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annotate presto_macros.xml @ 0:14e648d05cce draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
author iuc
date Wed, 30 May 2018 15:34:53 -0400
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14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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1 <macros>
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2 <xml name="citations">
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3 <citations>
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4 <citation type="doi">10.1093/bioinformatics/btu138</citation>
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5 <yield />
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6 </citations>
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7 </xml>
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9 <xml name="requirements">
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10 <requirements>
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11 <requirement type="package" version="0.5.4">presto</requirement>
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12 </requirements>
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13 </xml>
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15 <xml name="presto-coord-param">
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16 <param argument="--coord" type="select" value="presto" label="Coordinate" help="The format of the sequence identifier which defines shared coordinate information across mate pairs.">
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17 <option value="illumina">Illumina</option>
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18 <option value="solexa">Solexa</option>
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19 <option value="sra">SRA</option>
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20 <option value="454">454</option>
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21 <option value="presto">pRESTO</option>
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22 </param>
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23 </xml>
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25 <xml name="presto-log-param">
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26 <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/>
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27 </xml>
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29 <xml name="presto-log-output">
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30 <data name="log_out" format="txt" label="Log from ${tool.name} on ${on_string}">
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31 <filter>capture_log</filter>
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32 </data>
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33 </xml>
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35 <xml name="text-regex-validator">
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36 <validator type="regex" message="Value may include alphanumeric characters, underscores and spaces.">[A-Za-z0-9_ ]+</validator>
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37 </xml>
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39 <token name="@PRESTO_URL_BASE@">https://presto.readthedocs.io/en/latest/tools</token>
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41 <!-- When modifying this file ensure that the version here matches the version above in requirements. -->
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42 <token name="@PRESTO_VERSION@">0.5.4</token>
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44 <token name="@HELP_NOTE@"><![CDATA[
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45
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46 ====
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47
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48 **Note about limitations of pRESTO tools within Galaxy:**
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49
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50 pRESTO tools in galaxy have the following limitations vs. when run at the command line:
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51
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52 * Inputs must be FASTQ format and cannot be FASTA format.
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53 * Multiple inputs files are not supported per argument (e.g. ``-1``, ``-2`` or ``-s``), i.e.
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54 - Steps that take a pair of fastq inputs can only take two files, not two sets of files
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55 - Steps that take a single set of fastq inputs can only take a single file
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56 * The ``--outdir`` and ``--outname`` options are not supported; output files are named directly
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57 ]]></token>
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58 </macros>