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author devteam
date Mon, 09 Nov 2015 11:41:55 -0500
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643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 <tool id="lastz_paired_reads_wrapper" name="Lastz paired reads" version="1.1.1">
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2 <requirements>
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3 <requirement type="package" version="1.02.00">lastz</requirement>
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4 </requirements>
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5 <description> map short paired reads against reference sequence</description>
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6 <command interpreter="python">lastz_paired_reads_wrapper.py
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7 #if $seq_name.how_to_name=="yes":
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8 --ref_name=$seq_name.ref_name
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9 #end if
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10 --ref_source=$source.ref_source
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11 --input2=$input2
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12 --input3=$input3
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13 --input4=$input4
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14 #if $source.ref_source=="history":
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15 --input1=$source.input1
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16 --ref_sequences=$input1.metadata.sequences
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17 #else:
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18 --input1="${source.input1_2bit.fields.path}"
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19 #end if
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20 --output=$output1
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21 --lastz_seqs_file_dir=${GALAXY_DATA_INDEX_DIR}
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22 </command>
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23 <inputs>
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24 <param name="input2" format="fasta" type="data" label="Align sequencing reads in" />
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25 <conditional name="source">
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26 <param name="ref_source" type="select" label="Against reference sequences that are">
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27 <option value="cached">locally cached</option>
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28 <option value="history">in your history</option>
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29 </param>
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30 <when value="cached">
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31 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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32 <options from_data_table="lastz_seqs" />
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33 </param>
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34 </when>
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35 <when value="history">
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36 <param name="input1" type="data" format="fasta" label="Select a reference dataset" />
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37 </when>
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38 </conditional>
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39 <param name="input3" format="fasta" type="data" label="Linker file" />
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40 <param name="input4" format="qual454" type="data" label="Select a base quality score 454 dataset" />
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41 <conditional name="seq_name">
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42 <param name="how_to_name" type="select" label="Do you want to modify the reference name?">
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43 <option value="no">No</option>
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44 <option value="yes">Yes</option>
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45 </param>
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46 <when value="yes">
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47 <param name="ref_name" type="text" value="Type sequence name here" label="Enter name for the Reference sequence"/>
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48 </when>
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49 <when value="no" />
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50 </conditional>
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51 </inputs>
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52 <outputs>
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53 <data format="sam" name="output1" label="${tool.name} on ${on_string}: mapped reads" />
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54 </outputs>
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55 <tests>
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56 <test>
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57 <!--
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58 input1: a reference genome ( 2bit or fasta )
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59 input2: a collection of 454 paired end reads ( a fasta file )
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60 input3: a linker sequence ( a very small fasta file )
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61 input4: a base quality score 454 file ( qual454 )
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62 -->
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63 <param name="input2" value="lastz_paired_input2.fasta" ftype="fasta" />
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64 <param name="ref_source" value="cached" />
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65 <param name="input1_2bit" value="hg18chr21" />
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66 <param name="input3" value="lastz_paired_input3.fasta" ftype="fasta" />
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67 <param name="input4" value="lastz_paired_input4.qual454" ftype="qual454" />
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68 <param name="how_to_name" value="no" />
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69 <output name="output1" file="lastz_paired_out1.sam" />
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70 </test>
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71 </tests>
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72 <help>
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73
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74 **What it does**
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75
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76 **LASTZ** is a high performance pairwise sequence aligner derived from BLASTZ. It is written by Bob Harris in Webb Miller's laboratory at Penn State University. Special scoring sets were derived to improve runtime performance and quality. This Galaxy version of LASTZ is geared towards aligning short (Illumina/Solexa, AB/SOLiD) and medium (Roche/454) paired reads against a reference sequence. There is excellent, extensive documentation on LASTZ available here_.
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77
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78 .. _here: http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00.html
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79
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80 ------
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81
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82 **Input formats**
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83
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84 LASTZ accepts reference and reads in FASTA format. However, because Galaxy supports implicit format conversion the tool will recognize fastq and other method specific formats.
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85
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86 ------
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87
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88 **Outputs**
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89
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90 This LASTZ tool produces a SAM file showing sequence alignments.
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91
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92 **SAM output**
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93
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94 SAM has 12 columns::
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95
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96 1 2 3 4 5 6 7 8 9 10 11 12
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97 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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98 HWI-EAS91_1_30788AAXX:1:2:1670:915 99 chr9 58119878 60 36M = 58120234 392 GACCCCTACCCCACCGTGCTCTGGATCTCAGTGTTT IIIIIIIIIIIIIIIIEIIIIIII7IIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36
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99 HWI-EAS91_1_30788AAXX:1:2:1670:915 147 chr9 58120234 60 36M = 58119878 -392 ATGAGTCGAATTCTATTTTCCAAACTGTTAACAAAA IFIIDI;IIICIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36
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100
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101
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102 where::
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103
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104 Column Description
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105 --------- ---------------------------------------------------------------------
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106 1. QNAME Query (pair) NAME
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107 2. FLAG bitwise FLAG
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108 3. RNAME Reference sequence NAME
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109 4. POS 1-based leftmost POSition/coordinate of clipped sequence
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110 5. MAPQ MAPping Quality (Phred-scaled)
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111 6. CIGAR extended CIGAR string
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112 7. MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
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113 8. MPOS 1-based Mate POSition
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114 9. ISIZE Inferred insert SIZE
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115 10. SEQ query SEQuence on the same strand as the reference
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116 11. QUAL query QUALity (ASCII-33 gives the Phred base quality)
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117 12. OPT variable OPTional fields in the format TAG:VTYPE:VALUE, tab-separated
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118
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119 The flags are as follows::
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120
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121 Flag Description
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122 ------ -------------------------------------
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123 0x0001 the read is paired in sequencing
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124 0x0002 the read is mapped in a proper pair
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125 0x0004 the query sequence itself is unmapped
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126 0x0008 the mate is unmapped
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127 0x0010 strand of the query (1 for reverse)
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128 0x0020 strand of the mate
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129 0x0040 the read is the first read in a pair
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130 0x0080 the read is the second read in a pair
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131 0x0100 the alignment is not primary
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132
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133 ------
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134
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135 **Do you want to modify the reference name?**
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136
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137 This option allows you to set the name of the reference sequence manually. This is helpful when, for example, you would like to make the reference name compatible with the UCSC naming conventions to be able to display your lastz results as a custom track at the UCSC Genome Browser.
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138
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139 ------
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140
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141 **LASTZ parameter list**
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142
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143 This is an exhaustive list of LASTZ options. Once again, please note that not all parameters are included in this interface. If you would like to make additional options available through Galaxy, e-mail us at galaxy-bugs@bx.psu.edu::
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144
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145 target[[s..e]][-] spec/file containing target sequence (fasta or nib)
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146 [s..e] defines a subrange of the file
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147 - indicates reverse-complement
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148 (use --help=files for more details)
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149 query[[s..e]][-] spec/file containing query sequences (fasta or nib)
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150 if absent, queries come from stdin (unless they
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151 aren't needed, as for --self or --tableonly)
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152 (use --help=files for more details)
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153 --self the target sequence is also the query
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154 --quantum the query sequence contains quantum DNA
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155 --seed=match&lt;length&gt; use a word with no gaps instead of a seed pattern
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156 --seed=half&lt;length&gt; use space-free half-weight word instead of seed pattern
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157 --match=&lt;reward&gt;[,&lt;penalty&gt;] set the score values for a match (+&lt;reward&gt;)
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158 and mismatch (-&lt;penalty&gt;)
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159 --[no]trans[ition][=2] allow one or two transitions in a seed hit
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160 (by default a transition is allowed)
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161 --word=&lt;bits&gt; set max bits for word hash; use this to trade time for
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162 memory, eliminating thrashing for heavy seeds
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163 (default is 28 bits)
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164 --[no]filter=[&lt;T&gt;:]&lt;M&gt; filter half-weight seed hits, requiring at least M
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165 matches and allowing no more than T transversions
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166 (default is no filtering)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
167 --notwins require just one seed hit
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
168 --twins=[&lt;min&gt;:]&lt;maxgap&gt; require two nearby seed hits on the same diagonal
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
169 (default is twins aren't required)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
170 --notwins allow single, isolated seeds
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
171 --[no]recoverseeds avoid losing seeds in hash collisions. Cannot be used with --twins
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
172 --seedqueue=&lt;entries&gt; set number of entries in seed hit queue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
173 (default is 262144)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
174 --anchors=&lt;file&gt; read anchors from a file, instead of discovering anchors
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
175 via seeding
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
176 --recoverhits recover hash-collision seed hits
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
177 (default is not to recover seed hits)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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178 --step=&lt;length&gt; set step length (default is 1)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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179 --maxwordcount=&lt;limit&gt; words occurring more often than &lt;limit&gt; in the target
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
180 are not eligible for seeds
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
181 --strand=both search both strands
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
182 --strand=plus search + strand only (matching strand of query spec)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
183 --strand=minus search - strand only (opposite strand of query spec)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
184 (by default both strands are searched)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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185 --ambiguousn treat N as an ambiguous nucleotide
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
186 (by default N is treated as a sequence splicing character)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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187 --[no]gfextend perform gap-free extension of seed hits to HSPs
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
188 (by default no extension is performed)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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189 --[no]chain perform chaining
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
190 --chain=&lt;diag,anti&gt; perform chaining with given penalties for diagonal and
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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191 anti-diagonal
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
192 (by default no chaining is performed)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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193 --[no]gapped perform gapped alignment (instead of gap-free)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
194 (by default gapped alignment is performed)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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195 --score[s]=&lt;file&gt; read substitution scores from a file
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
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196 (default is HOXD70)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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197 --unitscore[s] scores are +1/-1 for match/mismatch
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
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198 --gap=&lt;[open,]extend&gt; set gap open and extend penalties (default is 400,30)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
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199 --xdrop=&lt;score&gt; set x-drop threshold (default is 10*sub[A][A])
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
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200 --ydrop=&lt;score&gt; set y-drop threshold (default is open+300extend)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
201 --infer[=&lt;control&gt;] infer scores from the sequences, then use them
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
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202 --inferonly[=&lt;control&gt;] infer scores, but don't use them (requires --infscores)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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203 all inference options are read from the control file
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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204 --infscores[=&lt;file&gt;] write inferred scores to a file
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
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205 --hspthresh=&lt;score&gt; set threshold for high scoring pairs (default is 3000)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
206 ungapped extensions scoring lower are discarded
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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207 &lt;score&gt; can also be a percentage or base count
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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208 --entropy adjust for entropy when qualifying HSPs in the x-drop extension
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
209 method
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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210 --noentropy don't adjust for entropy when qualifying HSPs
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
211 --exact=&lt;length&gt; set threshold for exact matches
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
212 if specified, exact matches are found rather than high
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
213 scoring pairs (replaces --hspthresh)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
214 --inner=&lt;score&gt; set threshold for HSPs during interpolation
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
215 (default is no interpolation)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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216 --gappedthresh=&lt;score&gt; set threshold for gapped alignments
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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217 gapped extensions scoring lower are discarded
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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218 &lt;score&gt; can also be a percentage or base count
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
219 (default is to use same value as --hspthresh)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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220 --ball=&lt;score&gt; set minimum score required of words 'in' a quantum ball
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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221 --[no]entropy involve entropy in filtering high scoring pairs
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
222 (default is "entropy")
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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223 --[no]mirror report/use mirror image of all gap-free alignments
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
224 (default is "mirror" for self-alignments only)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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225 --traceback=&lt;bytes&gt; space for trace-back information
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
226 (default is 80.0M)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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227 --masking=&lt;count&gt; mask any position in target hit this many times
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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228 zero indicates no masking
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
229 (default is no masking)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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230 --targetcapsule=&lt;capsule_file&gt; the target seed word position table and seed
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
231 (as well as the target sequence)are read from specified file
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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232 --segments=&lt;segment_file&gt; read segments from a file, instead of discovering
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
233 them via seeding. Replaces other seeding or gap-free extension
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
234 options
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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235 --[no]census[=&lt;file&gt;] count/report how many times each target base aligns
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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236 (default is to not report census)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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237 --identity=&lt;min&gt;[..&lt;max&gt;] filter alignments by percent identity
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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238 0&lt;=min&lt;=max&lt;=100; blocks (or HSPs) outside min..max
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
239 are discarded
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
240 (default is no identity filtering)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
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241 --coverage=&lt;min&gt;[..&lt;max&gt;] filter alignments by percentage pf query covered
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
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242 0&lt;=min&lt;=max&lt;=100; blocks (or HSPs) outside min..max
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
243 are discarded
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
244 (default is no query coverage filtering)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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245 --notrivial do not output trivial self-alignment block if the target and query
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
246 sequences are identical. Using --self enables this option automatically
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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247 --output=&lt;output_file&gt; write the alignments to the specified file name instead of stdout
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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248 --code=&lt;file&gt; give quantum code for query sequence (only for display)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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249 --format=&lt;type&gt; specify output format; one of lav, axt, maf, maf+, maf-, text,
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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250 lav+text, cigar, text, rdplot, general, or general:&lt;fields&gt;
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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251 (by default output is LAV)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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252 --rdotplot=&lt;file&gt; create an additional output file suitable for plotting the alignments
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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253 with the R statistical package.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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254 --markend Just before normal completion, write "# lastz end-of-file" to output file
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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255 --census[=&lt;output_file&gt;] count and report how many times each target base aligns, up
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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256 to 255. Ns are included in the count
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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257 --census16[=&lt;output_file&gt;] count and report how many times each target base aligns, up
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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258 up 65 thousand
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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259 --census32[=&lt;output_file&gt;] count and report how many times each target bas aligns, up
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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260 to 4 billion
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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261 --writecapsule=&lt;capsule_file&gt; just write out a targegt capsule file and quit; don't
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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262 search for seeds or perform subsequent stages
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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263 --verbosity=&lt;level&gt; set info level (0 is minimum, 10 is everything)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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264 (default is 0)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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265 --[no]runtime report runtime in the output file
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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266 (default is to not report runtime)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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267 --tableonly[=count] just produce the target position table, don't
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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268 search for seeds
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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269 --[no]stats[=&lt;file&gt;] show search statistics (or don't)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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270 (not available in this build)
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271 --version report the program version and quit
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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272 --help list all options
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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273 --help=files list information about file specifiers
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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274 --help=short[cuts] list blastz-compatible shortcuts
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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275 --help=yasra list yasra-specific shortcuts
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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276
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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277 </help>
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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278 </tool>