# HG changeset patch
# User iuc
# Date 1519067253 18000
# Node ID 48b414c7d38e7542e81ec385f201704d1deabb08

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e

diff -r 000000000000 -r 48b414c7d38e msaboot.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/msaboot.xml	Mon Feb 19 14:07:33 2018 -0500
@@ -0,0 +1,86 @@
+<?xml version="1.0"?>
+<tool id="msaboot" name="MSABOOT" version="@VERSION@">
+    <description>Output PHYLIP file with bootstrapped multiple sequence alignment data</description>
+    <macros>
+        <token name="@VERSION@">0.1.0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">msaboot</requirement>
+    </requirements>
+    <version_command>msaboot --version</version_command>
+    <command detect_errors="aggressive">
+        <![CDATA[
+msaboot -i '$input' -n $number -o '$output'
+#if $save_logfile:
+    > '$log' 2>&1
+#end if
+        ]]>
+    </command>
+    <inputs>
+        <param name="input" format="fasta" type="data" label="FASTA input file" />
+        <param name="number" type="integer" value="1" min="1" label="Specify the number of bootstrapping replicates to generate." />
+        <param name="save_logfile" type="boolean" truevalue="" falsevalue="" label="Output log file" />
+    </inputs>
+    <outputs>
+        <data name="output" format="phylip" label="${tool.name} on ${on_string}:out.phylip" />
+        <data name="log" format="txt" label="${tool.name} on ${on_string}:log_msabootpl_run.txt">
+            <filter>save_logfile</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="msa.fasta" />
+            <param name="number" value="10" />
+            <param name="save_logfile" value="true" />
+            <output name="log" file="log.txt" ftype="txt" compare="contains" />
+            <output name="output" file="out.phylip" ftype="phylip" compare="contains" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+===========
+Description
+===========
+
+.. class:: infomark
+
+A tool for creating bootstrapping replicates from Multiple Sequence Alignment data.
+
+.. _msaboot: https://github.com/phac-nml/msaboot
+
+-----
+
+-----
+Input
+-----
+Input file location of FASTA file containing Multiple Sequence Alignment data(-i)
+
+----------
+Parameters
+----------
+Number of bootstrapping replicates (-n)
+
+------
+Output
+------
+
+This tool produces two output files, one of which is optional (the log file).
+
+(A) The bootstrapped replicates in Phylip format.
+
+(B) The optional log file, containing information about the msaboot run to bootstrap the multiple sequence alignment data.
+
+]]>
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @misc{GitHubmsaboot,
+            title = {msaboot},
+            publisher = {phac-nml},
+            journal = {GitHub repository},
+            url = {https://github.com/phac-nml/msaboot},
+            }
+        </citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 48b414c7d38e test-data/log.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/log.txt	Mon Feb 19 14:07:33 2018 -0500
@@ -0,0 +1,1 @@
+msaboot v0.1.0
diff -r 000000000000 -r 48b414c7d38e test-data/msa.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/msa.fasta	Mon Feb 19 14:07:33 2018 -0500
@@ -0,0 +1,17 @@
+>1
+AAA
+>2
+CCC
+>3
+GGG
+>4
+TTT
+>5
+ACG
+>6
+CGT
+>7
+GTA
+>8
+TAC
+
diff -r 000000000000 -r 48b414c7d38e test-data/out.phylip
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.phylip	Mon Feb 19 14:07:33 2018 -0500
@@ -0,0 +1,1 @@
+