Mercurial > repos > peterjc > mummer
comparison tools/mummer/mummer.xml @ 6:d9f3d4779507 draft default tip
v0.0.7 stricter error checking; record gnuplot version
| author | peterjc |
|---|---|
| date | Wed, 10 May 2017 12:14:49 -0400 |
| parents | 683ea5ab0008 |
| children |
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| 5:683ea5ab0008 | 6:d9f3d4779507 |
|---|---|
| 1 <tool id="mummerplot_wrapper" name="MUMmer dotplot" version="0.0.6"> | 1 <tool id="mummerplot_wrapper" name="MUMmer dotplot" version="0.0.7"> |
| 2 <description>Combine mummer/nucmer/promer with mummerplot</description> | 2 <description>Combine mummer/nucmer/promer with mummerplot</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <!-- Needs ps2pdf from ghostscript --> | 4 <!-- Needs ps2pdf from ghostscript --> |
| 5 <requirement type="binary">ps2pdf</requirement> | |
| 6 <requirement type="package" version="9.10">ghostscript</requirement> | 5 <requirement type="package" version="9.10">ghostscript</requirement> |
| 7 <!-- Needs mummer, nucmer, promer and mummerplot from MUMmer --> | 6 <!-- Needs mummer, nucmer, promer and mummerplot from MUMmer --> |
| 8 <requirement type="binary">mummer</requirement> | |
| 9 <requirement type="binary">nucmer</requirement> | |
| 10 <requirement type="binary">promer</requirement> | |
| 11 <requirement type="binary">mummerplot</requirement> | |
| 12 <requirement type="package" version="3.23">mummer</requirement> | 7 <requirement type="package" version="3.23">mummer</requirement> |
| 13 <!-- mummerplot needs the gnuplot binary --> | 8 <!-- mummerplot needs the gnuplot binary --> |
| 14 <requirement type="binary">gnuplot</requirement> | |
| 15 <requirement type="package" version="4.6">gnuplot</requirement> | 9 <requirement type="package" version="4.6">gnuplot</requirement> |
| 16 </requirements> | 10 </requirements> |
| 17 <stdio> | 11 <version_command> |
| 18 <!-- Anything other than zero is an error --> | 12 python $__tool_directory__/mummer.py --version |
| 19 <exit_code range="1:" /> | |
| 20 <exit_code range=":-1" /> | |
| 21 </stdio> | |
| 22 <version_command interpreter="python"> | |
| 23 mummer.py --version | |
| 24 </version_command> | 13 </version_command> |
| 25 <command interpreter="python"> | 14 <command detect_errors="aggressive"> |
| 26 mummer.py "$fasta_a" "$fasta_b" $algorithm "$png_output" "$pdf_output" | 15 python $__tool_directory__/mummer.py '$fasta_a' '$fasta_b' $algorithm '$png_output' '$pdf_output' |
| 27 </command> | 16 </command> |
| 28 <inputs> | 17 <inputs> |
| 29 <!-- Galaxy does not have sub-types for protein vs nucletide FASTA --> | 18 <!-- Galaxy does not have sub-types for protein vs nucletide FASTA --> |
| 30 <param name="fasta_a" type="data" format="fasta" | 19 <param name="fasta_a" type="data" format="fasta" |
| 31 label="Species A" | 20 label="Species A" |