Mercurial > repos > devteam > clustalw
annotate rgClustalw.xml @ 1:ce785326df6e draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:14:40 -0400 |
| parents | de3662385a52 |
| children | bed27b5c0f63 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="clustalw" name="ClustalW" version="0.1"> |
| 2 <requirements> | |
| 3 <requirement type="package" version="2.1">clustalw2</requirement> | |
| 4 </requirements> | |
| 5 <description>multiple sequence alignment program for DNA or proteins</description> | |
| 6 <command interpreter="python"> | |
| 7 rgClustalw.py -i "$input" -o "$output" -s "$out_order" -l "$outlog" -t "$outname" -d "$dnarna" | |
| 8 #if ($range.mode=="part") | |
| 9 -b "$range.seq_range_start" -e "$range.seq_range_end" | |
| 10 #end if | |
| 11 #if ($outcontrol.outform=="clustal") | |
| 12 -f "CLUSTAL" | |
| 13 #if ($outcontrol.out_seqnos=="ON") | |
| 14 -q "ON" | |
| 15 #end if | |
| 16 #end if | |
| 17 #if ($outcontrol.outform=="phylip") | |
| 18 -f "PHYLIP" | |
| 19 #end if | |
| 20 #if ($outcontrol.outform=="fasta") | |
| 21 -f "FASTA" | |
| 22 #end if | |
| 23 </command> | |
| 24 <inputs> | |
| 25 <page> | |
| 26 <param format="fasta" name="input" type="data" label="Fasta File" /> | |
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27 <param name="outname" label="Name for output files to make it easy to remember what you did" type="text" value="Clustal_run" /> |
| 0 | 28 <param name="dnarna" type="select" label="Data Type"> |
| 29 <option value="DNA" selected="True">DNA nucleotide sequences</option> | |
| 30 <option value="PROTEIN">Protein sequences</option> | |
| 31 </param> | |
| 32 <conditional name="outcontrol"> | |
| 33 <param name="outform" type="select" label="Output alignment format"> | |
| 34 <option value="clustal" selected="True">Native Clustal output format</option> | |
| 35 <option value="phylip">Phylip format</option> | |
| 36 <option value="fasta">Fasta format</option> | |
| 37 </param> | |
| 38 <when value="fasta" /> | |
| 39 <when value="phylip" /> | |
| 40 <when value="clustal"> | |
| 41 <param name="out_seqnos" type="select" label="Show residue numbers in clustal format output"> | |
| 42 <option value="ON">yes</option> | |
| 43 <option value="OFF" selected="true">no</option> | |
| 44 </param> | |
| 45 </when> | |
| 46 </conditional> | |
| 47 <param name="out_order" type="select" label="Output Order"> | |
| 48 <option value="ALIGNED">aligned</option> | |
| 49 <option value="INPUT">same order as input file</option> | |
| 50 </param> | |
| 51 | |
| 52 <conditional name="range"> | |
| 53 <param name="mode" type="select" label="Output complete alignment (or specify part to output)"> | |
| 54 <option value="complete">complete alignment</option> | |
| 55 <option value="part">only part of the alignment</option> | |
| 56 </param> | |
| 57 <when value="complete"> | |
| 58 </when> | |
| 59 <when value="part"> | |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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60 <param name="seq_range_start" type="integer" value="1" label="start point" help="sequence range to write"> |
| 0 | 61 </param> |
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ce785326df6e
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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62 <param name="seq_range_end" type="integer" value="99999" label="end point" > |
| 0 | 63 </param> |
| 64 </when> | |
| 65 </conditional> | |
| 66 </page> | |
| 67 </inputs> | |
| 68 <outputs> | |
| 69 <data format="clustal" name="output" label="${outname}_output.${outcontrol.outform}"> | |
| 70 <change_format> | |
| 71 <when input="outcontrol.outform" value="phylip" format="phylip" /> | |
| 72 <when input="outcontrol.outform" value="fasta" format="fasta" /> | |
| 73 </change_format> | |
| 74 </data> | |
| 75 <data format="txt" name="outlog" label="${outname}_clustal_log.txt"/> | |
| 76 </outputs> | |
| 77 <tests> | |
| 78 <test> | |
| 79 <param name="input" value="rgClustal_testin.fasta" /> | |
| 80 <param name="outname" value="" /> | |
| 81 <param name="outform" value="fasta" /> | |
| 82 <param name="dnarna" value="DNA" /> | |
| 83 <param name="mode" value="complete" /> | |
| 84 <param name="out_order" value="ALIGNED" /> | |
| 85 <output name="output" file="rgClustal_testout.fasta" ftype="fasta" /> | |
| 86 <output name="outlog" file="rgClustal_testout.log" ftype="txt" lines_diff="5" /> | |
| 87 </test> | |
| 88 </tests> | |
| 89 <help> | |
| 90 | |
| 91 **Note** | |
| 92 | |
| 93 This tool allows you to run a multiple sequence alignment with ClustalW2 (see Clustsrc_) using the default options. | |
| 94 | |
| 95 For a tutorial introduction, see ClustalW2_ | |
| 96 | |
| 97 You can align DNA or protein sequences in the input file which should be multiple sequences to be aligned in a fasta file | |
| 98 | |
| 99 A log will be output to your history showing the output Clustal would normally write to standard output. | |
| 100 | |
| 101 The alignments will appear as a clustal format file or optionally, as phylip or fasta format files in your history. If you choose fasta as | |
| 102 the output format, you can create a 'Logo' image using the Sequence Logo tool. | |
| 103 | |
| 104 If Clustal format is chosen, you have the option of adding basepair counts to the output | |
| 105 | |
| 106 A subsequence of the alignment can be output by setting the Output complete parameter to "Partial" and defining the offset and end of the subsequence to be output | |
| 107 | |
| 108 ---- | |
| 109 | |
| 110 **Attribution** | |
| 111 | |
| 112 Clustal attribution and associated documentation are available at Clustsrc_ | |
| 113 | |
| 114 The first iteration of this Galaxy wrapper was written by Hans-Rudolf Hotz - see Clustfirst_ | |
| 115 | |
| 116 It was modified by Ross Lazarus for the rgenetics project - tests and some additional parameters were added | |
| 117 | |
| 118 This wrapper is released licensed under the LGPL_ | |
| 119 | |
| 120 .. _ClustalW2: http://www.ebi.ac.uk/2can/tutorials/protein/clustalw.html | |
| 121 | |
| 122 .. _Clustsrc: http://www.clustal.org | |
| 123 | |
| 124 .. _Clustfirst: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html | |
| 125 | |
| 126 .. _LGPL: http://www.gnu.org/copyleft/lesser.html | |
| 127 | |
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128 </help> |
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129 <citations> |
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130 <citation type="doi">10.1093/bioinformatics/btm404</citation> |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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131 </citations> |
| 0 | 132 </tool> |
| 133 |