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comparison emboss_transeq.xml @ 13:d5c3794bd246 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
author iuc
date Mon, 23 Apr 2018 13:04:47 -0400
parents 0e2484b6829b
children 27c43fb015f0
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12:ace31bbde4c0 13:d5c3794bd246
1 <tool id="EMBOSS: transeq101" name="transeq" version="5.0.0"> 1 <tool id="EMBOSS: transeq101" name="transeq" version="5.0.0">
2 <description>Translate nucleic acid sequences</description> 2 <description>Translate nucleic acid sequences</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" /> 7 <code file="emboss_format_corrector.py" />
8 <command><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 transeq 9 transeq
10 -sequence '$input1' 10 -sequence '$input1'
11 -outseq '$out_file1' 11 -outseq '$out_file1'
12 -frame $frame 12 -frame $frame
13 -table $table 13 -table $table
14 #if str($regions).strip(): 14 #if str($regions).strip():
15 -regions '$regions' 15 -regions '$regions'
16 #end if 16 #end if
17 -trim $trim 17 -trim $trim
18 -clean $clean 18 -clean $clean
19 -alternative $alternative 19 -alternative $alternative
20 -osformat2 '$out_format1' 20 -osformat2 '$out_format1'
21 -auto 21 -auto
22 ]]> 22 ]]></command>
23 </command> 23 <inputs>
24 <inputs> 24 <param name="input1" argument="-sequence" type="data" format="fasta" label="Sequences" />
25 <param name="input1" type="data" format="fasta" label="Sequences" /> 25 <param argument="-frame" type="select" label="Frame(s) to translate">
26 <param name="frame" type="select" label="Frame(s) to translate"> 26 <option value="1">Frame 1</option>
27 <option value="1">Frame 1</option> 27 <option value="2">Frame 2</option>
28 <option value="2">Frame 2</option> 28 <option value="3">Frame 3</option>
29 <option value="3">Frame 3</option> 29 <option value="F">Forward three frames</option>
30 <option value="F">Forward three frames</option> 30 <option value="-1">Frame -1</option>
31 <option value="-1">Frame -1</option> 31 <option value="-2">Frame -2</option>
32 <option value="-2">Frame -2</option> 32 <option value="-3">Frame -3</option>
33 <option value="-3">Frame -3</option> 33 <option value="R">Reverse three frames</option>
34 <option value="R">Reverse three frames</option> 34 <option value="6">All six frames</option>
35 <option value="6">All six frames</option> 35 </param>
36 </param> 36 <param argument="-table" type="select" label="Code to use">
37 <param name="table" type="select" label="Code to use"> 37 <option value="0">Standard</option>
38 <option value="0">Standard</option> 38 <option value="1">Standard (with alternative initiation codons)</option>
39 <option value="1">Standard (with alternative initiation codons)</option> 39 <option value="2">Vertebrate Mitochondrial</option>
40 <option value="2">Vertebrate Mitochondrial</option> 40 <option value="3">Yeast Mitochondrial</option>
41 <option value="3">Yeast Mitochondrial</option> 41 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
42 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> 42 <option value="5">Invertebrate Mitochondrial</option>
43 <option value="5">Invertebrate Mitochondrial</option> 43 <option value="6">Ciliate Macronuclear and Dasycladacean</option>
44 <option value="6">Ciliate Macronuclear and Dasycladacean</option> 44 <option value="9">Echinoderm Mitochondrial</option>
45 <option value="9">Echinoderm Mitochondrial</option> 45 <option value="10">Euplotid Nuclear</option>
46 <option value="10">Euplotid Nuclear</option> 46 <option value="11">Bacterial</option>
47 <option value="11">Bacterial</option> 47 <option value="12">Alternative Yeast Nuclear</option>
48 <option value="12">Alternative Yeast Nuclear</option> 48 <option value="13">Ascidian Mitochondrial</option>
49 <option value="13">Ascidian Mitochondrial</option> 49 <option value="14">Flatworm Mitochondrial</option>
50 <option value="14">Flatworm Mitochondrial</option> 50 <option value="15">Blepharisma Macronuclear</option>
51 <option value="15">Blepharisma Macronuclear</option> 51 <option value="16">Chlorophycean Mitochondrial</option>
52 <option value="16">Chlorophycean Mitochondrial</option> 52 <option value="21">Trematode Mitochondrial</option>
53 <option value="21">Trematode Mitochondrial</option> 53 <option value="22">Scenedesmus obliquus</option>
54 <option value="22">Scenedesmus obliquus</option> 54 <option value="23">Thraustochytrium Mitochondrial</option>
55 <option value="23">Thraustochytrium Mitochondrial</option> 55 </param>
56 </param> 56 <param argument="-regions" type="text" value="" label="Regions to translate" />
57 <param name="regions" type="text" value="" label="Regions to translate" /> 57 <param argument="-trim" type="select" label="Remove all 'X' and '*' characters from the right end of the translation">
58 <param name="trim" type="select" label="Remove all 'X' and '*' characters from the right end of the translation"> 58 <option value="no">No</option>
59 <option value="no">No</option> 59 <option value="yes">Yes</option>
60 <option value="yes">Yes</option> 60 </param>
61 </param> 61 <param argument="-clean" type="select" label="Change all STOP codon positions from the '*' character to 'X'">
62 <param name="clean" type="select" label="Change all STOP codon positions from the '*' character to 'X'"> 62 <option value="no">No</option>
63 <option value="no">No</option> 63 <option value="yes">Yes</option>
64 <option value="yes">Yes</option> 64 </param>
65 </param> 65 <param argument="-alternative" type="select" label="Define frame '-1' as using the set of codons starting with the last codon of the sequence">
66 <param name="alternative" type="select" label="Define frame '-1' as using the set of codons starting with the last codon of the sequence"> 66 <option value="no">No</option>
67 <option value="no">No</option> 67 <option value="yes">Yes</option>
68 <option value="yes">Yes</option> 68 </param>
69 </param> 69 <param name="out_format1" argument="-osformat2" type="select" label="Output sequence file format">
70 <param name="out_format1" type="select" label="Output sequence file format"> 70 <option value="fasta">FASTA (m)</option>
71 <option value="fasta">FASTA (m)</option> 71 <option value="acedb">ACeDB (m)</option>
72 <option value="acedb">ACeDB (m)</option> 72 <option value="asn1">ASN.1 (m)</option>
73 <option value="asn1">ASN.1 (m)</option> 73 <option value="clustal">Clustal (m)</option>
74 <option value="clustal">Clustal (m)</option> 74 <option value="codata">CODATA (m)</option>
75 <option value="codata">CODATA (m)</option> 75 <option value="embl">EMBL (m)</option>
76 <option value="embl">EMBL (m)</option> 76 <option value="fitch">Fitch (m)</option>
77 <option value="fitch">Fitch (m)</option> 77 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
78 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option> 78 <option value="genbank">GENBANK (m)</option>
79 <option value="genbank">GENBANK (m)</option> 79 <option value="gff">GFF (m)</option>
80 <option value="gff">GFF (m)</option> 80 <option value="hennig86">Hennig86 (m)</option>
81 <option value="hennig86">Hennig86 (m)</option> 81 <option value="ig">Intelligenetics (m)</option>
82 <option value="ig">Intelligenetics (m)</option> 82 <option value="jackknifer">Jackknifer (m)</option>
83 <option value="jackknifer">Jackknifer (m)</option> 83 <option value="jackknifernon">Jackknifernon (m)</option>
84 <option value="jackknifernon">Jackknifernon (m)</option> 84 <option value="mega">Mega (m)</option>
85 <option value="mega">Mega (m)</option> 85 <option value="meganon">Meganon (m)</option>
86 <option value="meganon">Meganon (m)</option> 86 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
87 <option value="msf">Wisconsin Package GCG's MSF (m)</option> 87 <option value="pir">NBRF (PIR) (m)</option>
88 <option value="pir">NBRF (PIR) (m)</option> 88 <option value="ncbi">NCBI style FASTA (m)</option>
89 <option value="ncbi">NCBI style FASTA (m)</option> 89 <option value="nexus">Nexus/PAUP (m)</option>
90 <option value="nexus">Nexus/PAUP (m)</option> 90 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
91 <option value="nexusnon">Nexusnon/PAUPnon (m)</option> 91 <option value="phylip">PHYLIP interleaved (m)</option>
92 <option value="phylip">PHYLIP interleaved (m)</option> 92 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
93 <option value="phylipnon">PHYLIP non-interleaved (m)</option> 93 <option value="selex">SELEX (m)</option>
94 <option value="selex">SELEX (m)</option> 94 <option value="staden">Staden (s)</option>
95 <option value="staden">Staden (s)</option> 95 <option value="strider">DNA strider (m)</option>
96 <option value="strider">DNA strider (m)</option> 96 <option value="swiss">SwisProt entry (m)</option>
97 <option value="swiss">SwisProt entry (m)</option> 97 <option value="text">Plain sequence (s)</option>
98 <option value="text">Plain sequence (s)</option> 98 <option value="treecon">Treecon (m)</option>
99 <option value="treecon">Treecon (m)</option> 99 </param>
100 </param> 100 </inputs>
101 </inputs> 101 <outputs>
102 <outputs> 102 <data name="out_file1" format="fasta" />
103 <data name="out_file1" format="fasta" /> 103 </outputs>
104 </outputs> 104 <tests>
105 <tests> 105 <test>
106 <test> 106 <param name="input1" value="2.fasta"/>
107 <param name="input1" value="2.fasta"/> 107 <param name="frame" value="1"/>
108 <param name="frame" value="1"/> 108 <param name="table" value="0"/>
109 <param name="table" value="0"/> 109 <param name="regions" value=""/>
110 <param name="regions" value=""/> 110 <param name="trim" value="no"/>
111 <param name="trim" value="no"/> 111 <param name="clean" value="no"/>
112 <param name="clean" value="no"/> 112 <param name="alternative" value="no"/>
113 <param name="alternative" value="no"/> 113 <param name="out_format1" value="fasta"/>
114 <param name="out_format1" value="fasta"/> 114 <output name="out_file1" file="emboss_transeq_out.fasta"/>
115 <output name="out_file1" file="emboss_transeq_out.fasta"/> 115 </test>
116 </test> 116 </tests>
117 </tests> 117 <help><![CDATA[
118 <help>
119 .. class:: warningmark 118 .. class:: warningmark
120 119
121 The input dataset needs to be sequences. 120 The input dataset needs to be sequences.
122 121
123 ----- 122 -----
124 123
125 You can view the original documentation here_. 124 You can view the original documentation here_.
126 125
127 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/transeq.html 126 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/transeq.html
128 </help> 127 ]]></help>
129 <expand macro="citations" /> 128 <expand macro="citations" />
130 </tool> 129 </tool>