Mercurial > repos > dfornika > augur

diff augur_align.xml @ 1:892c6690a1e8 draft default tip

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
author dfornika
date Mon, 08 Apr 2019 13:27:08 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/augur_align.xml	Mon Apr 08 13:27:08 2019 -0400
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+<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>