annotate presto_macros.xml @ 2:36ad790eda96 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 19e832988729a92be5426131fc6114e1f7237982"
author iuc
date Fri, 02 Jul 2021 15:33:02 +0000
parents 61c1ae41a6bd
children 98b0b4c22e69
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
1 <macros>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
2 <xml name="citations">
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
3 <citations>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
4 <citation type="doi">10.1093/bioinformatics/btu138</citation>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
5 <yield />
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
6 </citations>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
7 </xml>
2
36ad790eda96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 19e832988729a92be5426131fc6114e1f7237982"
iuc
parents: 1
diff changeset
8
36ad790eda96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 19e832988729a92be5426131fc6114e1f7237982"
iuc
parents: 1
diff changeset
9 <token name="@TOOL_VERSION@">0.6.2</token>
0
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
10
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
11 <xml name="requirements">
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
12 <requirements>
2
36ad790eda96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 19e832988729a92be5426131fc6114e1f7237982"
iuc
parents: 1
diff changeset
13 <requirement type="package" version="@TOOL_VERSION@">presto</requirement>
0
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
14 </requirements>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
15 </xml>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
16
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
17 <xml name="presto-coord-param">
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
18 <param argument="--coord" type="select" value="presto" label="Coordinate" help="The format of the sequence identifier which defines shared coordinate information across mate pairs.">
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
19 <option value="illumina">Illumina</option>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
20 <option value="solexa">Solexa</option>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
21 <option value="sra">SRA</option>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
22 <option value="454">454</option>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
23 <option value="presto">pRESTO</option>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
24 </param>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
25 </xml>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
26
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
27 <xml name="presto-log-param">
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
28 <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
29 </xml>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
30
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
31 <xml name="presto-log-output">
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
32 <data name="log_out" format="txt" label="Log from ${tool.name} on ${on_string}">
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
33 <filter>capture_log</filter>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
34 </data>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
35 </xml>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
36
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
37 <xml name="text-regex-validator">
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
38 <validator type="regex" message="Value may include alphanumeric characters, underscores and spaces.">[A-Za-z0-9_ ]+</validator>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
39 </xml>
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
40
1
61c1ae41a6bd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit a42c43c1528ae7b7efe2c5ef848681d574df0405"
iuc
parents: 0
diff changeset
41 <token name="@PRESTO_URL_BASE@">https://presto.readthedocs.io</token>
0
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
42
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
43 <token name="@HELP_NOTE@"><![CDATA[
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
44
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
45 ====
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
46
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
47 **Note about limitations of pRESTO tools within Galaxy:**
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
48
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
49 pRESTO tools in galaxy have the following limitations vs. when run at the command line:
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
50
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
51 * Inputs must be FASTQ format and cannot be FASTA format.
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
52 * Multiple inputs files are not supported per argument (e.g. ``-1``, ``-2`` or ``-s``), i.e.
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
53 - Steps that take a pair of fastq inputs can only take two files, not two sets of files
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
54 - Steps that take a single set of fastq inputs can only take a single file
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
55 * The ``--outdir`` and ``--outname`` options are not supported; output files are named directly
14e648d05cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
56 ]]></token>
1
61c1ae41a6bd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit a42c43c1528ae7b7efe2c5ef848681d574df0405"
iuc
parents: 0
diff changeset
57 </macros>