCAACATCACCAATCATAGAAGAACTA
+>Carp
+ATGGCACACCCAACGCAACTAGGTTTCAAGGACGCGGCCATACCCGTTATAGAGGAACTT
+>Chicken
+ATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTC
+>Human
+ATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTT
+>Loach
+ATGGCACATCCCACACAATTAGGATTCCAAGACGCGGCCTCACCCGTAATAGAAGAACTT
+>Mouse
+ATGGCCTACCCATTCCAACTTGGTCTACAAGACGCCACATCCCCTATTATAGAAGAGCTA
+>Rat
+ATGGCTTACCCATTTCAACTTGGCTTACAAGACGCTACATCACCTATCATAGAAGAACTT
+>Seal
+ATGGCATACCCCCTACAAATAGGCCTACAAGATGCAACCTCTCCCATTATAGAGGAGTTA
+>Whale
+ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTC
+>Frog
+ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTA
diff -r 000000000000 -r 9f4a66e22580 test-data/rapidnj-out1.nhx
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rapidnj-out1.nhx	Mon May 11 17:03:25 2020 -0400
@@ -0,0 +1,1 @@
+((('BRO2':0.00741,'BRO1_1':-1.9026e-05):9.5885e-06,'BRO4':0.0024584):1.0562e-06,((((('BRO11_1':0.014476,'BRO10':0.0028897):0.0014138,'BRO12':0.0060244):0.0055218,'BRO9':0.0044166):0.0003151,(('BRO7_1':-2.3261e-05,'BRO6':0.0049421):0.00018301,'BRO5':0.0022807):0.0021702):0.00030175,'BRO3_1':0.002458):1.0565e-06,'BRO8':0.0024584);
diff -r 000000000000 -r 9f4a66e22580 test-data/rapidnj-out2.nhx
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rapidnj-out2.nhx	Mon May 11 17:03:25 2020 -0400
@@ -0,0 +1,1 @@
+((((('Rat':0.091946,'Mouse':0.075881):0.021586,'Chicken':0.1511):0.015204,'Human':0.16846):0.03053,('Whale':0.059664,'Cow':0.087548):0.038075):0.006525,(('Loach':0.06275,'Carp':0.14804):0.070426,'Frog':0.09302):0.038865,'Seal':0.16782);