Mercurial > repos > peterjc > seq_select_by_id
changeset 12:9e9e3b860aa0 draft
Uploaded v0.0.7e, depend on Biopython 1.62, tabs to spaces in XML
| author | peterjc |
|---|---|
| date | Fri, 27 Sep 2013 06:14:51 -0400 |
| parents | 726dcfa94b2c |
| children | bedfe8f3d3fb |
| files | tools/seq_select_by_id/repository_dependencies.xml tools/seq_select_by_id/seq_select_by_id.xml |
| diffstat | 2 files changed, 42 insertions(+), 43 deletions(-) [+] |
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--- a/tools/seq_select_by_id/repository_dependencies.xml Thu Sep 26 10:09:17 2013 -0400 +++ b/tools/seq_select_by_id/repository_dependencies.xml Fri Sep 27 06:14:51 2013 -0400 @@ -2,5 +2,5 @@ <repositories description="This requires Biopython as a dependency."> <!-- Leave out the tool shed and revision to get the current tool shed and latest revision at the time of upload --> -<repository changeset_revision="2f6c871cfa35" name="package_biopython_1_61" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" /> +<repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </repositories>
--- a/tools/seq_select_by_id/seq_select_by_id.xml Thu Sep 26 10:09:17 2013 -0400 +++ b/tools/seq_select_by_id/seq_select_by_id.xml Fri Sep 27 06:14:51 2013 -0400 @@ -1,46 +1,45 @@ <tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.6"> - <description>from a tabular file</description> - <requirements> - <requirement type="package" version="1.61">biopython</requirement> - <requirement type="python-module">Bio</requirement> - </requirements> - <version_command interpreter="python">seq_select_by_id.py --version</version_command> - <command interpreter="python"> + <description>from a tabular file</description> + <requirements> + <requirement type="package" version="1.62">biopython</requirement> + <requirement type="python-module">Bio</requirement> + </requirements> + <version_command interpreter="python">seq_select_by_id.py --version</version_command> + <command interpreter="python"> seq_select_by_id.py $input_tabular $column $input_file $input_file.ext $output_file - </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <inputs> - <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file to select from" help="FASTA, QUAL, FASTQ, or SFF format." /> - <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> - <param name="column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing sequence identifiers"/> - </inputs> - <outputs> - <data name="output_file" format="fasta" label="Selected sequences"> - <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> - <change_format> - <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> - <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> - <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> - <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> - <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> - <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> - </change_format> - </data> - </outputs> - <tests> - <test> - <param name="input_file" value="k12_ten_proteins.fasta" ftype="fasta" /> - <param name="input_tabular" value="k12_hypothetical.tabular" ftype="tabular" /> - <param name="column" value="1" /> - <output name="output_file" file="k12_hypothetical.fasta" ftype="fasta" /> - </test> - </tests> - <help> - + </command> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <inputs> + <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file to select from" help="FASTA, QUAL, FASTQ, or SFF format." /> + <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> + <param name="column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing sequence identifiers"/> + </inputs> + <outputs> + <data name="output_file" format="fasta" label="Selected sequences"> + <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> + <change_format> + <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> + <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> + <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> + <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> + <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> + <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="input_file" value="k12_ten_proteins.fasta" ftype="fasta" /> + <param name="input_tabular" value="k12_hypothetical.tabular" ftype="tabular" /> + <param name="column" value="1" /> + <output name="output_file" file="k12_hypothetical.fasta" ftype="fasta" /> + </test> + </tests> + <help> **What it does** Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a @@ -69,5 +68,5 @@ This tool is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id - </help> + </help> </tool>