roche454_toolsuite: roche454/runMapping

annotate roche454/runMapping_cDNA.xml @ 1:584549c024c2 default tip

Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository

author	edward-kirton
date	Tue, 07 Jun 2011 17:23:39 -0400
parents	9e30cc10a6a3
children

rev	line source
1 584549c024c2 Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository edward-kirton parents: 0 diff changeset	1 <tool id="runMapping_cDNA" name="runMapping cDNA" version="1.0.1">
0 9e30cc10a6a3 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>
9e30cc10a6a3 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
9e30cc10a6a3 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
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	5 $alignment_info
9e30cc10a6a3 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
9e30cc10a6a3 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
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	8 $all_diffs
9e30cc10a6a3 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
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	10 $hc_diff
9e30cc10a6a3 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
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	12 $mapping_qc
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	13 $newbler_metrics
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	14 $pair_align
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	15 $read_status
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	16 $ref_status
9e30cc10a6a3 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
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	18 $trim_status
9e30cc10a6a3 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
9e30cc10a6a3 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
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	21 $contigs_ace
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	22 $gene_status
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	23 $isotigs_ace
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	24 $isotigs_fasta
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	25 $isotigs_qual
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	26 $isotigs_agp
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	27 $isotigs_layout
9e30cc10a6a3 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
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	29 -cpu 8
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	30 -a $a
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	31 -e $e
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	32 -mi $mi
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	33 -ml $ml
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	34 -minlen $minlen
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	35 $pair
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	36 $info
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	37 $notrim
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	38 $tr
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	39 $ace
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	40 $no
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	41 $qo
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	42 $nor
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	43 $ud
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	44 -ss $ss
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	45 -sl $sl
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	46 -sc $sc
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	47 -ais $ais
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	48 -rst $rst
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	49 -hsl $hsl
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	50 -mcf $mcf
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	51 -vs $vs
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	52 -vt $vt
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	53 -fi $fi
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	54 -fe $fe
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	55 -cdna
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	56 $srv
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	57 -ig $ig
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	58 -it $it
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	59 -icc $icc
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	60 -icl $icl
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	61 $ref_type
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	62 -ref
9e30cc10a6a3 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
9e30cc10a6a3 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}
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	65 #end for
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	66 -read
9e30cc10a6a3 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
9e30cc10a6a3 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}
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	69 #end for
9e30cc10a6a3 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
9e30cc10a6a3 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}
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	72 #end for
9e30cc10a6a3 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
9e30cc10a6a3 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}
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	75 #end for
9e30cc10a6a3 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
9e30cc10a6a3 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}
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	78 #end for
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	79 </command>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	80 <inputs>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	81 <!-- NEWBLER VERSION -->
9e30cc10a6a3 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'>
9e30cc10a6a3 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>
9e30cc10a6a3 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
9e30cc10a6a3 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>
9e30cc10a6a3 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>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	88 -->
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	89 </param>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	90
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	91 <!-- READSEQ INFILES -->
9e30cc10a6a3 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">
9e30cc10a6a3 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"/>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	94 </repeat>
9e30cc10a6a3 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">
9e30cc10a6a3 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"/>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	97 </repeat>
9e30cc10a6a3 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">
9e30cc10a6a3 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"/>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	100 </repeat>
9e30cc10a6a3 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">
9e30cc10a6a3 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"/>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	103 </repeat>
9e30cc10a6a3 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?'>
9e30cc10a6a3 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>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	107 </param>
9e30cc10a6a3 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'>
9e30cc10a6a3 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>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	111 </param>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	112
9e30cc10a6a3 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 -->
9e30cc10a6a3 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.'/>
9e30cc10a6a3 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.'/>
9e30cc10a6a3 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'/>
9e30cc10a6a3 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.'/>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	118
9e30cc10a6a3 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 -->
9e30cc10a6a3 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'>
9e30cc10a6a3 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'/>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	122 </repeat>
9e30cc10a6a3 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'>
9e30cc10a6a3 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>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	126 </param>
9e30cc10a6a3 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'/>
9e30cc10a6a3 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'/>
9e30cc10a6a3 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'/>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	130
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	131 <!-- OPTIONAL ARGUMENTS -->
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	132 <!-- NYI
9e30cc10a6a3 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' />
9e30cc10a6a3 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' />
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	135 -->
9e30cc10a6a3 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' />
9e30cc10a6a3 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' />
9e30cc10a6a3 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' />
9e30cc10a6a3 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)" />
9e30cc10a6a3 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" />
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	141
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	142 <!-- READ TRIMMING -->
9e30cc10a6a3 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)'/>
9e30cc10a6a3 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'/>
9e30cc10a6a3 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'>
9e30cc10a6a3 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>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	148 </param>
9e30cc10a6a3 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'/>
9e30cc10a6a3 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'/>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	151
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	152 <!-- ALIGNMENT PARAMETERS -->
9e30cc10a6a3 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'/>
9e30cc10a6a3 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'/>
9e30cc10a6a3 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'/>
9e30cc10a6a3 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"/>
9e30cc10a6a3 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"/>
9e30cc10a6a3 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'/>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	159
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	160 <!-- ASSEMBLY OPTIONS -->
9e30cc10a6a3 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"/>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	162
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	163 <!-- OUTPUT OPTIONS -->
9e30cc10a6a3 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'>
9e30cc10a6a3 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>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	167 </param>
9e30cc10a6a3 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'/>
9e30cc10a6a3 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."/>
9e30cc10a6a3 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'>
9e30cc10a6a3 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>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	173 </param>
9e30cc10a6a3 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'>
9e30cc10a6a3 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>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	177 </param>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	178 </inputs>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	179
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	180 <outputs>
9e30cc10a6a3 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 -->
9e30cc10a6a3 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' />
9e30cc10a6a3 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'/>
9e30cc10a6a3 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)'>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	186 </data>
9e30cc10a6a3 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)'>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	189 </data>
9e30cc10a6a3 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' -->
9e30cc10a6a3 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'/>
9e30cc10a6a3 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)'>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	194 </data>
9e30cc10a6a3 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)'>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	197 </data>
9e30cc10a6a3 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)'>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	200 </data>
9e30cc10a6a3 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'>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	203 </data>
9e30cc10a6a3 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'>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	206 </data>
9e30cc10a6a3 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)'>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	209 </data>
9e30cc10a6a3 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)'>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	212 </data>
9e30cc10a6a3 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)'>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	215 </data>
9e30cc10a6a3 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'>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	218 </data>
9e30cc10a6a3 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'/>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	220
9e30cc10a6a3 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 -->
9e30cc10a6a3 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'/>
9e30cc10a6a3 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'/>
9e30cc10a6a3 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'/>
9e30cc10a6a3 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'/>
9e30cc10a6a3 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'/>
9e30cc10a6a3 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)'/>
9e30cc10a6a3 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'/>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	229
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	230 <!-- ISOTIGS -->
9e30cc10a6a3 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)'>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	233 </data>
9e30cc10a6a3 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)'>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	236 </data>
9e30cc10a6a3 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)'>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	239 </data>
9e30cc10a6a3 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)'>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	242 </data>
9e30cc10a6a3 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'>
9e30cc10a6a3 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>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	245 </data>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	246
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	247 </outputs>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	248 <help>
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	249
9e30cc10a6a3 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
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	251
9e30cc10a6a3 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.
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	253
9e30cc10a6a3 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
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	255
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	256 .. class:: warningmark
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	257
9e30cc10a6a3 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.
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	259
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	260 </help>
9e30cc10a6a3 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 @ 1:584549c024c2 default tip