Mercurial > repos > iuc > last

annotate maf-convert.xml @ 10:a07c62dc88f9 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/last commit 88d7f81768f05f490f444b646f47241cf2547b44"
author iuc
date Sat, 27 Nov 2021 10:11:58 +0000
parents 18ff8319181f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
10
a07c62dc88f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 88d7f81768f05f490f444b646f47241cf2547b44"
iuc
parents: 9
diff changeset
1 <tool id="last_maf_convert" name="MAF-convert" version="@TOOL_VERSION@+galaxy0" profile="20.01">
0
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
2
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
3 <description>read MAF-format alignments and write them in another format.</description>
9
18ff8319181f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 8
diff changeset
4 <expand macro="bio_tools"/>
0
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
5 <macros>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
6 <import>macros_last.xml</import>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
7 </macros>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
8
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
9 <requirements>
10
a07c62dc88f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 88d7f81768f05f490f444b646f47241cf2547b44"
iuc
parents: 9
diff changeset
10 <requirement type="package" version="@TOOL_VERSION@">last</requirement>
0
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
11 </requirements>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
12
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
13 <command detect_errors="exit_code"><![CDATA[
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
14 maf-convert
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
15
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
16 $maf_convert.output_type.output_format
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
17
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
18 $maf_convert.noheader
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
19
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
20 #if $maf_convert.output_type.output_format == 'psl'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
21 $maf_convert.output_type.protein
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
22 -j $maf_convert.output_type.j
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
23 #end if
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
24
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
25 #if $maf_convert.output_type.output_format == 'sam'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
26 $maf_convert.output_type.sam_file.dictionary
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
27 #if $maf_convert.output_type.sam_file.dictionary == '-d'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
28 -f $maf_convert.output_type.sam_file.f
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
29 #end if
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
30 #if $maf_convert.output_type.readfile != ''
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
31 -r $maf_convert.output_type.r
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
32 #end if
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
33 #end if
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
34
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
35 #if $maf_convert.output_type.output_format == 'blast' or $maf_convert.output_type.output_format == 'html'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
36 -l $maf_convert.output_type.l
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
37 #end if
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
38
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
39 '$maf_file'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
40
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
41 > '$outfile'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
42
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
43 ]]></command>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
44 <inputs>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
45 <param name="maf_file" type="data" format="maf" label="MAF file to convert" />
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
46
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
47 <section name="maf_convert" title="MAF-convert arguments" expanded="true">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
48
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
49 <param name="noheader" argument="-n" type="boolean" truevalue="-n" falsevalue="" checked="false" label="No header." help="Omit any header lines from the output"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
50
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
51 <conditional name="output_type">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
52 <param name="output_format" type="select" multiple="false" label="Output format">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
53 <option value="axt">axt</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
54 <option value="blast">blast</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
55 <option value="blasttab">blasttab</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
56 <option value="chain">chain</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
57 <option value="html">html</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
58 <option value="psl" selected="true">psl</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
59 <option value="sam">sam</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
60 <option value="tab">tab</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
61 </param>
8
bd3a1cc88f0a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 4568799de240022f4058ec1602e08f536916e2af"
iuc
parents: 7
diff changeset
62 <when value="axt"/>
0
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
63 <when value="blast">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
64 <param argument="-l" type="integer" value="60" label="Line length"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
65 </when>
8
bd3a1cc88f0a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 4568799de240022f4058ec1602e08f536916e2af"
iuc
parents: 7
diff changeset
66 <when value="blasttab"/>
bd3a1cc88f0a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 4568799de240022f4058ec1602e08f536916e2af"
iuc
parents: 7
diff changeset
67 <when value="chain"/>
0
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
68 <when value="html">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
69 <param argument="-l" type="integer" value="60" label="Line length"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
70 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
71 <when value="psl">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
72 <param name="protein" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="false" label="Protein alignments." />
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
73 <param argument="-j" type="integer" value="1" label="Join neighboring alignments" help="Join neighboring alignments if they are co-linear and separated by at most N letters."/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
74 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
75 <when value="sam">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
76 <conditional name="sam_file">
8
bd3a1cc88f0a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 4568799de240022f4058ec1602e08f536916e2af"
iuc
parents: 7
diff changeset
77 <param name="dictionary" argument="-d" type="select" label="Include dictionary of sequence lengths in sam format">
bd3a1cc88f0a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 4568799de240022f4058ec1602e08f536916e2af"
iuc
parents: 7
diff changeset
78 <option value="-d">Yes</option>
bd3a1cc88f0a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 4568799de240022f4058ec1602e08f536916e2af"
iuc
parents: 7
diff changeset
79 <option value="" selected="true">No</option>
bd3a1cc88f0a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 4568799de240022f4058ec1602e08f536916e2af"
iuc
parents: 7
diff changeset
80 </param>
bd3a1cc88f0a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 4568799de240022f4058ec1602e08f536916e2af"
iuc
parents: 7
diff changeset
81 <when value=""/>
0
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
82 <when value="-d">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
83 <param argument="-f" type="data" format="dict" label="Get a sequence dictionary from DICTFILE" />
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
84 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
85 </conditional>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
86 <param argument="-r" type="text" value="" label="Specify read group information" help="Example: 'ID:1 PL:ILLUMINA SM:mysample'"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
87 </when>
8
bd3a1cc88f0a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 4568799de240022f4058ec1602e08f536916e2af"
iuc
parents: 7
diff changeset
88 <when value="tab"/>
0
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
89 </conditional>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
90 </section>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
91 </inputs>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
92
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
93 <outputs>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
94 <data format="maf" name="outfile" label="${on_string} to ${maf_convert.output_type.output_format}">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
95 <change_format>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
96 <when input="maf_convert.output_type.output_format" value="axt" format="axt" />
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
97 <when input="maf_convert.output_type.output_format" value="blast" format="blastxml" />
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
98 <when input="maf_convert.output_type.output_format" value="blasttab" format="blastxml" />
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
99 <when input="maf_convert.output_type.output_format" value="chain" format="txt" />
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
100 <when input="maf_convert.output_type.output_format" value="html" format="html" />
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
101 <when input="maf_convert.output_type.output_format" value="psl" format="tabular" />
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
102 <when input="maf_convert.output_type.output_format" value="sam" format="sam" />
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
103 <when input="maf_convert.output_type.output_format" value="tab" format="tabular" />
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
104 </change_format>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
105 </data>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
106 </outputs>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
107
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
108 <tests>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
109 <test>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
110 <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
111 <section name="maf_convert">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
112 <conditional name="output_type">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
113 <param name="output_format" value="axt"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
114 </conditional>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
115 </section>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
116 <output name="outfile" file="outfile_convert.axt"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
117 </test>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
118 <test>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
119 <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
120 <section name="maf_convert">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
121 <conditional name="output_type">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
122 <param name="output_format" value="blast"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
123 </conditional>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
124 </section>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
125 <output name="outfile" file="outfile_convert.blast"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
126 </test>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
127 <test>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
128 <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
129 <section name="maf_convert">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
130 <conditional name="output_type">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
131 <param name="output_format" value="html"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
132 </conditional>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
133 </section>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
134 <output name="outfile" file="outfile_convert.html"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
135 </test>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
136 <test>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
137 <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
138 <section name="maf_convert">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
139 <conditional name="output_type">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
140 <param name="output_format" value="tab"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
141 </conditional>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
142 </section>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
143 <output name="outfile" file="outfile_convert.tab"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
144 </test>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
145 </tests>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
146
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
147 <help><![CDATA[
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
148 This script reads alignments in maf format, and writes them in another format. It can write them in these formats: axt, blast, blasttab, chain, html, psl, sam, tab.
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
149 ]]></help>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
150 <citations><expand macro="citations"/></citations>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
151 </tool>