| Previous changeset 0:75cedeb179aa (2015-11-02) Next changeset 2:ea2f686dfd4a (2015-11-02) |
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vcf_to_snp.xml |
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| diff -r 75cedeb179aa -r 032d2c8cf8ae vcf_to_snp.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcf_to_snp.xml Mon Nov 02 12:45:32 2015 -0500 |
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| @@ -0,0 +1,55 @@ +<tool id="vcf_snp" name="vcf to snp" version="0.1"> + <description>vcf to snp for fasta</description> + <requirements> + <!-- Should just use the filter snp that's installed in the path --> + + </requirements> + +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +## ! We only have a simple single command here. + + <command interpreter="python"> + vcf_snp.py + -s ${vcf} + -o output.txt; + cut -f1 output.txt > header.txt | cut -f2- output.txt > seq.txt; + cat seq.txt | sed 's/[[:blank:]]//g' >seq2.txt; + paste header.txt seq2.txt >tab.txt; + + + </command> + + <inputs> + <param name="vcf" type="data" label="vcf" help=""/> + + </inputs> + + <outputs> + <data format="tabular" name="output_file" label="${vcf}" from_work_dir="tab.txt"> + </data> + </outputs> + + <tests> + <!-- Empty --> + </tests> + + <help> + +.. class:: infomark + +**What it does** + +Transforms a vcf into a snp tab file + +------------- + +.. class:: infomark + +**Tool Author** + +Brigida Rusconi + + + </help> +</tool> \ No newline at end of file |