Mercurial > repos > iracooke > sixframe_translate

comparison sixframe_translate.xml @ 2:e20c4df2bc28 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/sixframe-translate/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:40:02 -0400
parents 10465e20d9a2
children
comparison
equal deleted inserted replaced
1:10465e20d9a2 2:e20c4df2bc28
1 <tool id="sixframe_translate" name="Generate 6-frame translation" version="1.1.0"> 1 <tool id="sixframe_translate" name="Generate 6-frame translation" version="1.1.1">
2 <requirements> 2 <description>Translates DNA/RNA to protein</description>
3 <container type="docker">iracooke/protk-1.4.1</container> 3 <requirements>
4 <requirement type="package" version="1.4">protk</requirement> 4 <container type="docker">iracooke/protk-1.4.3</container>
5 </requirements> 5 <requirement type="package" version="1.4.3">protk</requirement>
6 </requirements>
7 <stdio>
8 <exit_code range="1:" level="fatal" description="Failure" />
9 </stdio>
10 <command>
11 sixframe.rb
12 $fasta_file
13 -o $output
14 $strip_header
15 $coords
16 $peptideshaker
17 --min-len $minlen
6 18
7 <description>Translates DNA/RNA to protein</description> 19 #if $gffoutput:
8 20 --gff
9 <command> 21 #end if
10 sixframe.rb $fasta_file -o $output $strip_header $coords 22 </command>
11 </command> 23 <inputs>
12 24 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
13 25 <param name="strip_header" type="boolean" label="Strip header info" help="" truevalue="--strip-header" falsevalue="" />
14 26 <param name="gffoutput" type="boolean" label="Produce gff instead of fasta" help="" truevalue="true" falsevalue="false" />
15 27 <param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--coords" falsevalue="" />
16 <stdio> 28 <param name="peptideshaker" type="boolean" label="Format fasta entries for PeptideShaker" help="" truevalue="--peptideshaker" falsevalue="" />
17 <exit_code range="1:" level="fatal" description="Failure" /> 29 <param name="minlen" type="integer" value="20" min="1" label="Minimum Peptide Length"/>
18 </stdio> 30 </inputs>
19 31 <outputs>
20 <inputs> 32 <data format="fasta" name="output">
21 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" /> 33 <change_format>
22 <param name="strip_header" type="boolean" label="Strip header info" help="" truevalue="--strip-header" falsevalue="" /> 34 <when input="gffoutput" value="true" format="gff3" />
23 <param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--coords" falsevalue="" /> 35 </change_format>
24 </inputs> 36 </data>
25 37 </outputs>
26 <outputs> 38 <tests>
27 <data format="fasta" name="output" /> 39 <test>
28 </outputs> 40 <param name="fasta_file" value="small_genome.fasta" format="fasta"/>
29 41 <output name="output" format="fasta">
30 <tests> 42 <assert_contents>
31 <test> 43 <has_text text="SVQHWFYRFQAGHPRVFCPKNGPRRLW" />
32 <param name="fasta_file" value="small_genome.fasta" format="fasta"/> 44 </assert_contents>
33 <output name="output" format="fasta"> 45 </output>
34 <assert_contents> 46 </test>
35 <has_text text="SVQHWFYRFQAGHPRVFCPKNGPRRLW" /> 47 </tests>
36 </assert_contents> 48 <help>
37 </output>
38 </test>
39 </tests>
40
41
42 <help>
43 49
44 **What it does** 50 **What it does**
45 51
46 Generates 6 frame translations suitable for proteogenomics workflows 52 Generates 6 frame translations suitable for proteogenomics workflows
47 53
48 ---- 54 </help>
49
50 **References**
51
52
53 </help>
54
55 </tool> 55 </tool>