mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Upgrading EMBOSS tools equicktandem, etandem and fuzznuc to version 5.0
This commit is contained in:
Chinmay Rao
@@ -0,0 +1,59 @@
|
||||
<tool id="EMBOSS_equicktandem31" name="equicktandem">
|
||||
<description>Finds tandem repeats</description>
|
||||
<command>equicktandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -maxrepeat $maxrepeat -threshold $threshold -rformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="fasta" name="input1" type="data">
|
||||
<label>Sequence</label>
|
||||
</param>
|
||||
<param name="maxrepeat" size="4" type="text" value="600">
|
||||
<label>Maximum repeat size</label>
|
||||
</param>
|
||||
<param name="threshold" size="4" type="text" value="20">
|
||||
<label>Threshold score</label>
|
||||
</param>
|
||||
<param name="out_format1" type="select">
|
||||
<label>Output Report File Format</label>
|
||||
<option value="table">Table</option>
|
||||
<option value="embl">EMBL</option>
|
||||
<option value="genbank">GENBANK</option>
|
||||
<option value="gff">GFF</option>
|
||||
<option value="pir">PIR</option>
|
||||
<option value="swiss">SwissProt</option>
|
||||
<option value="dbmotif">DbMotif</option>
|
||||
<option value="diffseq">Diffseq</option>
|
||||
<option value="excel">Excel (tab delimited)</option>
|
||||
<option value="feattable">FeatTable</option>
|
||||
<option value="motif">Motif</option>
|
||||
<option value="regions">Regions</option>
|
||||
<option value="seqtable">SeqTable</option>
|
||||
<option value="simple">SRS Simple</option>
|
||||
<option value="srs">SRS</option>
|
||||
<option value="tagseq">TagSeq</option>
|
||||
</param>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data format="table" name="out_file1" />
|
||||
<data format="equicktandem" name="ofile2" />
|
||||
</outputs>
|
||||
<tests>
|
||||
<test>
|
||||
<param name="input1" value="1.fasta"/>
|
||||
<param name="maxrepeat" value="600"/>
|
||||
<param name="threshold" value="20"/>
|
||||
<param name="out_format1" value="table"/>
|
||||
<output name="ofile2" file="emboss_equicktandem_out.equicktandem"/>
|
||||
</test>
|
||||
</tests>
|
||||
<code file="emboss_format_corrector.py" />
|
||||
<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/equicktandem.html
|
||||
</help>
|
||||
</tool>
|
||||
@@ -0,0 +1,77 @@
|
||||
<tool id="EMBOSS_etandem33" name="etandem">
|
||||
<description>Looks for tandem repeats in a nucleotide sequence</description>
|
||||
<command>etandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -minrepeat $minrepeat -maxrepeat $maxrepeat -threshold $threshold -mismatch $mismatch -uniform $uniform -rformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="fasta" name="input1" type="data">
|
||||
<label>Sequence</label>
|
||||
</param>
|
||||
<param name="minrepeat" size="4" type="text" value="10">
|
||||
<label>Minimum repeat size</label>
|
||||
</param>
|
||||
<param name="maxrepeat" size="4" type="text" value="10">
|
||||
<label>Maximum repeat size</label>
|
||||
</param>
|
||||
<param name="threshold" size="4" type="text" value="20">
|
||||
<label>Threshold score</label>
|
||||
</param>
|
||||
<param name="mismatch" type="select">
|
||||
<label>Allow N as a mismatch</label>
|
||||
<option value="no">No</option>
|
||||
<option value="yes">Yes</option>
|
||||
</param>
|
||||
<param name="uniform" type="select">
|
||||
<label>Allow uniform consensus</label>
|
||||
<option value="no">No</option>
|
||||
<option value="yes">Yes</option>
|
||||
</param>
|
||||
<param name="out_format1" type="select">
|
||||
<label>Output Report File Format</label>
|
||||
<option value="table">Table</option>
|
||||
<option value="embl">EMBL</option>
|
||||
<option value="genbank">GENBANK</option>
|
||||
<option value="gff">GFF</option>
|
||||
<option value="pir">PIR</option>
|
||||
<option value="swiss">SwissProt</option>
|
||||
<option value="dbmotif">DbMotif</option>
|
||||
<option value="diffseq">Diffseq</option>
|
||||
<option value="excel">Excel (tab delimited)</option>
|
||||
<option value="feattable">FeatTable</option>
|
||||
<option value="motif">Motif</option>
|
||||
<option value="regions">Regions</option>
|
||||
<option value="seqtable">SeqTable</option>
|
||||
<option value="simple">SRS Simple</option>
|
||||
<option value="srs">SRS</option>
|
||||
<option value="tagseq">TagSeq</option>
|
||||
</param>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data format="etandem" name="out_file1" />
|
||||
<data format="table" name="ofile2" />
|
||||
</outputs>
|
||||
<tests>
|
||||
<test>
|
||||
<param name="input1" value="1.fasta"/>
|
||||
<param name="minrepeat" value="10"/>
|
||||
<param name="maxrepeat" value="10"/>
|
||||
<param name="threshold" value="20"/>
|
||||
<param name="mismatch" value="no"/>
|
||||
<param name="uniform" value="no"/>
|
||||
<param name="out_format1" value="table"/>
|
||||
<output name="ofile2" file="emboss_etandem_out.table"/>
|
||||
</test>
|
||||
</tests>
|
||||
<code file="emboss_format_corrector.py" />
|
||||
<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/etandem.html
|
||||
</help>
|
||||
</tool>
|
||||
|
||||
|
||||
@@ -0,0 +1,66 @@
|
||||
<tool id="EMBOSS_fuzznuc37" name="fuzznuc">
|
||||
<description>Nucleic acid pattern search</description>
|
||||
<command>fuzznuc -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="fasta" name="input1" type="data">
|
||||
<label>Sequences</label>
|
||||
</param>
|
||||
<param name="pattern" size="5" type="text" value="">
|
||||
<label>Search pattern</label>
|
||||
</param>
|
||||
<param name="mismatch" size="5" type="text" value="0">
|
||||
<label>Number of mismatches</label>
|
||||
</param>
|
||||
<param name="complement" type="select">
|
||||
<label>Search complementary strand</label>
|
||||
<option value="no">No</option>
|
||||
<option value="yes">Yes</option>
|
||||
</param>
|
||||
<param name="out_format1" type="select">
|
||||
<label>Output Report File Format</label>
|
||||
<option value="seqtable">SeqTable</option>
|
||||
<option value="embl">EMBL</option>
|
||||
<option value="genbank">GENBANK</option>
|
||||
<option value="gff">GFF</option>
|
||||
<option value="pir">PIR</option>
|
||||
<option value="swiss">SwissProt</option>
|
||||
<option value="dbmotif">DbMotif</option>
|
||||
<option value="diffseq">Diffseq</option>
|
||||
<option value="excel">Excel (tab delimited)</option>
|
||||
<option value="feattable">FeatTable</option>
|
||||
<option value="motif">Motif</option>
|
||||
<option value="regions">Regions</option>
|
||||
<option value="simple">SRS Simple</option>
|
||||
<option value="fuzznuc">Fuzznuc Output File</option>
|
||||
<option value="srs">SRS</option>
|
||||
<option value="table">Table</option>
|
||||
<option value="tagseq">TagSeq</option>
|
||||
</param>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data format="fuzznuc" name="out_file1" />
|
||||
</outputs>
|
||||
<tests>
|
||||
<test>
|
||||
<param name="input1" value="2.fasta"/>
|
||||
<param name="pattern" value="AA"/>
|
||||
<param name="mismatch" value="0"/>
|
||||
<param name="complement" value="no"/>
|
||||
<param name="out_format1" value="excel"/>
|
||||
<output name="out_file1" file="emboss_fuzznuc_out.tabular"/>
|
||||
</test>
|
||||
</tests>
|
||||
<code file="emboss_format_corrector.py" />
|
||||
<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/fuzznuc.html
|
||||
</help>
|
||||
</tool>
|
||||
Reference in New Issue
Block a user