Mercurial > repos > iuc > presto_parseheaders

comparison presto_macros.xml.orig @ 3:c18b607fec09 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
parents
children
comparison
equal deleted inserted replaced
2:7f3467910eb5 3:c18b607fec09
1 <macros>
2 <xml name="citations">
3 <citations>
4 <citation type="doi">10.1093/bioinformatics/btu138</citation>
5 <yield />
6 </citations>
7 </xml>
8 <<<<<<< HEAD
9
10 <token name="@TOOL_VERSION@">0.6.2</token>
11
12 =======
13 <xml name="bio_tools">
14 <xrefs>
15 <xref type='bio.tools'>presto</xref>
16 </xrefs>
17 </xml>
18 >>>>>>> 7abad681f (add tools up until P)
19 <xml name="requirements">
20 <requirements>
21 <requirement type="package" version="@TOOL_VERSION@">presto</requirement>
22 </requirements>
23 </xml>
24
25 <xml name="presto-coord-param">
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.">
27 <option value="illumina">Illumina</option>
28 <option value="solexa">Solexa</option>
29 <option value="sra">SRA</option>
30 <option value="454">454</option>
31 <option value="presto">pRESTO</option>
32 </param>
33 </xml>
34
35 <xml name="presto-log-param">
36 <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/>
37 </xml>
38
39 <xml name="presto-log-output">
40 <data name="log_out" format="txt" label="Log from ${tool.name} on ${on_string}">
41 <filter>capture_log</filter>
42 </data>
43 </xml>
44
45 <xml name="text-regex-validator">
46 <validator type="regex" message="Value may include alphanumeric characters, underscores and spaces.">[A-Za-z0-9_ ]+</validator>
47 </xml>
48
49 <token name="@PRESTO_URL_BASE@">https://presto.readthedocs.io</token>
50
51 <token name="@HELP_NOTE@"><![CDATA[
52
53 ====
54
55 **Note about limitations of pRESTO tools within Galaxy:**
56
57 pRESTO tools in galaxy have the following limitations vs. when run at the command line:
58
59 * Inputs must be FASTQ format and cannot be FASTA format.
60 * Multiple inputs files are not supported per argument (e.g. ``-1``, ``-2`` or ``-s``), i.e.
61 - Steps that take a pair of fastq inputs can only take two files, not two sets of files
62 - Steps that take a single set of fastq inputs can only take a single file
63 * The ``--outdir`` and ``--outname`` options are not supported; output files are named directly
64 ]]></token>
65 </macros>