Mercurial > repos > iuc > last
comparison maf-convert.xml @ 0:9a7e91fc6562 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
author | iuc |
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date | Wed, 17 Jun 2020 14:50:21 -0400 |
parents | |
children | 8705e0d74a0f |
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-1:000000000000 | 0:9a7e91fc6562 |
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1 <tool id="last_maf_convert" name="MAF-convert" version="@LAST_CONDA_VERSION@+galaxy0" profile="18.01"> | |
2 | |
3 <description>read MAF-format alignments and write them in another format.</description> | |
4 | |
5 <macros> | |
6 <import>macros_last.xml</import> | |
7 </macros> | |
8 | |
9 <requirements> | |
10 <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement> | |
11 </requirements> | |
12 | |
13 <command detect_errors="exit_code"><![CDATA[ | |
14 maf-convert | |
15 | |
16 $maf_convert.output_type.output_format | |
17 | |
18 $maf_convert.noheader | |
19 | |
20 #if $maf_convert.output_type.output_format == 'psl' | |
21 $maf_convert.output_type.protein | |
22 -j $maf_convert.output_type.j | |
23 #end if | |
24 | |
25 #if $maf_convert.output_type.output_format == 'sam' | |
26 $maf_convert.output_type.sam_file.dictionary | |
27 #if $maf_convert.output_type.sam_file.dictionary == '-d' | |
28 -f $maf_convert.output_type.sam_file.f | |
29 #end if | |
30 #if $maf_convert.output_type.readfile != '' | |
31 -r $maf_convert.output_type.r | |
32 #end if | |
33 #end if | |
34 | |
35 #if $maf_convert.output_type.output_format == 'blast' or $maf_convert.output_type.output_format == 'html' | |
36 -l $maf_convert.output_type.l | |
37 #end if | |
38 | |
39 '$maf_file' | |
40 | |
41 > '$outfile' | |
42 | |
43 ]]></command> | |
44 <inputs> | |
45 <param name="maf_file" type="data" format="maf" label="MAF file to convert" /> | |
46 | |
47 <section name="maf_convert" title="MAF-convert arguments" expanded="true"> | |
48 | |
49 <param name="noheader" argument="-n" type="boolean" truevalue="-n" falsevalue="" checked="false" label="No header." help="Omit any header lines from the output"/> | |
50 | |
51 <conditional name="output_type"> | |
52 <param name="output_format" type="select" multiple="false" label="Output format"> | |
53 <option value="axt">axt</option> | |
54 <option value="blast">blast</option> | |
55 <option value="blasttab">blasttab</option> | |
56 <option value="chain">chain</option> | |
57 <option value="html">html</option> | |
58 <option value="psl" selected="true">psl</option> | |
59 <option value="sam">sam</option> | |
60 <option value="tab">tab</option> | |
61 </param> | |
62 <when value="blast"> | |
63 <param argument="-l" type="integer" value="60" label="Line length"/> | |
64 </when> | |
65 <when value="html"> | |
66 <param argument="-l" type="integer" value="60" label="Line length"/> | |
67 </when> | |
68 <when value="psl"> | |
69 <param name="protein" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="false" label="Protein alignments." /> | |
70 <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."/> | |
71 </when> | |
72 <when value="sam"> | |
73 <conditional name="sam_file"> | |
74 <param name="dictionary" argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false" label="Include dictionary of sequence lengths in sam format"/> | |
75 <when value="-d"> | |
76 <param argument="-f" type="data" format="dict" label="Get a sequence dictionary from DICTFILE" /> | |
77 </when> | |
78 </conditional> | |
79 <param argument="-r" type="text" value="" label="Specify read group information" help="Example: 'ID:1 PL:ILLUMINA SM:mysample'"/> | |
80 </when> | |
81 </conditional> | |
82 </section> | |
83 </inputs> | |
84 | |
85 <outputs> | |
86 <data format="maf" name="outfile" label="${on_string} to ${maf_convert.output_type.output_format}"> | |
87 <change_format> | |
88 <when input="maf_convert.output_type.output_format" value="axt" format="axt" /> | |
89 <when input="maf_convert.output_type.output_format" value="blast" format="blastxml" /> | |
90 <when input="maf_convert.output_type.output_format" value="blasttab" format="blastxml" /> | |
91 <when input="maf_convert.output_type.output_format" value="chain" format="txt" /> | |
92 <when input="maf_convert.output_type.output_format" value="html" format="html" /> | |
93 <when input="maf_convert.output_type.output_format" value="psl" format="tabular" /> | |
94 <when input="maf_convert.output_type.output_format" value="sam" format="sam" /> | |
95 <when input="maf_convert.output_type.output_format" value="tab" format="tabular" /> | |
96 </change_format> | |
97 </data> | |
98 </outputs> | |
99 | |
100 <tests> | |
101 <test> | |
102 <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/> | |
103 <section name="maf_convert"> | |
104 <conditional name="output_type"> | |
105 <param name="output_format" value="axt"/> | |
106 </conditional> | |
107 </section> | |
108 <output name="outfile" file="outfile_convert.axt"/> | |
109 </test> | |
110 <test> | |
111 <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/> | |
112 <section name="maf_convert"> | |
113 <conditional name="output_type"> | |
114 <param name="output_format" value="blast"/> | |
115 </conditional> | |
116 </section> | |
117 <output name="outfile" file="outfile_convert.blast"/> | |
118 </test> | |
119 <test> | |
120 <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/> | |
121 <section name="maf_convert"> | |
122 <conditional name="output_type"> | |
123 <param name="output_format" value="html"/> | |
124 </conditional> | |
125 </section> | |
126 <output name="outfile" file="outfile_convert.html"/> | |
127 </test> | |
128 <test> | |
129 <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/> | |
130 <section name="maf_convert"> | |
131 <conditional name="output_type"> | |
132 <param name="output_format" value="tab"/> | |
133 </conditional> | |
134 </section> | |
135 <output name="outfile" file="outfile_convert.tab"/> | |
136 </test> | |
137 </tests> | |
138 | |
139 <help><![CDATA[ | |
140 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. | |
141 ]]></help> | |
142 <citations><expand macro="citations"/></citations> | |
143 </tool> |