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annotate macros.xml @ 1:ab2cf85b9ae8 draft

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planemo upload commit f86fb54b98f0dbed260735675219e64882f08efe
author nml
date Mon, 13 Mar 2017 15:36:43 -0400
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1 <macros>
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2 <token name="@VERSION@">2.3</token>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="2.3.1">kat</requirement>
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6 </requirements>
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7 </xml>
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8 <xml name="stdio">
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9 <stdio>
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10 <exit_code range="1:" />
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11 <exit_code range=":-1" />
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12 <regex match="Error:" />
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13 <regex match="Exception:" />
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14 </stdio>
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15 </xml>
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16 <xml name="version_command">
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17 <version_command>kat --version</version_command>
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18 </xml>
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19 <xml name="citations">
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20 <citations>
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21 <citation type="doi">10.1101/064733</citation>
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22 <yield />
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23 </citations>
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24 </xml>
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25 <token name="@THREADS@">
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26 --threads \${GALAXY_SLOTS:-4}
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27 </token>
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28 <xml name="macro_input">
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29 <conditional name="single_or_paired">
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30 <param name="type" type="select" label="Read type">
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31 <option value="single">Single-end</option>
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32 <option value="paired">Paired-end</option>
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33 <option value="collection">Collection Paired-end</option>
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34 </param>
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35 <when value="single">
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36 <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/>
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37 </when>
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38 <when value="paired">
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39 <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/>
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40 <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/>
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41 </when>
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42 <when value="collection">
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43 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger" collection_type="paired" />
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44 </when>
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45 </conditional>
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46 </xml>
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47 <xml name="macro_kmers">
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48 <param name="kmer" type="integer" value='27' label="Kmer size" help="The kmer length to use in the kmer hashes. Larger values will provide more discriminating power between kmers but at the expense of additional memory and lower coverage."/>
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49 </xml>
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50 </macros>