Mercurial > repos > yating-l > snap

annotate snap.xml @ 23:ba64ea834baf draft

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author yating-l
date Fri, 12 Aug 2016 18:57:05 -0400
parents ab843488e9ea
children 9a7a53f902e7
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1 <tool id="snap" name="Semi-HMM-based Nucleic Acid Parser (SNAP)" version="1.0">
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2 <requirements>
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3 <requirement type="package" version="1.0">snap</requirement>
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4 </requirements>
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5 <stdio>
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6 <exit_code range="1:" />
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7 </stdio>
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8 <command><![CDATA[
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9 snap
0
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10 #if $settings.advanced == "advanced"
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11 $settings.lcmask
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12 #if $settings.strand == "true"
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13 $settings.strand.onestrand
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14 #end if
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15 #end if
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16 #if $proteins == "-aa":
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17 $proteins "$output2"
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18 #end if
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19 #if $transcripts == "-tx":
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20 $transcripts "$output3"
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21 #end if
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22 -gff
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23 -quiet
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24 $organism
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25 $input1
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26 | python $__tool_directory__/gff2Togff3.py --output $output1
0
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27 ]]></command>
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28 <inputs>
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29 <param type="data" name="input1" format="dna.gz" />
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30 <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset.">
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31 <option value="A.gambiae.hmm">A.gambiae</option>
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32 <option value="A.mellifera.hmm">A.mellifera</option>
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33 <option value="A.thaliana.hmm">Arabidopsis thaliana</option>
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34 <option value="Acanium.hmm">Acanium</option>
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35 <option value="At.hmm">Thale</option>
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36 <option value="B.malayi.hmm">Brugia</option>
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37 <option value="B.mori.hmm">B.mori</option>
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38 <option value="C.elegans.hmm">C.elegans</option>
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39 <option value="C.intestinalis.hmm">Ciona</option>
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40 <option value="Ce.hmm">Ce</option>
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41 <option value="D.melanogaster.hmm">Drosophila melanogaster</option>
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42 <option value="Dm.hmm">Dm</option>
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43 <option value="ixodesA.hmm">ixodesA</option>
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44 <option value="ixodesB.hmm">ixodesB</option>
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45 <option value="mam39-ro.hmm">mam39-ro</option>
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46 <option value="mam39.hmm">mam39</option>
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47 <option value="mam46-ro.hmm">mam46-ro</option>
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48 <option value="mam46.hmm">mam46</option>
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49 <option value="mam54-ro.hmm">mam54-ro</option>
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50 <option value="mam54.hmm">mam54</option>
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51 <option value="mamiso.hmm">mamiso</option>
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52 <option value="minimal.hmm">minimal</option>
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53 <option value="Nasonia.hmm">Nasonia</option>
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54 <option value="nGASP.hmm">nGASP</option>
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55 <option value="nGASPr.hmm">nGASPr</option>
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56 <option value="O.sativa.hmm">O.sativa</option>
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57 <option value="Os.hmm">Os</option>
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58 </param>
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59 <param name="proteins" type="select" label="Create FASTA file of proteins">
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60 <option value=>No</option>
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61 <option value="-aa">Yes</option>
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62 </param>
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63 <param name="transcripts" type="select" label="Create FASTA file of transcripts">
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64 <option value="">No</option>
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65 <option value="-tx">Yes</option>
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66 </param>
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67 <conditional name="settings">
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68 <param name="advanced" type="select" label="Specify advanced parameters">
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69 <option value="simple" selected="true">No, use program defaults.</option>
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70 <option value="advanced">Yes, see full parameter list.</option>
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71 </param>
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72 <when value="simple">
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73 </when>
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74 <when value="advanced">
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75 <param name="lcmask" type="boolean" label="treat lowercase as N" truevalue="-lcmask" falsevalue="" />
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76 <conditional name="strand">
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77 <param name="strand" type="boolean" label="predict on one strand only" />
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78 <when value="true">
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79 <param name="onestrand" type="select" label="Specify which strand to predict">
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80 <option value="-plus">predict on plus strand only.</option>
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81 <option value="-minus">predict on minus strand only.</option>
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82 </param>
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83 </when>
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84 <when value="false">
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85 </when>
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86 </conditional>
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87 </when>
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88 </conditional>
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89 </inputs>
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90 <outputs>
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91 <data name="output1" format="gff3" label="${tool.name} on ${on_string}: GTF/GFF3">
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92 </data>
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93 <data name="output2" format="fasta" label="${tool.name} on ${on_string}: Protein sequence">
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94 <filter>proteins == "-aa"</filter>
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95 </data>
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96 <data name="output3" format="fasta" label="${tool.name} on ${on_string}: Coding sequence">
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97 <filter>transcripts == "-tx"</filter>
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98 </data>
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99 </outputs>
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100 <tests>
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101 <test>
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102 <param name="input1" value="thale.dna.gz"/>
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103 <param name="organism" value="At.hmm" />
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104 <output name="output1" file="thale.gff3"/>
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105 </test>
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106 </tests>
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107 <help><![CDATA[
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108 The general form of the snap command line is:
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109
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110 snap <HMM file> <FASTA file> [options]
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111
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112 HMM file:
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113
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114 The most convenient way to specify the HMM file is by name. This requires
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115 that the ZOE environment variable is set. In this case, snap will look
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116 for the HMM file in $ZOE/HMM. You may also specify the HMM file by an
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117 explicit path. The following are equivalent if $ZOE is in /usr/local:
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118
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119 snap C.elegans.hmm ...
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120 snap /usr/local/Zoe/HMM/C.elegans.hmm ...
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121 snap worm ... # there are a few convenient aliases in $ZOE/HMM
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122
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123 FASTA file:
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124
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125 If you have several sequences to analyze, it is more efficient to run
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126 snap on a concatenated FASTA file rather than separate runs on single
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127 sequence files. The seqeuence may be in a compressed format
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128
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129 If sequences have been masked with lowercase letters, use -lcmask to
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130 prevent exons from appearing in masked DNA.
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131
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132 Output:
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133
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134 Annotation is reported to stdout in a non-standard format (ZFF). You can
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135 change to GFF or ACEDB with the -gff or -ace options. Proteins and
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136 transcripts are reported to FASTA files with the -aa and -tx options.
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137
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138 External definitions:
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139
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140 SNAP allows you to adjust the score of any sequence model at any point
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141 in a sequence. This behavior is invoked by giving a ZFF file to SNAP:
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142
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143 snap <hmm> <sequence> -xdef <ZFF file>
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144
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145 Each feature description uses the 'group' field to issue a command:
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146
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147 SET set the score
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148 ADJ adjust the score up or down
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149 OK set non-cannonical scores
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150
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151 >FOO
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152 Acceptor 120 120 + +50 . . . SET (sets an Acceptor to 50)
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153 Donor 212 212 + -20 . . . ADJ (lowers a Donor by -20)
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154 Inter 338 579 + -2 . . . ADJ (lowers Inter by -2 in a range)
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155 Coding 440 512 - +3 . . . ADJ (raises Coding by +3 in a range)
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156 Donor 625 638 + -5 . . . OK (sets range of odd Donors to -5)
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157
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158 If the output has scrolled off your screen, try 'snap -help | more'
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159
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160 ]]></help>
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161 <citations>
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162 <citation type="bibtex">
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163 @misc{renameTODO,
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164 author = {LastTODO, FirstTODO},
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165 year = {TODO},
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166 title = {TODO},
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167 url = {http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz},
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168 }</citation>
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169 </citations>
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170 </tool>