Mercurial > repos > iuc > presto_pairseq

comparison presto_macros.xml @ 0:d08bfab1c8fc 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 15:34:01 -0400
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children c50b8441ac36
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-1:000000000000 0:d08bfab1c8fc
1 <macros>
2 <xml name="citations">
3 <citations>
4 <citation type="doi">10.1093/bioinformatics/btu138</citation>
5 <yield />
6 </citations>
7 </xml>
8
9 <xml name="requirements">
10 <requirements>
11 <requirement type="package" version="0.5.4">presto</requirement>
12 </requirements>
13 </xml>
14
15 <xml name="presto-coord-param">
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.">
17 <option value="illumina">Illumina</option>
18 <option value="solexa">Solexa</option>
19 <option value="sra">SRA</option>
20 <option value="454">454</option>
21 <option value="presto">pRESTO</option>
22 </param>
23 </xml>
24
25 <xml name="presto-log-param">
26 <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/>
27 </xml>
28
29 <xml name="presto-log-output">
30 <data name="log_out" format="txt" label="Log from ${tool.name} on ${on_string}">
31 <filter>capture_log</filter>
32 </data>
33 </xml>
34
35 <xml name="text-regex-validator">
36 <validator type="regex" message="Value may include alphanumeric characters, underscores and spaces.">[A-Za-z0-9_ ]+</validator>
37 </xml>
38
39 <token name="@PRESTO_URL_BASE@">https://presto.readthedocs.io/en/latest/tools</token>
40
41 <!-- When modifying this file ensure that the version here matches the version above in requirements. -->
42 <token name="@PRESTO_VERSION@">0.5.4</token>
43
44 <token name="@HELP_NOTE@"><![CDATA[
45
46 ====
47
48 **Note about limitations of pRESTO tools within Galaxy:**
49
50 pRESTO tools in galaxy have the following limitations vs. when run at the command line:
51
52 * Inputs must be FASTQ format and cannot be FASTA format.
53 * Multiple inputs files are not supported per argument (e.g. ``-1``, ``-2`` or ``-s``), i.e.
54 - Steps that take a pair of fastq inputs can only take two files, not two sets of files
55 - Steps that take a single set of fastq inputs can only take a single file
56 * The ``--outdir`` and ``--outname`` options are not supported; output files are named directly
57 ]]></token>
58 </macros>