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annotate presto_macros.xml.orig @ 3:c18b607fec09 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 08:09:53 +0000
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c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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1 <macros>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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2 <xml name="citations">
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <citations>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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4 <citation type="doi">10.1093/bioinformatics/btu138</citation>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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5 <yield />
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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6 </citations>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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7 </xml>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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8 <<<<<<< HEAD
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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10 <token name="@TOOL_VERSION@">0.6.2</token>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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12 =======
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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13 <xml name="bio_tools">
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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14 <xrefs>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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15 <xref type='bio.tools'>presto</xref>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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16 </xrefs>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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17 </xml>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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18 >>>>>>> 7abad681f (add tools up until P)
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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19 <xml name="requirements">
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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20 <requirements>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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21 <requirement type="package" version="@TOOL_VERSION@">presto</requirement>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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22 </requirements>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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23 </xml>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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24
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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25 <xml name="presto-coord-param">
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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26 <param argument="--coord" type="select" value="presto" label="Coordinate" help="The format of the sequence identifier which defines shared coordinate information across mate pairs.">
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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27 <option value="illumina">Illumina</option>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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28 <option value="solexa">Solexa</option>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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29 <option value="sra">SRA</option>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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30 <option value="454">454</option>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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31 <option value="presto">pRESTO</option>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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32 </param>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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33 </xml>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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34
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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35 <xml name="presto-log-param">
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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36 <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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37 </xml>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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38
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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39 <xml name="presto-log-output">
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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40 <data name="log_out" format="txt" label="Log from ${tool.name} on ${on_string}">
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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41 <filter>capture_log</filter>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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42 </data>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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43 </xml>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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44
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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45 <xml name="text-regex-validator">
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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46 <validator type="regex" message="Value may include alphanumeric characters, underscores and spaces.">[A-Za-z0-9_ ]+</validator>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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47 </xml>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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48
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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49 <token name="@PRESTO_URL_BASE@">https://presto.readthedocs.io</token>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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51 <token name="@HELP_NOTE@"><![CDATA[
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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52
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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53 ====
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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54
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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55 **Note about limitations of pRESTO tools within Galaxy:**
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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56
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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57 pRESTO tools in galaxy have the following limitations vs. when run at the command line:
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58
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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59 * Inputs must be FASTQ format and cannot be FASTA format.
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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60 * Multiple inputs files are not supported per argument (e.g. ``-1``, ``-2`` or ``-s``), i.e.
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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61 - Steps that take a pair of fastq inputs can only take two files, not two sets of files
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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62 - Steps that take a single set of fastq inputs can only take a single file
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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63 * The ``--outdir`` and ``--outname`` options are not supported; output files are named directly
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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64 ]]></token>
c18b607fec09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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65 </macros>