Mercurial > repos > iuc > prestor_abseq3

annotate presto_macros.xml @ 4:2b2e40162269 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 08:15:11 +0000
parents 92829bcb3e49
children 9ada370c9d68
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87ae065762f3 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">
87ae065762f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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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>
87ae065762f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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7 </xml>
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8 <xml name="bio_tools">
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9 <xrefs>
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10 <xref type="bio.tools">presto</xref>
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11 </xrefs>
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12 </xml>
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13 <token name="@TOOL_VERSION@">0.6.2</token>
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87ae065762f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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15 <xml name="requirements">
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16 <requirements>
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17 <requirement type="package" version="@TOOL_VERSION@">presto</requirement>
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18 </requirements>
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19 </xml>
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87ae065762f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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21 <xml name="presto-coord-param">
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22 <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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23 <option value="illumina">Illumina</option>
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24 <option value="solexa">Solexa</option>
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25 <option value="sra">SRA</option>
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26 <option value="454">454</option>
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27 <option value="presto">pRESTO</option>
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28 </param>
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29 </xml>
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87ae065762f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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31 <xml name="presto-log-param">
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32 <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/>
87ae065762f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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33 </xml>
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87ae065762f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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35 <xml name="presto-log-output">
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36 <data name="log_out" format="txt" label="Log from ${tool.name} on ${on_string}">
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37 <filter>capture_log</filter>
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38 </data>
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39 </xml>
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87ae065762f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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41 <xml name="text-regex-validator">
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42 <validator type="regex" message="Value may include alphanumeric characters, underscores and spaces.">[A-Za-z0-9_ ]+</validator>
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43 </xml>
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44
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45 <token name="@PRESTO_URL_BASE@">https://presto.readthedocs.io</token>
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87ae065762f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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47 <token name="@HELP_NOTE@"><![CDATA[
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48
87ae065762f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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49 ====
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50
87ae065762f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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51 **Note about limitations of pRESTO tools within Galaxy:**
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52
87ae065762f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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53 pRESTO tools in galaxy have the following limitations vs. when run at the command line:
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54
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55 * Inputs must be FASTQ format and cannot be FASTA format.
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56 * Multiple inputs files are not supported per argument (e.g. ``-1``, ``-2`` or ``-s``), i.e.
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57 - Steps that take a pair of fastq inputs can only take two files, not two sets of files
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58 - Steps that take a single set of fastq inputs can only take a single file
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59 * The ``--outdir`` and ``--outname`` options are not supported; output files are named directly
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60 ]]></token>
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61 </macros>