segemehl: segemehl.xml annotate

annotate segemehl.xml @ 3:039547ad8fb8 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053

author	rnateam
date	Fri, 16 Dec 2016 07:37:24 -0500
parents	0da425524259
children	db367d012fa3

rev	line source
3 039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	1 <tool id="segemehl" name="segemehl" version="0.2.0">
0 e97db054a88d Uploaded rnateam parents: diff changeset	2 <description>based short read aligner</description>
e97db054a88d Uploaded rnateam parents: diff changeset	3 <requirements>
3 039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	4 <requirement type="package" version="0.2.0">segemehl</requirement>
0 e97db054a88d Uploaded rnateam parents: diff changeset	5 </requirements>
3 039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	6 <stdio>
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	7 <regex match="Exit forced"
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	8 source="both"
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	9 level="fatal"
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	10 description="Execution halted." />
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	11 </stdio>
0 e97db054a88d Uploaded rnateam parents: diff changeset	12 <command>
1 df7c7d732d31 Uploaded rnateam parents: 0 diff changeset	13 <![CDATA[
0 e97db054a88d Uploaded rnateam parents: diff changeset	14 ## prepare segemehl index if no reference genome is supplied
e97db054a88d Uploaded rnateam parents: diff changeset	15 #if $refGenomeSource.genomeSource == "history":
3 039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	16 mkdir ./temp_index/ &&
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	17 #set $temp_index = './temp_index/temp.idx'
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	18 segemehl.x -x $temp_index -d $refGenomeSource.own_reference_genome &&
0 e97db054a88d Uploaded rnateam parents: diff changeset	19 #else:
2 0da425524259 Uploaded bgruening parents: 1 diff changeset	20 #set $temp_index = $refGenomeSource.index.fields.index_path
0 e97db054a88d Uploaded rnateam parents: diff changeset	21 #end if
e97db054a88d Uploaded rnateam parents: diff changeset	22
e97db054a88d Uploaded rnateam parents: diff changeset	23
e97db054a88d Uploaded rnateam parents: diff changeset	24 ## execute segemehl
e97db054a88d Uploaded rnateam parents: diff changeset	25 segemehl.x
1 df7c7d732d31 Uploaded rnateam parents: 0 diff changeset	26
0 e97db054a88d Uploaded rnateam parents: diff changeset	27 ## number of threads
e97db054a88d Uploaded rnateam parents: diff changeset	28 -t "\${GALAXY_SLOTS:-12}"
e97db054a88d Uploaded rnateam parents: diff changeset	29
3 039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	30 #if $refGenomeSource.genomeSource == "history":
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	31 -d $refGenomeSource.own_reference_genome
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	32 #else:
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	33 -d ${refGenomeSource.index.fields.db_path}
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	34 #end if
0 e97db054a88d Uploaded rnateam parents: diff changeset	35
e97db054a88d Uploaded rnateam parents: diff changeset	36 -i $temp_index
e97db054a88d Uploaded rnateam parents: diff changeset	37
e97db054a88d Uploaded rnateam parents: diff changeset	38 ## check for single/pair-end
e97db054a88d Uploaded rnateam parents: diff changeset	39 #if str( $library.type ) == "single":
e97db054a88d Uploaded rnateam parents: diff changeset	40 #set $query_list = list()
e97db054a88d Uploaded rnateam parents: diff changeset	41 ## prepare inputs
3 039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	42 #for $fastq in $library.input_query:
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	43 $query_list.append('%s' % $fastq )
0 e97db054a88d Uploaded rnateam parents: diff changeset	44 #end for
e97db054a88d Uploaded rnateam parents: diff changeset	45 -q "#echo ' '.join( $query_list )#"
e97db054a88d Uploaded rnateam parents: diff changeset	46 #else
e97db054a88d Uploaded rnateam parents: diff changeset	47 ## prepare inputs
1 df7c7d732d31 Uploaded rnateam parents: 0 diff changeset	48
0 e97db054a88d Uploaded rnateam parents: diff changeset	49 #set $mate1 = list()
e97db054a88d Uploaded rnateam parents: diff changeset	50 #set $mate2 = list()
e97db054a88d Uploaded rnateam parents: diff changeset	51 #for $mate_pair in $library.mate_list:
e97db054a88d Uploaded rnateam parents: diff changeset	52 $mate1.append( str($mate_pair.first_strand_query) )
e97db054a88d Uploaded rnateam parents: diff changeset	53 $mate2.append( str($mate_pair.second_strand_query) )
e97db054a88d Uploaded rnateam parents: diff changeset	54 #end for
e97db054a88d Uploaded rnateam parents: diff changeset	55
e97db054a88d Uploaded rnateam parents: diff changeset	56 -q #echo ','.join($mate1)
e97db054a88d Uploaded rnateam parents: diff changeset	57 -p #echo ','.join($mate2)
e97db054a88d Uploaded rnateam parents: diff changeset	58
e97db054a88d Uploaded rnateam parents: diff changeset	59 -I $library.maxinsertsize
e97db054a88d Uploaded rnateam parents: diff changeset	60 #end if
e97db054a88d Uploaded rnateam parents: diff changeset	61 -m $minsize
e97db054a88d Uploaded rnateam parents: diff changeset	62 -A $accuracy
e97db054a88d Uploaded rnateam parents: diff changeset	63 -H $hitstrategy
e97db054a88d Uploaded rnateam parents: diff changeset	64 #if str( $prime5 ).strip():
2 0da425524259 Uploaded bgruening parents: 1 diff changeset	65 -P "$prime5"
0 e97db054a88d Uploaded rnateam parents: diff changeset	66 #end if
e97db054a88d Uploaded rnateam parents: diff changeset	67 #if str( $prime3 ).strip():
2 0da425524259 Uploaded bgruening parents: 1 diff changeset	68 -Q "$prime3"
0 e97db054a88d Uploaded rnateam parents: diff changeset	69 #end if
e97db054a88d Uploaded rnateam parents: diff changeset	70 $polyA
e97db054a88d Uploaded rnateam parents: diff changeset	71 $autoclip
e97db054a88d Uploaded rnateam parents: diff changeset	72 $hardclip
e97db054a88d Uploaded rnateam parents: diff changeset	73 $order
3 039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	74 $splits
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	75 #if $maxout:
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	76 --maxout $maxout
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	77 #end if
0 e97db054a88d Uploaded rnateam parents: diff changeset	78 -s
3 039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	79
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	80 --minsplicecover $minsplicecover
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	81 --minfragscore $minfragscore
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	82 --minfraglen $minfraglen
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	83 --splicescorescale $splicescorescale
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	84
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	85 -o '$segemehl_out'
1 df7c7d732d31 Uploaded rnateam parents: 0 diff changeset	86 ]]>
0 e97db054a88d Uploaded rnateam parents: diff changeset	87 </command>
e97db054a88d Uploaded rnateam parents: diff changeset	88 <inputs>
e97db054a88d Uploaded rnateam parents: diff changeset	89 <conditional name="refGenomeSource">
e97db054a88d Uploaded rnateam parents: diff changeset	90 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
e97db054a88d Uploaded rnateam parents: diff changeset	91 <option value="indexed">Use a built-in index</option>
e97db054a88d Uploaded rnateam parents: diff changeset	92 <option value="history">Use one from the history</option>
e97db054a88d Uploaded rnateam parents: diff changeset	93 </param>
e97db054a88d Uploaded rnateam parents: diff changeset	94 <when value="indexed">
e97db054a88d Uploaded rnateam parents: diff changeset	95 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">
e97db054a88d Uploaded rnateam parents: diff changeset	96 <options from_data_table="segemehl_indexes">
e97db054a88d Uploaded rnateam parents: diff changeset	97 <column name="value" index="0"/>
e97db054a88d Uploaded rnateam parents: diff changeset	98 <column name="dbkey" index="1"/>
e97db054a88d Uploaded rnateam parents: diff changeset	99 <column name="name" index="2"/>
e97db054a88d Uploaded rnateam parents: diff changeset	100 <column name="db_path" index="3"/>
e97db054a88d Uploaded rnateam parents: diff changeset	101 <column name="index_path" index="4"/>
e97db054a88d Uploaded rnateam parents: diff changeset	102 <filter type="sort_by" column="2"/>
e97db054a88d Uploaded rnateam parents: diff changeset	103 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
e97db054a88d Uploaded rnateam parents: diff changeset	104 </options>
e97db054a88d Uploaded rnateam parents: diff changeset	105 </param>
e97db054a88d Uploaded rnateam parents: diff changeset	106 </when> <!-- build-in -->
e97db054a88d Uploaded rnateam parents: diff changeset	107 <when value="history">
3 039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	108 <param name="own_reference_genome" type="data" format="fasta" label="Select the reference genome" />
0 e97db054a88d Uploaded rnateam parents: diff changeset	109 </when> <!-- history -->
e97db054a88d Uploaded rnateam parents: diff changeset	110 </conditional> <!-- refGenomeSource -->
e97db054a88d Uploaded rnateam parents: diff changeset	111
e97db054a88d Uploaded rnateam parents: diff changeset	112 <conditional name="library">
e97db054a88d Uploaded rnateam parents: diff changeset	113 <param name="type" type="select" label="Is this library paired-end?">
e97db054a88d Uploaded rnateam parents: diff changeset	114 <option value="single">Single-end</option>
e97db054a88d Uploaded rnateam parents: diff changeset	115 <option value="paired">Paired-end</option>
e97db054a88d Uploaded rnateam parents: diff changeset	116 </param>
e97db054a88d Uploaded rnateam parents: diff changeset	117 <when value="single">
3 039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	118 <param name="input_query" type="data" multiple="True" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads in FASTQ/FASTA files" />
0 e97db054a88d Uploaded rnateam parents: diff changeset	119 </when>
e97db054a88d Uploaded rnateam parents: diff changeset	120 <when value="paired">
3 039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	121 <!-- ToDo paired coolections -->
0 e97db054a88d Uploaded rnateam parents: diff changeset	122 <repeat name="mate_list" title="Paired End Pairs" min="1">
e97db054a88d Uploaded rnateam parents: diff changeset	123 <param name="first_strand_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads from first strand" />
e97db054a88d Uploaded rnateam parents: diff changeset	124 <param name="second_strand_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads from second strand" />
e97db054a88d Uploaded rnateam parents: diff changeset	125 </repeat>
e97db054a88d Uploaded rnateam parents: diff changeset	126 <param name="maxinsertsize" type="integer" value="5000" label="Maximum size of the inserts (paired end)" help="default: 5000 (-I)" />
e97db054a88d Uploaded rnateam parents: diff changeset	127 </when>
e97db054a88d Uploaded rnateam parents: diff changeset	128 </conditional>
e97db054a88d Uploaded rnateam parents: diff changeset	129
3 039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	130 <param name="minsplicecover" type="integer" value="80" label="Min coverage for spliced transcripts" help="(--minsplicecover)" />
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	131 <param name="minfragscore" type="integer" value="18" label="Min coverage for spliced transcripts" help="(--minfragscore)" />
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	132 <param name="minfraglen" type="integer" value="20" label="Min length of a spliced fragment" help="(--minfraglen)" />
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	133 <param name="splicescorescale" type="float" value="1.0" label="Report spliced alignment with score greater than this scale times the score"
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	134 help="Report only if this value x score is larger than next best spliced alignment (--splicescorescale)" />
0 e97db054a88d Uploaded rnateam parents: diff changeset	135
3 039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	136 <param name="minsize" type="integer" value="12" min="1" label="Minimum size of queries" help="(-m)" />
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	137
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	138 <param name="maxout" type="integer" min="0" value="0" optional="True"
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	139 label="Maximum number of alignments that will be reported" help="(--maxout)" />
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	140 <param name="accuracy" type="integer" value="85" min="1" max="100" label="Min percentage of matches per read in semi-global alignment" help="(-A)" />
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	141
0 e97db054a88d Uploaded rnateam parents: diff changeset	142 <param name="hitstrategy" type="select" label="Hits to report?" help="(-H)">
e97db054a88d Uploaded rnateam parents: diff changeset	143 <option value="1">report only best scoring hits</option>
e97db054a88d Uploaded rnateam parents: diff changeset	144 <option value="0">report all scoring hits</option>
e97db054a88d Uploaded rnateam parents: diff changeset	145 </param>
3 039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	146 <param name="prime5" type="text" label="add 5' adapter" help="default: none (-Q)" />
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	147 <param name="prime3" type="text" label="add 3' adapter" help="default: none (-P)"/>
0 e97db054a88d Uploaded rnateam parents: diff changeset	148 <param name="polyA" type="boolean" truevalue="--polyA" falsevalue="" checked="false" label="Clip polyA tail" help="(-T)"/>
e97db054a88d Uploaded rnateam parents: diff changeset	149 <param name="autoclip" type="boolean" truevalue="--autoclip" falsevalue="" checked="false" label="Autoclip unknown 3prime adapter" help="(-Y)"/>
3 039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	150 <param name="hardclip" type="boolean" truevalue="--hardclip" falsevalue="" checked="false" label="Enable hard clipping" help="(-C)"/>
0 e97db054a88d Uploaded rnateam parents: diff changeset	151 <param name="order" type="boolean" truevalue="--order" falsevalue="" checked="false" label="Sorts the output by chromsome and position" help="(-O)"/>
3 039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	152 <param name="splits" type="boolean" truevalue="--splits" falsevalue="" checked="false" label="Detect split/spliced reads" help="(--splits)"/>
0 e97db054a88d Uploaded rnateam parents: diff changeset	153 </inputs>
e97db054a88d Uploaded rnateam parents: diff changeset	154 <outputs>
e97db054a88d Uploaded rnateam parents: diff changeset	155 <data format="sam" name="segemehl_out" label="Read alignments on ${on_string}"/>
e97db054a88d Uploaded rnateam parents: diff changeset	156 </outputs>
3 039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	157 <tests>
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	158 <test>
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	159 <param name="genomeSource" value="history" />
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	160 <param name="own_reference_genome" value="chr1.fa" />
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	161 <param name="library" value="single" />
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	162 <param name="input_query" value="test.fastq" />
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	163 <param name="splits" value="true" />
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	164 <output name="segemehl_out" file="testmap.sam" lines_diff="2" />
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	165 </test>
039547ad8fb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: 2 diff changeset	166 </tests>
0 e97db054a88d Uploaded rnateam parents: diff changeset	167 <help>
1 df7c7d732d31 Uploaded rnateam parents: 0 diff changeset	168 <![CDATA[
0 e97db054a88d Uploaded rnateam parents: diff changeset	169
e97db054a88d Uploaded rnateam parents: diff changeset	170 .. class:: infomark
e97db054a88d Uploaded rnateam parents: diff changeset	171
1 df7c7d732d31 Uploaded rnateam parents: 0 diff changeset	172 What it does
0 e97db054a88d Uploaded rnateam parents: diff changeset	173
e97db054a88d Uploaded rnateam parents: diff changeset	174 Segemehl_ is a short read mapper with gaps.
e97db054a88d Uploaded rnateam parents: diff changeset	175
1 df7c7d732d31 Uploaded rnateam parents: 0 diff changeset	176 Segemehl_ is a software to map short sequencer reads to reference genomes.
df7c7d732d31 Uploaded rnateam parents: 0 diff changeset	177 Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions.
df7c7d732d31 Uploaded rnateam parents: 0 diff changeset	178 Furthermore, segemehl is not limited to a specific read length and is able to mapprimer- or polyadenylation contaminated reads correctly.
0 e97db054a88d Uploaded rnateam parents: diff changeset	179 segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl_ allows bisulfite sequencing mapping and split read mapping.
e97db054a88d Uploaded rnateam parents: diff changeset	180
e97db054a88d Uploaded rnateam parents: diff changeset	181 .. _Segemehl: http://www.bioinf.uni-leipzig.de/Software/segemehl/
e97db054a88d Uploaded rnateam parents: diff changeset	182
e97db054a88d Uploaded rnateam parents: diff changeset	183
1 df7c7d732d31 Uploaded rnateam parents: 0 diff changeset	184 ]]>
0 e97db054a88d Uploaded rnateam parents: diff changeset	185 </help>
1 df7c7d732d31 Uploaded rnateam parents: 0 diff changeset	186 <citations>
df7c7d732d31 Uploaded rnateam parents: 0 diff changeset	187 <citation type="doi">10.1371/journal.pcbi.1000502</citation>
df7c7d732d31 Uploaded rnateam parents: 0 diff changeset	188 </citations>
0 e97db054a88d Uploaded rnateam parents: diff changeset	189 </tool>

Mercurial > repos > rnateam > segemehl

annotate segemehl.xml @ 3:039547ad8fb8 draft