Mercurial > repos > iuc > meme_fimo

annotate fimo.xml @ 1:fdf47de5bdbc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit d84a6599817ce37c2548cc98b6a01beb7fe4020a
author iuc
date Wed, 20 Jan 2016 08:46:01 -0500
parents fd522a964017
children 0fce5521bb96
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fdf47de5bdbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit d84a6599817ce37c2548cc98b6a01beb7fe4020a
iuc
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1 <tool id="meme_fimo" name="FIMO" version="4.11.0.1">
0
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2 <description>- Scan a set of sequences for motifs.</description>
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3 <requirements>
1
fdf47de5bdbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit d84a6599817ce37c2548cc98b6a01beb7fe4020a
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4 <requirement type="package" version="4.11.0">meme</requirement>
0
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5 </requirements>
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6 <command>
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7 <![CDATA[
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8 python $__tool_directory__/fimo_wrapper.py
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9 --input_motifs "${input_motifs}"
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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10 #if str($fasta_type.fasta_type_selector) == 'history':
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11 --input_fasta "${fasta_type.input_database}"
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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12 #else:
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13 --input_fasta "${fasta_type.input_database.fields.path}"
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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14 #end if
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15 --options_type $options_type.options_type_selector
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16 #if str($options_type.options_type_selector) == 'advanced':
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17 --alpha "${options_type.alpha}"
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18 #if str($options_type.bgfile_type.bgfile_type_selector) == 'motif_file':
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19 --bgfile "motif-file"
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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20 #elif str($options_type.bgfile_type.bgfile_type_selector) == 'bgfile':
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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21 --bgfile "${options_type.bgfile_type.bgfile}"
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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22 #end if
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23 ${options_type.max_strand}
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24 --max_stored_scores "${options_type.max_stored_scores}"
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25 #if str($options_type.motifs_cond.motifs_selector) == 'no':
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26 #for $motif in $options_type.motifs:
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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27 --motif "${motif.motif}"
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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28 #end for
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29 #end if
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30 --motif_pseudo "${options_type.motif_pseudo}"
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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31 ${options_type.no_qvalue}
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32 ${options_type.norc}
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33 ${options_type.parse_genomic_coord}
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34 #if str($options_type.psp_cond.psp_selector) == 'yes':
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35 --input_psp "${input_psp}"
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36 #end if
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37 #if str($options_type.prior_dist_cond.prior_dist_selector) == 'yes':
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38 --input_prior_dist "${input_prior_dist}"
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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39 #end if
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40 ${options_type.qv_thresh}
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41 --thresh ${options_type.thresh}
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42 #end if
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43 --output_path '${html_outfile.files_path}'
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44 --html_output "${html_outfile}"
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45 --interval_output '${interval_outfile}'
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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46 --txt_output "${txt_outfile}"
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47 --xml_output "${xml_outfile}"
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48 --gff_output "${gff_outfile}"
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49 ]]>
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50 </command>
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51 <inputs>
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52 <param name="input_motifs" type="data" format="memexml" label="'MEME output' formatted file"/>
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53 <conditional name="fasta_type">
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54 <param name="fasta_type_selector" type="select" label="Source for sequence to search">
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55 <option value="cached">Locally Cached sequences</option>
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56 <option value="history" selected="true">Sequences from your history</option>
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57 </param>
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58 <when value="cached">
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59 <param name="input_database" type="select" label="Genome to search">
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60 <options from_data_table="all_fasta" />
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61 </param>
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62 </when>
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63 <when value="history">
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64 <param format="fasta" name="input_database" type="data" label="Sequences"/>
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65 </when>
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66 </conditional>
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67 <conditional name="options_type">
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68 <param name="options_type_selector" type="select" label="Options configuration">
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69 <option value="basic" selected="true">Basic</option>
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70 <option value="advanced">Advanced</option>
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71 </param>
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72 <when value="basic" />
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73 <when value="advanced">
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74 <param name="alpha" type="float" value="1.0" min="0" max="1.0" label="Alpha parameter for calculating position specific priors" help="Represents the fraction of all transcription factor binding sites that are binding sites for the TF of interest (must be between 0 and 1)."/>
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75 <conditional name="bgfile_type">
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76 <param name="bgfile_type_selector" type="select" label="Background file type">
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77 <option value="default" selected="true">Use frequencies embedded in the application from the non-redundant database</option>
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78 <option value="motif_file">Use frequencies from motif file</option>
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79 <option value="bgfile">Use frequencies from background file</option>
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80 </param>
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81 <when value="motif_file" />
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82 <when value="default" />
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83 <when value="bgfile">
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84 <param name="bgfile" type="data" format="txt" optional="True" label="Background Model" help="File must be in MEME background file format."/>
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85 </when>
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86 </conditional>
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87 <param name="max_strand" label="If matches on both strands at a given position satisfy the output threshold, only report the match for the strand with the higher score" type="boolean" truevalue="--max_strand" falsevalue="" checked="False" help="If the scores are tied, the matching strand is chosen at random. Leave unchecked to report both matches."/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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88 <param name="max_stored_scores" type="integer" value="100000" label="Maximum number of scores that will be stored" />
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89 <conditional name="motifs_cond">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
90 <param name="motifs_selector" type="select" label="Use all motifs in input?">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
91 <option value="yes" selected="true">Yes</option>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
92 <option value="no">No</option>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
93 </param>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
94 <when value="yes"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
95 <when value="no">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
96 <repeat name="motifs" title="Limit to specified motif">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
97 <param name="motif" type="text" value="" label="Specify motif by id" />
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
98 </repeat>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
99 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
100 </conditional>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
101 <param name="motif_pseudo" type="float" value="0.1" label="Pseudocount to add to counts in motif matrix" help="A pseudocount to be added to each count in the motif matrix, after first multiplying by the corresponding background frequency"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
102 <param name="no_qvalue" label="Do not compute a q-value for each p-value" type="boolean" truevalue="--no_qvalue" falsevalue="" checked="True" help="The q-value calculation is that of Benjamini and Hochberg (1995)."/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
103 <param name="norc" label="Do not score the reverse complement DNA strand" type="boolean" truevalue="--norc" falsevalue="" checked="False" />
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
104 <param name="parse_genomic_coord" label="Check each sequence header for UCSC style genomic coordinates" type="boolean" truevalue="--parse_genomic_coord" falsevalue="" checked="False" />
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
105 <conditional name="psp_cond">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
106 <param name="psp_selector" type="select" label="Use position-specific priors?">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
107 <option value="no" selected="true">No</option>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
108 <option value="yes">Yes</option>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
109 </param>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
110 <when value="no"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
111 <when value="yes">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
112 <param name="input_psp" type="data" format="txt" label="Select dataset containing position specific priors" help="Format must be meme psp or wiggle."/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
113 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
114 </conditional>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
115 <conditional name="prior_dist_cond">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
116 <param name="prior_dist_selector" type="select" label="Use binned distribution of priors?">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
117 <option value="no" selected="true">No</option>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
118 <option value="yes">Yes</option>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
119 </param>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
120 <when value="no"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
121 <when value="yes">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
122 <param name="input_prior_dist" type="data" format="txt" label="Select dataset containing binned distribution of priors"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
123 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
124 </conditional>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
125 <param name="qv_thresh" label="Use q-values for the output threshold" type="boolean" truevalue="--qv_thresh" falsevalue="" checked="False" help="Leave unchecked to use p-values for the output threshold."/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
126 <param name="thresh" type="float" value="1e-4" label="Output threshold for displaying search results" help="Only search results with a p-value less than the threshold will be output. The threshold can be set to use q-values rather than p-values via the option above."/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
127 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
128 </conditional>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
129 <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
130 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
131 </param>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
132 </inputs>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
133 <outputs>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
134 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
135 <actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
136 <conditional name="fasta_type.fasta_type_selector">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
137 <when value="cached">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
138 <action type="metadata" name="dbkey">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
139 <option type="from_data_table" name="all_fasta" column="1" offset="0">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
140 <filter type="param_value" column="0" value="seq" keep="True"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
141 <filter type="param_value" ref="fasta_type.input_database" column="1"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
142 </option>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
143 </action>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
144 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
145 </conditional>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
146 </actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
147 </data>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
148 <data format="tabular" name="txt_outfile" label="${tool.name} on ${on_string} (text)">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
149 <actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
150 <conditional name="fasta_type.fasta_type_selector">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
151 <when value="cached">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
152 <action type="metadata" name="dbkey">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
153 <option type="from_data_table" name="all_fasta" column="1" offset="0">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
154 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
155 </option>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
156 </action>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
157 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
158 </conditional>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
159 </actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
160 </data>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
161 <data format="tabular" name="gff_outfile" label="${tool.name} on ${on_string} (almost-gff)">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
162 <actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
163 <conditional name="fasta_type.fasta_type_selector">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
164 <when value="cached">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
165 <action type="metadata" name="dbkey">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
166 <option type="from_data_table" name="all_fasta" column="1" offset="0">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
167 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
168 </option>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
169 </action>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
170 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
171 </conditional>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
172 </actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
173 </data>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
174 <data format="cisml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
175 <actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
176 <conditional name="fasta_type.fasta_type_selector">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
177 <when value="cached">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
178 <action type="metadata" name="dbkey">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
179 <option type="from_data_table" name="all_fasta" column="1" offset="0">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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180 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
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181 </option>
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182 </action>
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183 </when>
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184 </conditional>
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185 </actions>
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186 </data>
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187 <data format="interval" name="interval_outfile" label="${tool.name} on ${on_string} (interval)">
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188 <actions>
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189 <conditional name="fasta_type.fasta_type_selector">
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190 <when value="cached">
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191 <action type="metadata" name="dbkey">
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192 <option type="from_data_table" name="all_fasta" column="1" offset="0">
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193 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
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194 </option>
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195 </action>
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196 </when>
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197 </conditional>
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198 </actions>
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199 </data>
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200 </outputs>
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201 <tests>
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202 <test>
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203 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/>
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204 <param name="fasta_type_selector" value="history"/>
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205 <param name="input_database" value="phiX.fasta" ftype="fasta"/>
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206 <param name="options_type_selector" value="basic"/>
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207 <param name="non_commercial_use" value="True"/>
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208 <output name="html_outfile" file="fimo_output_html_1.html" compare="contains"/>
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209 <output name="txt_outfile" file="fimo_output_txt_1.txt" compare="contains"/>
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210 <output name="gff_outfile" file="fimo_output_almost-gff_1.txt" compare="contains"/>
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211 <output name="xml_outfile" file="fimo_output_xml_1.xml" lines_diff="8"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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212 <output name="interval_outfile" file="fimo_output_interval_1.txt" compare="contains"/>
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213 </test>
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214 <test>
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215 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/>
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216 <param name="fasta_type_selector" value="history"/>
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217 <param name="input_database" value="phiX.fasta" ftype="fasta"/>
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218 <param name="options_type_selector" value="advanced"/>
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219 <param name="non_commercial_use" value="True"/>
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220 <output name="html_outfile" file="fimo_output_html_2.html" compare="contains"/>
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221 <output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/>
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222 <output name="gff_outfile" file="fimo_output_almost-gff_2.txt" compare="contains"/>
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223 <output name="xml_outfile" file="fimo_output_xml_2.xml" lines_diff="8"/>
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224 <output name="interval_outfile" file="fimo_output_interval_2.txt" compare="contains"/>
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225 </test>
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226 </tests>
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227 <help>
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228
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229 .. class:: warningmark
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230
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231 **WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted.
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232 Before using, be sure to review, agree, and comply with the license.**
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233
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234 FIMO scans a sequence database for individual matches to each of the motifs you provide (sample output for motifs and sequences).
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235 The name FIMO stands for 'Find Individual Motif Occurrences'. The program searches a database of sequences for occurrences of
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236 known motifs, treating each motif independently. Motifs must be in MEME Motif Format. You can define the statistical threshold
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237 (p-value) for motifs and whether FIMO scans just the given sequences or their reverse complements (where applicable), too.
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238
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239 .. class:: infomark
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240
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241 For detailed information on FIMO, click here_, or view the license_.
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242
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243 .. _here: http://meme-suite.org/doc/fimo.html?man_type=web
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244 .. _license: http://meme-suite.org/doc/copyright.html?man_type=web
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245
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246 </help>
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247 <citations>
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248 <citation type="doi">10.1093/bioinformatics/btr064</citation>
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249 </citations>
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250 </tool>