Mercurial > repos > iuc > obi_ngsfilter

annotate macros.xml @ 4:91a1ed0b486f draft default tip

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/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
author iuc
date Wed, 20 Mar 2024 13:16:28 +0000
parents 3bf57dadf7cd
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
2 <macros>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
3 <xml name="requirements">
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
4 <requirements>
1
e6ccf97b3d39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 0
diff changeset
5 <requirement type="package" version="@TOOL_VERSION@">obitools</requirement>
0
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
6 </requirements>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
7 </xml>
4
91a1ed0b486f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
8 <xml name="bio_tools">
91a1ed0b486f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
9 <xrefs>
91a1ed0b486f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
10 <xref type="bio.tools">obitools</xref>
91a1ed0b486f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
11 </xrefs>
91a1ed0b486f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
12 </xml>
3
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
13 <token name="@TOOL_VERSION@">1.2.13</token>
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
14 <token name="@PROFILE@">21.01</token>
0
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
15
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
16 <xml name="stdio">
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
17 <stdio>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
18 <exit_code range="1:" level="fatal" description="Error in Obitools execution" />
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
19 </stdio>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
20 </xml>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
21
3
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
22 <token name="@INPUT_FORMATS@">fastqsanger,fastqsanger.gz,fastqsolexa,fastqsolexa.gz,fasta,fasta.gz</token>
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
23 <token name="@GUNZIP_INPUT@"><![CDATA[
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
24 #if $input.ext.endswith(".gz")
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
25 gunzip -c '$input' > input &&
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
26 #else
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
27 ln -s '$input' input &&
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
28 #end if
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
29 ]]></token>
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
30 <token name="@GZIP_OUTPUT@"><![CDATA[
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
31 #if $input.ext.endswith(".gz")
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
32 | gzip -c
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
33 #end if
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
34 ]]></token>
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
35
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
36 <!-- generate galaxy.json to determine output format
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
37 - by default same as input
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
38 - if out_format can be specified
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
39 - fasta/fastq depending on $out_format (if != "")
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
40 - or fasta if the tool does not support choosing the output format, e.g. obiuniq which always outputs fasta
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
41 - gz if $input is zipped
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
42
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
43 A list of outputs to include in the json can be given by
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
44 setting a variable $outputs = [...] listing pairs of output names and the actual output
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
45 (defaults to [("output", $output)])
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
46 -->
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
47 <token name="@GENERATE_GALAXY_JSON@"><![CDATA[
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
48 #import json
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
49
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
50 #try:
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
51 #silent $outputs[0]
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
52 #except
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
53 #set outputs = [("output", $output)]
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
54 #end try
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
55
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
56 #if $input.ext.startswith("fastq")
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
57 #set ext = "fastqsanger"
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
58 #else if $input.ext.startswith("fasta")
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
59 #set ext = "fasta"
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
60 #end if
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
61
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
62 #try
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
63 #if $out_format == "fasta"
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
64 #set ext = "fasta"
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
65 #else if $out_format == "fastq"
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
66 #set ext = "fastqsanger"
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
67 #end if
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
68 #except
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
69 #set ext = "fasta"
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
70 #end try
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
71
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
72 #if $input.ext.endswith(".gz")
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
73 #set ext = ext + ".gz"
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
74 #end if
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
75
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
76 #set gxy_json = {}
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
77 #for oname, o in $outputs
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
78 #silent gxy_json[oname] = {"ext": ext}
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
79 #end for
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
80 && echo '${json.dumps(gxy_json)}' >> galaxy.json
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
81 ]]></token>
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
82
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
83 <token name="@OUT_FORMAT@"><![CDATA[
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
84 #if $out_format
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
85 --${out_format}-output
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
86 #end if
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
87 ]]></token>
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
88
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
89 <xml name="out_format_macro">
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
90 <param name="out_format" type="select" optional="true" label="Output data type" help="For FASTA/Q the the default output type is the same as the input type">
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
91 <option value="fasta">fasta</option>
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
92 <option value="fastq">fastq</option>
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
93 </param>
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
94 </xml>
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
95
0
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
96 <token name="@OBITOOLS_LINK@">
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
97 <![CDATA[
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
98 --------
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
99
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
100 **Project links:**
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
101
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
102 `OBITools`_
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
103
2
76e69de726b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
iuc
parents: 1
diff changeset
104 .. _OBITools: https://pythonhosted.org/OBITools/
0
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
105 ]]>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
106 </token>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
107
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
108 <xml name="attributes">
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
109 <option value="ali_dir" selected="true">ali_dir</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
110 <option value="ali_length">ali_length</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
111 <option value="avg_quality">avg_quality</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
112 <option value="best_match">best_match</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
113 <option value="best_identity">best_identity</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
114 <option value="class">class</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
115 <option value="cluster">cluster</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
116 <option value="complemented">complemented</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
117 <option value="count">count</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
118 <option value="cut">cut</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
119 <option value="direction">direction</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
120 <option value="distance">distance</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
121 <option value="error">error</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
122 <option value="experiment">experiment</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
123 <option value="family">family</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
124 <option value="family_name">family_name</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
125 <option value="forward_error">forward_error</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
126 <option value="forward_match">forward_match</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
127 <option value="forward_primer">forward_primer</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
128 <option value="forward_score">forward_score</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
129 <option value="forward_tag">forward_tag</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
130 <option value="forward_tm">forward_tm</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
131 <option value="genus">genus</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
132 <option value="genus_name">genus_name</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
133 <option value="head_quality">head_quality</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
134 <option value="id_status">id_status</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
135 <option value="merged_star">merged_star</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
136 <option value="merged">merged</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
137 <option value="mid_quality">mid_quality</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
138 <option value="mode">mode</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
139 <option value="obiclean_cluster">obiclean_cluster</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
140 <option value="obiclean_count">obiclean_count</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
141 <option value="obiclean_head">obiclean_head</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
142 <option value="obiclean_headcount">obiclean_headcount</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
143 <option value="obiclean_internalcount">obiclean_internalcount</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
144 <option value="obiclean_samplecount">obiclean_samplecount</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
145 <option value="obiclean_singletoncount">obiclean_singletoncount</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
146 <option value="obiclean_status">obiclean_status</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
147 <option value="occurrence">occurrence</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
148 <option value="order">order</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
149 <option value="order_name">order_name</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
150 <option value="pairend_limit ">pairend_limit </option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
151 <option value="partial ">partial </option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
152 <option value="rank">rank</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
153 <option value="reverse_error">reverse_error</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
154 <option value="reverse_match">reverse_match</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
155 <option value="reverse_primer">reverse_primer</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
156 <option value="reverse_score">reverse_score</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
157 <option value="reverse_tag">reverse_tag</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
158 <option value="reverse_tm">reverse_tm</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
159 <option value="sample">sample</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
160 <option value="scientific_name">scientific_name</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
161 <option value="score">score</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
162 <option value="score_norm">score_norm</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
163 <option value="select">select</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
164 <option value="seq_ab_match">seq_ab_match</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
165 <option value="seq_a_single">seq_a_single</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
166 <option value="seq_a_mismatch">seq_a_mismatch</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
167 <option value="seq_a_deletion">seq_a_deletion</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
168 <option value="seq_a_insertion">seq_a_insertion</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
169 <option value="seq_b_single">seq_b_single</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
170 <option value="seq_b_mismatch">seq_b_mismatch</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
171 <option value="seq_b_deletion">seq_b_deletion</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
172 <option value="seq_b_insertion">seq_b_insertion</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
173 <option value="seq_length">seq_length</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
174 <option value="seq_length_ori">seq_length_ori</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
175 <option value="seq_rank">seq_rank</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
176 <option value="sminL">sminL</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
177 <option value="sminR">sminR</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
178 <option value="species">species</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
179 <option value="species_list">species_list</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
180 <option value="species_name">species_name</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
181 <option value="status">status</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
182 <option value="strand">strand</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
183 <option value="tail_quality">tail_quality</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
184 <option value="taxid">taxid</option>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
185 </xml>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
186
3
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
187 <xml name="input_format_options_macro">
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
188 <section name="input_format_options" title="Input format options" expanded="false">
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
189 <param name="options_inputtype" type="select" optional="true" label="Specify the input datatype" help="default: determine automatically (should only be necessay for non FASTA/FASTQ datasets)">
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
190 <option value="--genbank">genbank</option>
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
191 <option value="--embl">embl</option>
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
192 <option value="--sanger">sanger</option>
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
193 <option value="--solexa">solexa</option>
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
194 <option value="--ecopcr">ecopcr</option>
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
195 <option value="--ecopcrdb">ecopcrdb</option>
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
196 <option value="--fasta">fasta (including obitools fasta extentions)</option>
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
197 <option value="--raw-fasta">raw fasta (more tolerant format variant)</option>
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
198 </param>
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
199 <param name="options_seqtype" type="select" optional="true" label="Specify the sequence datatype" >
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
200 <option value="--nuc">nucleic</option>
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
201 <option value="--prot">protein</option>
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
202 </param>
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
203 </section>
0
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
204 </xml>
3
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
205
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
206 <token name="@INPUT_FORMAT@"><![CDATA[
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
207 #if $input_format_options.options_inputtype
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
208 $input_format_options.options_inputtype
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
209 #else
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
210 #if $input.ext.startswith("fasta")
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
211 --fasta
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
212 #else if $input.ext.startswith("fastqsolexa")
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
213 ## input file is in fastq nucleic format produced by solexa sequencer
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
214 --solexa
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
215 #else
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
216 ## input file is in sanger fastq nucleic format (standard fastq)
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
217 --sanger
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
218 #end if
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
219 #end if
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
220 #if $input_format_options.options_seqtype
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
221 $input_format_options.options_seqtype
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
222 #end if
3bf57dadf7cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
parents: 2
diff changeset
223 ]]></token>
0
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
224
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
225 <xml name="sanitizer">
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
226 <sanitizer invalid_char="test">
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
227 <valid initial="default">
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
228 <!--add value="&quot;"/-->
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
229 </valid>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
230 <mapping initial="default">
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
231 <add source="&gt;" target="\&gt;"/>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
232 <add source="&quot;" target="\&quot;"/>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
233 </mapping>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
234 </sanitizer>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
235 </xml>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
236
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
237 <xml name="citation">
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
238 <citations>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
239 <citation type="doi">10.1111/1755-0998.12428</citation>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
240 </citations>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
241 </xml>
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
242
4df964e14378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
243 </macros>