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1 <tool id="PHYLO_alignment" name="Align query sequences" version="1.0.0">
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2 <description>with sequences in a reference package</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6
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6 <requirements>
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7 <requirement type="package">yapp_env</requirement>
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8 </requirements>
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9 <stdio>
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10 <expand macro="basic_errors"/>
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11 </stdio>
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12 <version_command>echo "$(taxit -V); $(cmalign -h | grep INFERNAL); $(esl-alimerge -h | grep Easel)"</version_command>
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3
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13 <command interpreter="bash">
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14 alignment-wrapper.sh ${config}
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15 </command>
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16 <inputs>
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17 <param name="refpkg" type="data" format="refpkg" label="Reference package"/>
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18 <param name="input_seqs" type="data" format="fasta" label="Input sequences"/>
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19 </inputs>
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20 <outputs>
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21 <data name="aligned_seqs" format="fasta" label="Aligned sequences"/>
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22 <data name="aligned_scores" format="txt" label="Alignment scores"/>
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23 </outputs>
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24 <configfiles>
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25 <configfile name="config">
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26 REFPKG="${refpkg.extra_files_path}"
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27 INPUT_SEQS="${input_seqs}"
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28
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29 ALIGNED_SEQS="${aligned_seqs}"
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30 ALIGNED_SCORES="${aligned_scores}"
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31 </configfile>
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32 </configfiles>
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33 <!-- The contents of the help tag is parsed as reStructuredText. Please see
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34 help-template.rst for examples of commonly-used sections in other Galaxy
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35 tools. -->
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36 <help>
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37
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38 .. class:: infomark
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39
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40 **What it does**
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41
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42 This tool aligns query sequences with the reference sequences used to make the
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43 reference tree contained in the reference package and then merges the query and
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44 reference sequences.
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45
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46 </help>
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6
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47 <citations>
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48 <expand macro="cite_taxtastic"/>
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49 <expand macro="cite_infernal"/>
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50 </citations>
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3
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51 </tool>
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