diff fasttree.xml @ 0:614a12d56e58 draft default tip

planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc/tree/master/tools/fasttree commit 4db125fcd73327813d7bd511852bbe9ffc68a25c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasttree.xml	Mon Jan 09 08:07:45 2017 -0500
@@ -0,0 +1,137 @@
+<tool id="fasttree" name="FastTree" version="0.1">
+  <description>infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.</description>
+
+  <requirements>
+      <requirement type="package" version="2.1.9">fasttree</requirement>
+  </requirements>
+
+  <command detect_errors="aggressive">
+  <![CDATA[
+    OMP_NUM_THREADS=\${GALAXY_SLOTS:-1} &&
+    export OMP_NUM_THREADS &&
+    FastTreeMP
+    #if ( ( str( $advanced_options.advanced_options_selector ) == 'false'
+           and str( $advanced_options.alignment_type1 ) == 'nucl' ) or
+          ( str( $advanced_options.advanced_options_selector ) == 'true'
+             and str( $advanced_options.alignment_type_selection.alignment_type2 ) == 'nucl' ) ):
+      -nt
+    #end if
+    #if str( $advanced_options.advanced_options_selector ) == 'true':
+      $advanced_options.fastest
+      $advanced_options.gamma
+      $advanced_options.noml
+      $advanced_options.nosupport
+      $advanced_options.log
+      #if str( $advanced_options.alignment_type_selection.alignment_type2 ) == 'nucl':
+        $advanced_options.alignment_type_selection.nucl_alignment_model
+      #else
+        $advanced_options.alignment_type_selection.prot_alignment_model
+      #end if
+    #end if
+    '${input_alignment}' > '${output_tree}'
+  ]]>
+  </command>
+
+  <inputs>
+    <param name="input_alignment" type="data" format="fasta,phylip"
+      label="Multiple sequence alignment"/>
+    <conditional name="advanced_options">
+      <param name="advanced_options_selector" type="select" label="Advanced options">
+        <option value="true">Yes</option>
+        <option value="false" selected="True">No</option>
+      </param>
+      <when value="true">
+        <param argument="-fastest" type="boolean" truevalue="-fastest" falsevalue=""
+          label="Fastest mode (recommended for > 50,000 sequences)"/>
+        <param argument="-gamma" type="boolean" truevalue="-gamma" falsevalue=""
+          label="Rescale likelihoods using Gamma20 model" />
+        <param argument="-noml" type="boolean" truevalue="-noml" falsevalue=""
+          label="Disable Maximum-Likelihood topology refinement step" />
+        <param argument="-nosupport" type="boolean" truevalue="-nosupport" falsevalue=""
+          label="Disable computation of support values for tree splits" />
+        <param argument="-log" type="boolean" truevalue="-log output_log.txt" falsevalue=""
+          label="Save log file" />
+        <conditional name="alignment_type_selection">
+        <param name="alignment_type2" type="select" label="Alignment type">
+          <option value="nucl">Nucleotide</option>
+          <option value="prot" selected="True">Protein</option>
+        </param>
+        <when value="nucl">
+          <param name="nucl_alignment_model" label="Alignment model" type="select">
+            <option value="" selected="True">Jukes-Cantor+CAT</option>
+            <option value="-gtr">GTR+CAT</option>
+          </param>
+        </when>
+        <when value="prot">
+          <param name="prot_alignment_model" label="Alignment model" type="select">
+            <option value="">JTT+CAT</option>
+            <option value="-wag">WAG+CAT</option>
+            <option value="-lg">LG+CAT</option>
+          </param>
+        </when>
+        </conditional>
+      </when>
+      <when value="false">
+        <param name="alignment_type1" type="select" label="Alignment type">
+          <option value="nucl">Nucleotide</option>
+          <option value="prot" selected="True">Protein</option>
+        </param>
+      </when>
+    </conditional>
+
+  </inputs>
+
+  <outputs>
+    <data name="output_tree" format="nhx" />
+    <data name="output_log" format="txt" label="Log from ${tool.name} on ${on_string}" from_work_dir="output_log.txt">
+      <filter>advanced_options['advanced_options_selector'] == 'true' and advanced_options['log'] is True</filter>
+    </data>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input_alignment" value="sample_aln1.fasta" ftype="fasta" />
+      <param name="advanced_options_selector" value="false" />
+      <param name="alignment_type1" value="nucl" />
+      <output name="output_tree">
+        <assert_contents>
+          <has_text_matching expression="^^\(\(\(471528:[^,]+,\(\(484305:[^,]+,\(471785:[^,]+,\(484347:[^,]+,484343:" />
+        </assert_contents>
+      </output>
+    </test>
+    <test>
+      <param name="input_alignment" value="sample_aln2.fasta" ftype="fasta" />
+      <param name="advanced_options_selector" value="false" />
+      <output name="output_tree">
+        <assert_contents>
+          <has_text_matching expression="^\(\(N3970:\d\.\d+,N3339:\d\.\d+\)\d+\.\d+:\d\.\d+,\(\(\(\(N3243:\d\.\d+,\(\(N3234:\d\.\d+,\(N500:" />
+        </assert_contents>
+      </output>
+    </test>
+    <test>
+      <param name="input_alignment" value="sample_aln2.fasta" ftype="fasta" />
+      <param name="advanced_options_selector" value="true" />
+      <param name="log" value="True" />
+      <output name="output_log">
+        <assert_contents>
+          <has_text text="Amino acid distances: BLOSUM45 Joins: balanced Support: SH-like 1000" />
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+
+  <help>
+  <![CDATA[
+    FastTree infers approximately-maximum-likelihood phylogenetic trees from
+    alignments of nucleotide or protein sequences. For more information see
+    the `FastTree`_ website.
+
+    .. _FastTree: http://www.microbesonline.org/fasttree
+  ]]>
+  </help>
+
+  <citations>
+    <citation type="doi">10.1093/molbev/msp077</citation>
+    <citation type="doi">10.1371/journal.pone.0009490</citation>
+  </citations>
+</tool>