roche454_toolsuite: roche454/runMapping

annotate roche454/runMapping_cDNA.xml @ 0:f036c7107601

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

author	edward-kirton
date	Tue, 07 Jun 2011 17:50:32 -0400
parents
children	368a6ebebdde

rev	line source
0 f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	1 <tool id="runMapping_cDNA" name="runMapping cDNA" version="1.0.0">
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	2 <description>Map Roche/454 reads to a reference using Newbler</description>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	3 <command interpreter='perl'>runMapping_cDNA_wrapper.pl
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	4 $newbler_metrics.extra_files_path
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	5 $alignment_info
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	6 $all_contigs_fasta
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	7 $all_contigs_qual
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	8 $all_diffs
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	9 $all_struct_vars
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	10 $hc_diff
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	11 $hc_struct_vars
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	12 $mapping_qc
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	13 $newbler_metrics
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	14 $pair_align
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	15 $read_status
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	16 $ref_status
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	17 $tag_pair_align
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	18 $trim_status
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	19 $trimmed_reads_fasta
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	20 $trimmed_reads_qual
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	21 $contigs_ace
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	22 $gene_status
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	23 $isotigs_ace
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	24 $isotigs_fasta
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	25 $isotigs_qual
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	26 $isotigs_agp
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	27 $isotigs_layout
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	28 $newbler_exe -o $newbler_metrics.extra_files_path
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	29 -cpu 8
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	30 -a $a
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	31 -e $e
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	32 -mi $mi
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	33 -ml $ml
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	34 -minlen $minlen
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	35 $pair
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	36 $info
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	37 $notrim
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	38 $tr
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	39 $ace
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	40 $no
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	41 $qo
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	42 $nor
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	43 $ud
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	44 -ss $ss
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	45 -sl $sl
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	46 -sc $sc
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	47 -ais $ais
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	48 -rst $rst
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	49 -hsl $hsl
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	50 -mcf $mcf
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	51 -vs $vs
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	52 -vt $vt
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	53 -fi $fi
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	54 -fe $fe
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	55 -cdna
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	56 $srv
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	57 -ig $ig
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	58 -it $it
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	59 -icc $icc
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	60 -icl $icl
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	61 $ref_type
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	62 -ref
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	63 #for $i in $ref_inputs
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	64 ${i.ref_input}
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	65 #end for
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	66 -read
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	67 #for $i in $sff_paired_inputs
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	68 -p ${i.sff_paired_input}
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	69 #end for
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	70 #for $i in $sanger_paired_inputs
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	71 -p ${i.sanger_paired_input}
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	72 #end for
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	73 #for $i in $sff_inputs
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	74 ${i.sff_input}
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	75 #end for
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	76 #for $i in $sanger_inputs
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	77 ${i.sanger_input}
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	78 #end for
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	79 </command>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	80 <inputs>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	81 <!-- NEWBLER VERSION -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	82 <param name='newbler_exe' type='select' display='radio' label='Newbler version'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	83 <option value='runMapping' selected='true'>default</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	84 <!-- OTHER VERSIONS MAY BE INCLUDED HERE; OR SIMPLY EDIT TO REMOVE THIS ENTIRE SECTION
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	85 <option value='/jgi/tools/454/rig-DataProcessing_2.3/bin/runMapping'>2.3</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	86 <option value='/jgi/tools/454/rig-DataProcessing_2.4pre-20091204/bin/runMapping'>2.4</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	87 <option value='/home/copeland/local/x86_64/newbler/v2.5p1-internal-10Jun23-1/runMapping'>2.5</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	88 -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	89 </param>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	90
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	91 <!-- READSEQ INFILES -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	92 <repeat name="sff_inputs" title="Unpaired Reads Sff Files">
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	93 <param name="sff_input" type="data" format="sff" label="SE Sff file"/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	94 </repeat>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	95 <repeat name="sanger_inputs" title="Unpaired Reads Fasta Files">
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	96 <param name="sanger_input" type="data" format="fasta" label="SE Fasta file"/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	97 </repeat>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	98 <repeat name="sff_paired_inputs" title="Paired Reads Sff Files">
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	99 <param name="sff_paired_input" type="data" format="sff" label="PE Sff file"/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	100 </repeat>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	101 <repeat name="sanger_paired_inputs" title="Paired Reads Fasta Files">
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	102 <param name="sanger_paired_input" type="data" format="fasta" label="PE Fasta file"/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	103 </repeat>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	104 <param name='paired_reads' type='select' display='radio' label='[-paired_reads] If supplying paired reads (above), do you want paired-read info?'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	105 <option value='false'>no</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	106 <option value='true'>[-paired_reads] yes</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	107 </param>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	108 <param name='pair' type='select' display='radio' label='[-pair] Output pairwise overlaps'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	109 <option value=''>no</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	110 <option value='-pair'>[-pair] yes</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	111 </param>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	112
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	113 <!-- SOURCE DNA TYPE -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	114 <param name='it' type='integer' value='100' label='[-it] Specify the maximum number of isotigs in an isogroup. Maximum is 10,000.'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	115 <param name='ig' type='integer' value='500' label='[-ig] Specify the maximum number of contigs in an isogroup.'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	116 <param name='icc' type='integer' value='100' label='[-icc] Specify the maximum number of contigs in an isotig. Maximum is 200 and corresponds to the recursion depth during graph traversal'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	117 <param name='icl' type='integer' value='3' label='[-icl] Specify the minimum length a contig must be to be part of an isotig. Minimum is 3bp.'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	118
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	119 <!-- INPUTS SPECIFIC TO MAPPING -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	120 <repeat name='ref_inputs' title='Reference Sequence'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	121 <param name='ref_input' type='data' format='fasta' label='Fasta file'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	122 </repeat>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	123 <param name='ref_type' type='select' display='radio' label='Reference type'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	124 <option value='-gref'>[-gref] Genomic reference sequence</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	125 <option value='-cref'>[-cref] cDNA reference sequence</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	126 </param>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	127 <param name='rst' type='integer' value='12' label='[-rst] Repeat score threshold parameter. Allowed values: 0 or greater'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	128 <param name='hsl' type='integer' value='70' label='[-hsl] Hit-per-seed limit parameter'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	129 <param name='srv' type='boolean' truevalue='-srv' falsevalue='' checked='false' label='[-srv] Single read variant output'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	130
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	131 <!-- OPTIONAL ARGUMENTS -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	132 <!-- NYI
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	133 <param name='accno' type='data' format='tabular' optional='true' label='[-accno] Specify annotation data. Required only if reference sequence headers do not contain gene=NAME pairs' />
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	134 <param name='annot' type='data' format='tabular' optional='true' label='[-annot] Supply gene, transcript, and protein information' />
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	135 -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	136 <param name='mcf' type='data' format='tabular' optional='true' label='[-mcf] Specify non-default MID config file' />
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	137 <param name='fi' type='data' format='txt' optional='true' label='[-fi] Include filter file to be specified' />
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	138 <param name='fe' type='data' format='txt' optional='true' label='[-fe] Exclude filter file to be specified' />
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	139 <param name='vt' type='data' format='fasta' optional='true' label="[-vt] This option specifies a vector trimming database, or FASTA file of sequences to be used to trim the ends of input reads (for cloning vectors, primers, adapters or other end sequences)" />
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	140 <param name='vs' type='data' format='fasta' optional='true' label="[-vs] This option specifies a vector screening database, or FASTA file of sequences to be used to screen the input reads for contaminants. Reads that completely align against the screening database are trimmed completely (so that it is not used in the computation), but otherwise the read trimpoints are not changed" />
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	141
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	142 <!-- READ TRIMMING -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	143 <param name='minlen' type='integer' value='20' label='[-minlen] Minimum length of reads to use (15-45 allowed)'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	144 <param name='notrim' type='boolean' truevalue='-notrim' falsevalue='' checked='false' label='[-notrim] Do not perform default quality and primer trimming of input reads'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	145 <param name='tr' type='select' display='radio' label='[-tr] Output trimmed reads'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	146 <option value=''>no</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	147 <option value='-tr'>[-tr] yes</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	148 </param>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	149 <param name='nor' type='boolean' truevalue='-nor' falsevalue='' label='[-nor] Turn off the automatic rescore function for read quality scores'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	150 <param name='ud' type='boolean' truevalue='-ud' falsevalue='' label='[-ud] Treat each read separately, with no grouping of duplicates'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	151
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	152 <!-- ALIGNMENT PARAMETERS -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	153 <param name='ss' type='integer' value='12' label='[-ss] Seed step parameter - The number of bases between seed generation locations used in the exact k-mer matching part of the overlap detection. Allow values: 1 or greater'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	154 <param name='sl' type='integer' value='16' label='[-sl] Seed length parameter - The number of bases used for each seed in the exact k-mer matching part of the overlap detection (i.e. the "k" value of the k-mer matching). Allowed values: 6-16'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	155 <param name='sc' type='integer' value='1' label='[-sc] Seed count parameter - The number of seeds required in a window before an extension is made. Allowed values: 1 or greater'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	156 <param name='ml' type="text" value='40' label="[-ml] Minimum overlap length - The minimum length of overlaps used for the pairwise alignment step. The value can either be a minimum length in bases or a percentage of read length. In the case of a percentage, simply include '%' immediately following the numeric value. Allowed values: 1 or greater"/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	157 <param name='mi' type="integer" value='90' label="[-mi] Minimum overlap identity - The percent identity of overlaps used for the pairwise alignment step. Allowed values: 0 or greater"/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	158 <param name='ais' type='integer' value='2' label='[-ais] Alignment identity score - When multiple overlaps are found, the per-overlap column identity score used to sort the overlaps for use in the progressive alignment. Allowed values: 0 or greater'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	159
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	160 <!-- ASSEMBLY OPTIONS -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	161 <param name='e' type="integer" value='0' label="[-e] This option tells the assembler that the expected depth of the data is at a certain level. The assembler has been optimized for datasets in the 10-50x oversampling size, and this option helps the assembler with datasets that have a higher oversampling level. A value of 0 resets the assembler computation to use its default algorithms"/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	162
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	163 <!-- OUTPUT OPTIONS -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	164 <param name='no' type='select' display='radio' label='[-no] Do complete assembly'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	165 <option value=''>do complete assembly</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	166 <option value='-no'>[-no] do not assemble; do alignments only</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	167 </param>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	168 <param name='qo' type='boolean' truevalue='' falsevalue='-qo' checked='false' label='[-qo] Generate quick output for mapping and assembly. Disables signal distribution computation for calling consensus sequences and can decrease accuracy'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	169 <param name='a' type="integer" value='100' label="[-a] This option sets the minimum length for a contig to appear in the 454AllContigs.fna file."/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	170 <param name='info' type='select' display='radio' label='Output Alignment Info'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	171 <option value='-info'>[-info] yes</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	172 <option value='-infoall'>[-infoall] yes, including 0-coverage positions</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	173 </param>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	174 <param name='ace' type='select' display='radio' label='Produce Ace assembly file'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	175 <option value=''>no</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	176 <option value='-ace'>[-ace] yes</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	177 </param>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	178 </inputs>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	179
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	180 <outputs>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	181 <!-- the following are common to runMapping and runAssembly -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	182 <data name='newbler_metrics' format='txt' />
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	183 <data name='read_status' format='tabular' label='Read Status'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	184 <data name='trimmed_reads_fasta' format='fasta' label='Trimmed Reads (Fasta)'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	185 <filter>tr == '-tr'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	186 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	187 <data name='trimmed_reads_qual' format='qual454' label='Trimmed Reads (Qual)'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	188 <filter>tr == '-tr'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	189 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	190 <!-- the following produced only if no != '-no' -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	191 <data name='alignment_info' format='tabular' label='Alignment Info'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	192 <data name='all_contigs_fasta' format='fasta' label='All Contigs (Fasta)'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	193 <filter>no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	194 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	195 <data name='all_contigs_qual' format='qual454' label='All Contigs (Qual454)'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	196 <filter>no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	197 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	198 <data name='contigs_ace' format='ace' label='Contigs (Ace)'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	199 <filter>ace == '-ace' and no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	200 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	201 <data name='pair_align' format='txt' label='Pairwise Alignments'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	202 <filter>pair == '-pair' and no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	203 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	204 <data name='pair_status' format='tabular' label='Paired-End Read Status'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	205 <filter>paired_reads == 'true' and no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	206 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	207 <data name='scaffolds_fasta' format='fasta' label='Scaffolds (Fasta)'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	208 <filter>paired_reads == 'true' and no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	209 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	210 <data name='scaffolds_qual' format='qual454' label='Scaffolds (Qual454)'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	211 <filter>paired_reads == 'true' and no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	212 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	213 <data name='scaffolds_agp' format='tabular' label='Scaffolds (Agp)'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	214 <filter>paired_reads == 'true' and no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	215 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	216 <data name='tag_pair_align' format='txt' label='Tag Pair Alignments'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	217 <filter>pair == '-pair' and paired_reads == 'true' and no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	218 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	219 <data name='trim_status' format='tabular' label='Trim Status'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	220
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	221 <!-- THE FOLLOWING ARE LIMITED TO MAPPING -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	222 <data name='all_diffs' format='tabular' label='All Diffs'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	223 <data name='all_struct_vars' format='tabular' label='All Struct Vars'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	224 <data name='hc_diff' format='tabular' label='High Confidence Diff'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	225 <data name='hc_struct_vars' format='tabular' label='High Confidence Struct Vars'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	226 <data name='gene_status' format='tabular' label='Gene Status'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	227 <data name='mapping_qc' format='xls' label='Mapping QC (Excel)'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	228 <data name='ref_status' format='tabular' label='Ref Status'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	229
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	230 <!-- ISOTIGS -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	231 <data name='isotigs_ace' format='ace' label='Isotigs (Ace)'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	232 <filter>ace != '' and no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	233 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	234 <data name='isotigs_fasta' format='fasta' label='Isotigs (Fasta)'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	235 <filter>no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	236 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	237 <data name='isotigs_qual' format='qual454' label='Isotigs (Qual454)'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	238 <filter>no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	239 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	240 <data name='isotigs_agp' format='tabular' label='Isotigs (Agp)'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	241 <filter>no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	242 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	243 <data name='isotigs_layout' format='txt' label='Isotig Layout'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	244 <filter>no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	245 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	246
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	247 </outputs>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	248 <help>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	249
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	250 What it does
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	251
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	252 Map (Roche/454) reads to a reference using Newbler.
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	253
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	254 Download the manual here: http://galaxy.jgi-psf.org/static/manuals/GSFLXSystemSoftwareManual_PartC_Assembler-Mapper-SFFTools.pdf
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	255
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	256 .. class:: warningmark
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	257
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	258 Fasta Header Format Fasta input must provide any pairing information in the header using the expected key=value format. Use the 'Sanger tab to Newbler Fasta' tool.
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	259
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	260 </help>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	261 </tool>

Mercurial > repos > edward-kirton > roche454_toolsuite

annotate roche454/runMapping_cDNA.xml @ 0:f036c7107601