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1 <tool id="PHYLO_preprocessing" name="Preprocess sequences" version="2.0.0">
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2 <description>in preparation for phylogenetic placement</description>
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3 <requirements>
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4 <requirement type="package">yapp_env</requirement>
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5 </requirements>
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9 <version_command>echo "guppy $(guppy --version)"</version_command>
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10 <command interpreter="bash">
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11 preprocessing-wrapper.sh ${config}
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12 </command>
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13 <stdio>
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14 <expand macro="basic_errors"/>
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15 </stdio>
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16 <inputs>
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17 <param name="refpkg" type="data" format="refpkg" label="Reference package"/>
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18 <param name="input_seqs" type="data" format="fasta" label="Input sequences"/>
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19 <param name="split_map" type="data" format="csv" label="Read-to-specimen map"/>
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20 </inputs>
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21 <outputs>
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22 <data name="dedup_seqs" format="fasta" label="Deduplicated sequences"/>
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23 <data name="dedup_info" format="csv" label="Deduplication info"/>
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24 <data name="aligned_seqs" format="fasta" label="Aligned sequences"/>
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25 <data name="aligned_scores" format="txt" label="Alignment scores"/>
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26 </outputs>
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27 <configfiles>
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28 <configfile name="config">
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29 REFPKG="${refpkg.extra_files_path}"
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30 INPUT_SEQS="${input_seqs}"
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31 SPLIT_MAP="${split_map}"
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32
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33 DEDUP_SEQS="${dedup_seqs}"
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34 DEDUP_INFO="${dedup_info}"
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35 ALIGNED_SEQS="${aligned_seqs}"
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36 ALIGNED_SCORES="${aligned_scores}"
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37 </configfile>
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38 </configfiles>
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39 <!-- The contents of the help tag is parsed as reStructuredText. Please see
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40 help-template.rst for examples of commonly-used sections in other Galaxy
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41 tools. -->
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42 <help>
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43
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44 .. class:: infomark
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45
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46 **What it does**
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47
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48 This tool aligns query sequences with the reference sequences used to make the
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49 reference tree contained in the reference package and then merges the query and
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50 reference sequences.
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51
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52 </help>
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53 </tool>
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