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comparison maf-convert.xml @ 0:9a7e91fc6562 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
author iuc
date Wed, 17 Jun 2020 14:50:21 -0400
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children 8705e0d74a0f
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-1:000000000000 0:9a7e91fc6562
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>