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comparison emboss_trimest.xml @ 11:0e2484b6829b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
author iuc
date Mon, 30 Jan 2017 13:27:40 -0500
parents 9b98d3d903c6
children 27c43fb015f0
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10:9b98d3d903c6 11:0e2484b6829b
1 <tool id="EMBOSS: trimest102" name="trimest" version="5.0.0"> 1 <tool id="EMBOSS: trimest102" name="trimest" version="5.0.0.1">
2 <description>Trim poly-A tails off EST sequences</description> 2 <description>Trim poly-A tails off EST sequences</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>trimest -sequence $input1 -outseq $out_file1 -minlength "$minlength" -mismatches "$mismatches" -reverse $reverse -tolower $tolower -fiveprime $fiveprime -osformat2 $out_format1 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>trimest -sequence '$input1' -outseq '$out_file1' -minlength $minlength -mismatches $mismatches -reverse $reverse -tolower $tolower -fiveprime $fiveprime -osformat2 $out_format1
5 -auto</command> 9 -auto</command>
6 <inputs> 10 <inputs>
7 <param format="fasta" name="input1" type="data"> 11 <param name="input1" type="data" format="fasta" label="Sequences" />
8 <label>Sequences</label> 12 <param name="minlength" type="integer" value="4" label="Minimum length that a poly-A (or poly-T) tail must have before it is removed" />
9 </param> 13 <param name="mismatches" type="integer" value="1" label="Number of fewer mismatched non-A bases in a poly-A tail" />
10 <param name="minlength" type="text" value="4"> 14 <param name="reverse" type="select" label="Change the sequence to the forward sense when it is written out">
11 <label>Minimum length that a poly-A (or poly-T) tail must have before it is removed</label>
12 </param>
13 <param name="mismatches" type="text" value="1">
14 <label>Number of fewer mismatched non-A bases in a poly-A tail</label>
15 </param>
16 <param name="reverse" type="select">
17 <label>Change the sequence to the forward sense when it is written out</label>
18 <option value="yes">Yes</option> 15 <option value="yes">Yes</option>
19 <option value="no">No</option> 16 <option value="no">No</option>
20 </param> 17 </param>
21 <param name="tolower" type="select"> 18 <param name="tolower" type="select" label="Mask poly-A by converting to lowercase">
22 <label>Mask poly-A by converting to lowercase</label>
23 <option value="no">No</option> 19 <option value="no">No</option>
24 <option value="yes">Yes</option> 20 <option value="yes">Yes</option>
25 </param> 21 </param>
26 <param name="fiveprime" type="select"> 22 <param name="fiveprime" type="select" label="Inspect 5' end of the sequence for poly-T tails">
27 <label>Inspect 5' end of the sequence for poly-T tails</label>
28 <option value="yes">Yes</option> 23 <option value="yes">Yes</option>
29 <option value="no">No</option> 24 <option value="no">No</option>
30 </param> 25 </param>
31 <param name="out_format1" type="select"> 26 <param name="out_format1" type="select" label="Output sequence file format">
32 <label>Output Sequence File Format</label>
33 <option value="fasta">FASTA (m)</option> 27 <option value="fasta">FASTA (m)</option>
34 <option value="acedb">ACeDB (m)</option> 28 <option value="acedb">ACeDB (m)</option>
35 <option value="asn1">ASN.1 (m)</option> 29 <option value="asn1">ASN.1 (m)</option>
36 <option value="clustal">Clustal (m)</option> 30 <option value="clustal">Clustal (m)</option>
37 <option value="codata">CODATA (m)</option> 31 <option value="codata">CODATA (m)</option>
60 <option value="text">Plain sequence (s)</option> 54 <option value="text">Plain sequence (s)</option>
61 <option value="treecon">Treecon (m)</option> 55 <option value="treecon">Treecon (m)</option>
62 </param> 56 </param>
63 </inputs> 57 </inputs>
64 <outputs> 58 <outputs>
65 <data format="fasta" name="out_file1" /> 59 <data name="out_file1" format="fasta" />
66 </outputs> 60 </outputs>
67 <tests> 61 <tests>
68 <test> 62 <test>
69 <param name="input1" value="2.fasta"/> 63 <param name="input1" value="2.fasta"/>
70 <param name="minlength" value="4"/> 64 <param name="minlength" value="4"/>
74 <param name="fiveprime" value="yes"/> 68 <param name="fiveprime" value="yes"/>
75 <param name="out_format1" value="fasta"/> 69 <param name="out_format1" value="fasta"/>
76 <output name="out_file1" file="emboss_trimest_out.fasta"/> 70 <output name="out_file1" file="emboss_trimest_out.fasta"/>
77 </test> 71 </test>
78 </tests> 72 </tests>
79 <code file="emboss_format_corrector.py" />
80 <help> 73 <help>
81
82 .. class:: warningmark 74 .. class:: warningmark
83 75
84 The input dataset needs to be sequences. 76 The input dataset needs to be sequences.
85 77
86 ----- 78 -----
87 79
88 You can view the original documentation here_. 80 You can view the original documentation here_.
89
90 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/trimest.html
91 81
92 ------ 82 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/trimest.html
93
94 **Citation**
95
96 For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
97
98 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
99 </help> 83 </help>
84 <expand macro="citations" />
100 </tool> 85 </tool>