Mercurial > repos > greg > ensure_synced
diff ensure_synced.xml @ 0:9180906544b6 draft
Uploaded
author | greg |
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date | Thu, 15 Aug 2019 10:37:49 -0400 |
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children | 281f38df3c58 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ensure_synced.xml Thu Aug 15 10:37:49 2019 -0400 @@ -0,0 +1,40 @@ +<tool id="ensure_synced" name="Ensure synchronized" version="1.0.0"> + <description>analysis components</description> + <command detect_errors="exit_code"><![CDATA[ +#set affy_ids_from_file = 'affy_ids_from_file.txt' +grep "#CHROM" $input > test.head && +tr '\t' '\n' < test.head > $affy_ids_from_file +python '$__tool_directory__/ensure_synced.py' +--database_connection_string '$__app__.config.corals_database_connection' +--affy_ids_from_file '$affy_ids_from_file' +--output '$output']]></command> + <inputs> + <param name="input" format="vcf" type="data" label="All genotyped samples file"/> + </inputs> + <outputs> + <data name="output" format="txt" label="${tool.name} (process log) on ${on_string}"/> + </outputs> + <tests> + <test> + <!--Testing this tool is a bit difficult at the current time.--> + </test> + </tests> + <help> +**What it does** + +Compares the set of Affymetrix id strings contained within a selected VCF file with the set of Affymetrix ids contained +in the affy_id column of the sample table in the corals (stag) database for all samples not in a failed state. If these +sets are equivalent, the file and the database are considered to be in sync with each other. + </help> + <citations> + <citation type="bibtex"> + @misc{None, + journal = {None}, + author = {Baums I}, + title = {Manuscript in preparation}, + year = {None}, + url = {http://baumslab.org} + </citation> + </citations> +</tool> +