Mercurial > repos > iracooke > make_protein_decoys
changeset 2:bd4844c664f2 draft default tip
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
| author | iracooke |
|---|---|
| date | Tue, 20 Oct 2015 19:37:19 -0400 |
| parents | 354e820eb485 |
| children | |
| files | make_decoy.xml repository_dependencies.xml tool_dependencies.xml |
| diffstat | 3 files changed, 40 insertions(+), 48 deletions(-) [+] |
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--- a/make_decoy.xml Thu Mar 26 21:27:53 2015 -0400 +++ b/make_decoy.xml Tue Oct 20 19:37:19 2015 -0400 @@ -1,51 +1,41 @@ -<tool id="make_decoy" name="Generate protein decoy sequences" version="1.0.0"> - <requirements> - <container type="docker">iracooke/protk-1.4.1</container> - <requirement type="package" version="1.4">protk</requirement> - </requirements> - - <description> - Generate random protein sequences with the same AA composition as input sequences - </description> - - <command> - make_decoy.rb $fasta_file -o $output -P $prefix_string $append - </command> - - <stdio> - <exit_code range="1:" level="fatal" description="Failure" /> - </stdio> - - <inputs> - <param name="fasta_file" type="data" format="fasta" label="Fasta file contain protein sequences" /> - <param name="prefix_string" help="Prefix String to use for Decoys" type="text" value="decoy_" label="Prefix String" size="20"/> - <param name="append" type="boolean" label="Append input sequences to the generated sequences" help="" truevalue="--append" falsevalue="" /> - </inputs> - - <outputs> - <data format="fasta" name="output" /> - </outputs> - - <tests> - <test> - <param name="fasta_file" value="testdb.fasta" format="fasta"/> - <output name="output" format="fasta"> - <assert_contents> - <has_text text="decoy_rp3" /> - </assert_contents> - </output> - </test> - </tests> - - - - <help> +<tool id="make_decoy" name="Generate protein decoy sequences" version="1.0.1"> + <description> + Generate random protein sequences with the same AA composition as input sequences + </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> + make_decoy.rb $fasta_file -o $output -P $prefix_string $append + </command> + <inputs> + <param name="fasta_file" type="data" format="fasta" label="Fasta file contain protein sequences" /> + <param name="prefix_string" help="Prefix String to use for Decoys" type="text" value="decoy_" label="Prefix String" size="20"/> + <param name="append" type="boolean" label="Append input sequences to the generated sequences" help="" truevalue="--append" falsevalue="" /> + </inputs> + <outputs> + <data format="fasta" name="output" /> + </outputs> + <tests> + <test> + <param name="fasta_file" value="testdb.fasta" format="fasta"/> + <output name="output" format="fasta"> + <assert_contents> + <has_text text="decoy_rp3" /> + </assert_contents> + </output> + </test> + </tests> + <help> **What it does** Generates random protein sequences based on the amino acid composition of a given set of input sequences. To be used for decoy proteomics searches - </help> - + </help> </tool>
--- a/repository_dependencies.xml Thu Mar 26 21:27:53 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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Oct 20 19:37:19 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>