mummer_toolsuite: MUMmer/mummer

annotate MUMmer/mummer_tool.xml @ 0:6753195df9e0 default tip

Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

author	abossers
date	Tue, 07 Jun 2011 17:49:58 -0400
parents
children

rev	line source
0 6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	1 <tool id="mummer_tool" name="MUMmer" version="0.4.alx" force_history_refresh="True">
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	2 <description>: Compare genomes (Nucmer or Promer)</description>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	3 <command interpreter="bash">
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	4 mummer_tool.sh
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	5 $input_ref $input_query
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	6 $out_delta $out_coords $out_png $out_log
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	7 $algorithm
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	8 $keep_delta $make_coords $keep_log $make_image
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	9 $cmd_extra
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	10 </command>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	11 <inputs>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	12 <param name="algorithm" type="select" format="text" value="nucmer" label="Algorithm" help="Nucmer dna or Promer protein (FASTA: protein. Dna is six frame translated)">
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	13 <option value="nucmer">Nucmer DNA</option>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	14 <option value="promer">Promer</option>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	15 </param>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	16 <param name="input_ref" type="data" format="fasta" label="Reference sequence" />
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	17 <param name="input_query" type="data" format="fasta" label="Sequence query file"/>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	18 <param name="make_image" type="select" format="text" value="yes" label="Generate MUMmerplot" help="MUMmerplot will be run with default settings and --large --png as fixed image.">
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	19 <option value="yes">Yes</option>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	20 <option value="no">No</option>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	21 </param>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	22 <param name="keep_delta" type="select" format="text" value="no" label="Keep delta file" help="i.e. for further processing">
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	23 <option value="no">No</option>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	24 <option value="yes">Yes</option>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	25 </param>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	26 <param name="make_coords" type="select" format="text" value="yes" label="Make coords file" help="Uses the -r argument to sort lines by reference.">
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	27 <option value="no">No</option>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	28 <option value="yes">Yes</option>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	29 </param>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	30 <param name="keep_log" type="select" format="text" value="no" label="Keep console log file" help="i.e. for debugging">
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	31 <option value="no">No</option>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	32 <option value="yes">Yes</option>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	33 </param>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	34 <param name="cmd_extra" type="text" size="40" value="" label="Extra cmd line options" help="the --coords is run by default" />
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	35 </inputs>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	36 <outputs>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	37 <data name="out_coords" format="tabular" label="${algorithm.value_label} coords">
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	38 <filter>make_coords=="yes"</filter>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	39 </data>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	40 <data name="out_delta" format="tabular" label="${algorithm.value_label} delta">
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	41 <filter>keep_delta=="yes"</filter>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	42 </data>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	43 <data name="out_png" format="png" label="${algorithm.value_label} mummerplot">
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	44 <filter>make_image=="yes"</filter>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	45 </data>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	46 <data name="out_log" format="tabular" label="Console log file">
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	47 <filter>keep_log=="yes"</filter>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	48 </data>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	49 </outputs>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	50 <requirements>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	51 <requirement type="binary">nucmer</requirement>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	52 <requirement type="binary">promer</requirement>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	53 </requirements>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	54 <tests>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	55 <test>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	56 </test>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	57 </tests>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	58 <help>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	59 \|
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	60
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	61
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	62 Reference
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	63 -------------
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	64
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	65 - Nucmer Galaxy tool wrapper: Alex Bossers, CVI of Wageningen UR, The Netherlands.
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	66
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	67 - Nucmer or Promer of MUMmer suite: v3.22 http://mummer.sourceforge.net/manual/
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	68
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	69 - MUMmer tutorials: http://mummer.sourceforge.net/examples/
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	70
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	71
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	72 If you found these tools/wrappers useful in your research, please acknowledge our work. If you improve
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	73 or modify the wrappers please add instead of substitute yourself into the acknowlegement section :)
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	74
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	75
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	76 Command line arguments
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	77 --------------------------
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	78
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	79 --mum Use anchor matches that are unique in both the reference and query
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	80 --mumreference Use anchor matches that are unique in the reference but not necessarily unique in the query (default behavior)
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	81 --maxmatch Use all anchor matches regardless of their uniqueness
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	82 --breaklen Distance an alignment extension will attempt to extend poor scoring regions before giving up (default 200)
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	83 --mincluster Minimum cluster length (default 65)
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	84 --delta Toggle the creation of the delta file. Setting --nodelta prevents the alignment extension step and only outputs the match clusters (default --delta)
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	85 --depend Print the dependency information and exit
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	86 --diagfactor Maximum diagonal difference factor for clustering, i.e. diagonal difference / match separation (default 0.12)
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	87 --extend Toggle the outward extension of alignments from their anchoring clusters. Setting --noextend will prevent alignment extensions but still align the DNA between clustered matches and create the .delta file (default --extend)
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	88 --forward Align only the forward strands of each sequence
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	89 --maxgap Maximum gap between two adjacent matches in a cluster (default 90)
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	90 --help Print the help information and exit
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	91 --minmatch Minimum length of an maximal exact match (default 20)
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	92 --optimize Toggle alignment score optimization. Setting --nooptimize will prevent alignment score optimization and result in sometimes longer, but lower scoring alignments (default --optimize)
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	93 --reverse Align only the reverse strand of the query sequence to the forward strand of the reference
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	94 --simplify Simplify alignments by removing shadowed clusters. Turn this option off (--nosimplify) if aligning a sequence to itself to look for repeats (default --simplify)
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	95 --version Print the version information and exit
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	96 --coords Automatically ON in galaxy wrapper! It generates the .coords file using the 'show-coords' program with the -r option.
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	97 --prefix Do NOT use in Galaxy wrapper! Set the output file prefix (default out)
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	98
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	99 \|
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	100 \|
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	101
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	102 </help>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	103 </tool>
6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository abossers parents: diff changeset	104

Mercurial > repos > abossers > mummer_toolsuite

annotate MUMmer/mummer_tool.xml @ 0:6753195df9e0 default tip