diff tree.xml @ 9:7bf54edaba24 draft

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty

--- a/tree.xml	Mon Aug 23 09:25:07 2021 +0000
+++ b/tree.xml	Thu May 12 10:44:30 2022 +0000
@@ -1,73 +1,46 @@
-<?xml version="1.0"?>
-<!--
-# Copyright (C) 2017 INRA
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
--->
-<tool id="FROGS_Tree" name="FROGS Tree" version="@TOOL_VERSION@+galaxy2">
+<tool id="FROGS_Tree" name="FROGS Tree" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05">
     <description>Reconstruction of phylogenetic tree </description>
-
-      <macros>
-          <import>macros.xml</import>
-      </macros>
-
-      <expand macro="requirements" >
-          <requirement type="package" version="7.407">mafft</requirement>
-          <requirement type="package" version="2.1.9">fasttree</requirement>
-          <requirement type="package" version="4.0">r-essentials</requirement>
-          <requirement type="package" version="2.7.0">r-phangorn</requirement>
-      </expand>
-
-    <stdio>
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <command>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="7.407">mafft</requirement>
+        <requirement type="package" version="2.1.9">fasttree</requirement>
+        <requirement type="package" version="4.1.2">r-base</requirement>
+        <requirement type="package" version="4.1">r-essentials</requirement>
+        <requirement type="package" version="2.7.0">r-phangorn</requirement>
+    </expand>
+    <command detect_errors="exit_code">
         tree.py
             --input-sequences '$input_otu'
             --biom-file '$biomfile'
-            --nb-cpus \${GALAXY_SLOTS:-1}
+            @CPUS@
             --out-tree '$out_tree'
             --html '$html'
     </command>
     <inputs>
-    <!-- Files -->
-        <param format="fasta" name="input_otu" type="data" label="OTUs sequence file" help="OTUs sequence file (format: fasta). Warning: FROGS Tree does not work on more than 10000 sequences!" optional="false">
-            <validator type="empty_field" message="This parameter is required." />
-        </param>
-        <param format="biom1" name="biomfile" type="data" label="Biom file" help="The abundance table of OTUs (format: biom)." optional="false">
-            <validator type="empty_field" message="This parameter is required." />
-        </param>
+        <!-- Files -->
+        <param format="fasta" name="input_otu" type="data" label="OTUs sequence file" help="OTUs sequence file (format: FASTA). Warning: FROGS Tree does not work on more than 10000 sequences!"/>
+        <param format="biom1" name="biomfile" type="data" label="Biom file" help="The abundance table of OTUs (format: BIOM)"/>
     </inputs>
     <outputs>
-        <data format="nhx" name="out_tree" label="${tool.name}: tree.nwk" from_work_dir="tree.nwk"/>
-        <data format="html" name="html" label="${tool.name}: report.html" from_work_dir="summary.html"/>
+        <data format="nhx" name="out_tree" label="${tool.name}: tree.nwk" from_work_dir="tree.nwk" />
+        <data format="html" name="html" label="${tool.name}: report.html" from_work_dir="summary.html" />
     </outputs>
     <tests>
         <test>
-            <param name="input_otu" value="references/09-normalisation.fasta"/>
-            <param name="biomfile" value="references/09-normalisation.biom"/>
-            <output name="out_tree" value="references/15-tree-mafft.nwk" compare="sim_size" delta="30"/>
-            <output name="html" value="references/15-tree-mafft.html" compare="diff" lines_diff="2"/>
-            <output name="html" value="references/15-tree-mafft.html" compare="sim_size" delta="30"/>
+            <param name="input_otu" value="references/09-normalisation.fasta" />
+            <param name="biomfile" value="references/09-normalisation.biom" />
+            <output name="out_tree" value="references/15-tree-mafft.nwk" compare="sim_size" delta="30" />
+            <output name="html" value="references/15-tree-mafft.html" compare="diff" lines_diff="2" />
+            <output name="html" value="references/15-tree-mafft.html" compare="sim_size" delta="30" />
             <output name="html">
-                 <assert_contents>
+                <assert_contents>
                     <has_text_matching expression="FROGS\sTree" />
                     <has_text_matching expression="abundance_removed.*:\s0" />
                     <has_text_matching expression="abundance_kept.*:\s300" />
                     <has_text_matching expression="otu_removed.*:\s0" />
-                    <has_text_matching expression="otu_kept.*:\s52" />
+                    <has_text_matching expression="otu_kept.*:\s50" />
                 </assert_contents>
             </output>
         </test>
@@ -123,9 +96,5 @@
 
 
     </help>
-
-    <citations>
-        <expand macro="citations" />
-    </citations>
-    
+    <expand macro="citations" />
 </tool>