Mercurial > repos > iracooke > sixframe_translate
changeset 2:e20c4df2bc28 draft default tip
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 | |
| files | repository_dependencies.xml sixframe_translate.xml tool_dependencies.xml |
| diffstat | 3 files changed, 54 insertions(+), 52 deletions(-) [+] |
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--- a/repository_dependencies.xml Thu Mar 26 19:56:34 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories description="Proteomics datatypes"> - <repository changeset_revision="ac51d9dbfb4d" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> - </repositories>
--- a/sixframe_translate.xml Thu Mar 26 19:56:34 2015 -0400 +++ b/sixframe_translate.xml Tue Oct 20 20:40:02 2015 -0400 @@ -1,55 +1,55 @@ -<tool id="sixframe_translate" name="Generate 6-frame translation" version="1.1.0"> - <requirements> - <container type="docker">iracooke/protk-1.4.1</container> - <requirement type="package" version="1.4">protk</requirement> - </requirements> - - <description>Translates DNA/RNA to protein</description> - - <command> - sixframe.rb $fasta_file -o $output $strip_header $coords - </command> - - - - - <stdio> - <exit_code range="1:" level="fatal" description="Failure" /> - </stdio> +<tool id="sixframe_translate" name="Generate 6-frame translation" version="1.1.1"> + <description>Translates DNA/RNA to protein</description> + <requirements> + <container type="docker">iracooke/protk-1.4.3</container> + <requirement type="package" version="1.4.3">protk</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Failure" /> + </stdio> + <command> + sixframe.rb + $fasta_file + -o $output + $strip_header + $coords + $peptideshaker + --min-len $minlen - <inputs> - <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" /> - <param name="strip_header" type="boolean" label="Strip header info" help="" truevalue="--strip-header" falsevalue="" /> - <param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--coords" falsevalue="" /> - </inputs> - - <outputs> - <data format="fasta" name="output" /> - </outputs> - - <tests> - <test> - <param name="fasta_file" value="small_genome.fasta" format="fasta"/> - <output name="output" format="fasta"> - <assert_contents> - <has_text text="SVQHWFYRFQAGHPRVFCPKNGPRRLW" /> - </assert_contents> - </output> - </test> - </tests> - - - <help> + #if $gffoutput: + --gff + #end if + </command> + <inputs> + <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" /> + <param name="strip_header" type="boolean" label="Strip header info" help="" truevalue="--strip-header" falsevalue="" /> + <param name="gffoutput" type="boolean" label="Produce gff instead of fasta" help="" truevalue="true" falsevalue="false" /> + <param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--coords" falsevalue="" /> + <param name="peptideshaker" type="boolean" label="Format fasta entries for PeptideShaker" help="" truevalue="--peptideshaker" falsevalue="" /> + <param name="minlen" type="integer" value="20" min="1" label="Minimum Peptide Length"/> + </inputs> + <outputs> + <data format="fasta" name="output"> + <change_format> + <when input="gffoutput" value="true" format="gff3" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="fasta_file" value="small_genome.fasta" format="fasta"/> + <output name="output" format="fasta"> + <assert_contents> + <has_text text="SVQHWFYRFQAGHPRVFCPKNGPRRLW" /> + </assert_contents> + </output> + </test> + </tests> + <help> **What it does** Generates 6 frame translations suitable for proteogenomics workflows ----- - -**References** - - - </help> - + </help> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Oct 20 20:40:02 2015 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="protk" version="1.4.3"> + <repository changeset_revision="74bf855be117" name="package_protk_1_4_3" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>