/tools/emboss_5/emboss_einverted.xml
https://bitbucket.org/h_morita_dbcls/galaxy-central · XML · 49 lines · 45 code · 4 blank · 0 comment · 0 complexity · 33c7f16d7050bb725685d1c13b65c0b2 MD5 · raw file
- <tool id="EMBOSS: einverted28" name="einverted" version="5.0.0">
- <description>Finds DNA inverted repeats</description>
- <command>einverted -sequence $input1 -outfile $out_file1 -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command>
- <inputs>
- <param format="fasta" name="input1" type="data">
- <label>On query</label>
- </param>
- <param name="gap" size="4" type="text" value="12">
- <label>Gap penalty</label>
- </param>
- <param name="threshold" size="4" type="text" value="50">
- <label>Minimum score threshold</label>
- </param>
- <param name="match" size="4" type="text" value="3">
- <label>Match score</label>
- </param>
- <param name="mismatch" size="4" type="text" value="-4">
- <label>Mismatch score</label>
- </param>
- <param name="maxrepeat" size="4" type="text" value="2000">
- <label>Maximum separation between the start of repeat and the end of the inverted repeat</label>
- </param>
- </inputs>
- <outputs>
- <data format="einverted" name="out_file1" />
- </outputs>
- <tests>
- <test>
- <param name="input1" value="1.fasta"/>
- <param name="gap" value="12"/>
- <param name="threshold" value="50"/>
- <param name="match" value="3"/>
- <param name="mismatch" value="-4"/>
- <param name="maxrepeat" value="2000"/>
- <output name="out_file1" file="emboss_einverted_out.einverted"/>
- </test>
- </tests>
- <help>
- .. class:: warningmark
- The input dataset needs to be sequences.
- -----
- You can view the original documentation here_.
-
- .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/einverted.html
- </help>
- </tool>