Mercurial > repos > iuc > meme_fimo

annotate fimo.xml @ 6:cdcc4bb60bc3 draft

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author iuc
date Wed, 29 Jun 2016 08:35:04 -0400
parents eca84de658b0
children b3f7ff168b9a
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1 <tool id="meme_fimo" name="FIMO" version="4.11.0.3">
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2 <description>- Scan a set of sequences for motifs.</description>
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3 <requirements>
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4 <requirement type="package" version="6.9.3">imagemagick</requirement>
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5 <requirement type="package" version="4.11.0">meme</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9 mkdir -p output &&
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10 python $__tool_directory__/fimo_wrapper.py
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11 --input_motifs "${input_motifs}"
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12 #if str($fasta_type.fasta_type_selector) == 'history':
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13 --input_fasta "${fasta_type.input_database}"
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14 #else:
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15 --input_fasta "${fasta_type.input_database.fields.path}"
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16 #end if
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17 --options_type $options_type.options_type_selector
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18 #if str($options_type.options_type_selector) == 'advanced':
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19 --alpha "${options_type.alpha}"
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20 #if str($options_type.bgfile_type.bgfile_type_selector) == 'motif_file':
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21 --bgfile "motif-file"
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22 #elif str($options_type.bgfile_type.bgfile_type_selector) == 'bgfile':
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23 --bgfile "${options_type.bgfile_type.bgfile}"
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24 #end if
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25 ${options_type.max_strand}
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26 --max_stored_scores "${options_type.max_stored_scores}"
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27 #if str($options_type.motifs_cond.motifs_selector) == 'no':
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28 #for $motif in $options_type.motifs:
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29 --motif "${motif.motif}"
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30 #end for
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31 #end if
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32 --output_separate_motifs ${options_type.output_separate_motifs}
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33 --motif_pseudo "${options_type.motif_pseudo}"
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34 ${options_type.no_qvalue}
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35 ${options_type.norc}
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36 #if str($options_type.parse_genomic_coord_cond.parse_genomic_coord) == 'yes':
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37 --parse_genomic_coord 'yes'
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38 --remove_duplicate_coords ${options_type.parse_genomic_coord_cond.remove_duplicate_coords}
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39 #end if
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40 #if str($options_type.psp_cond.psp_selector) == 'yes':
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41 --input_psp "${input_psp}"
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42 #end if
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43 #if str($options_type.prior_dist_cond.prior_dist_selector) == 'yes':
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44 --input_prior_dist "${input_prior_dist}"
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45 #end if
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46 ${options_type.qv_thresh}
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47 --thresh ${options_type.thresh}
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48 #end if
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49 --output_path '${html_outfile.files_path}'
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50 --html_output "${html_outfile}"
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51 --interval_output '${interval_outfile}'
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52 --txt_output "${txt_outfile}"
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53 --xml_output "${xml_outfile}"
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54 --gff_output "${gff_outfile}"
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55 ]]>
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56 </command>
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57 <inputs>
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58 <param name="input_motifs" type="data" format="memexml" label="'MEME output' formatted file"/>
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59 <conditional name="fasta_type">
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60 <param name="fasta_type_selector" type="select" label="Source for sequence to search">
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61 <option value="cached">Locally Cached sequences</option>
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62 <option value="history" selected="true">Sequences from your history</option>
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63 </param>
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64 <when value="cached">
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65 <param name="input_database" type="select" label="Genome to search">
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66 <options from_data_table="all_fasta" />
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67 </param>
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68 </when>
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69 <when value="history">
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70 <param format="fasta" name="input_database" type="data" label="Sequences"/>
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71 </when>
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72 </conditional>
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73 <conditional name="options_type">
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74 <param name="options_type_selector" type="select" label="Options configuration">
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75 <option value="basic" selected="true">Basic</option>
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76 <option value="advanced">Advanced</option>
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77 </param>
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78 <when value="basic" />
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79 <when value="advanced">
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80 <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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81 <conditional name="bgfile_type">
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82 <param name="bgfile_type_selector" type="select" label="Background file type">
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83 <option value="default" selected="true">Use frequencies embedded in the application from the non-redundant database</option>
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84 <option value="motif_file">Use frequencies from motif file</option>
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85 <option value="bgfile">Use frequencies from background file</option>
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86 </param>
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87 <when value="motif_file" />
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88 <when value="default" />
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89 <when value="bgfile">
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90 <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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91 </when>
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92 </conditional>
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93 <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
iuc
parents:
diff changeset
94 <param name="max_stored_scores" type="integer" value="100000" label="Maximum number of scores that will be stored" />
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
95 <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
96 <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
97 <option value="yes" selected="true">Yes</option>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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parents:
diff changeset
98 <option value="no">No</option>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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parents:
diff changeset
99 </param>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
100 <when value="yes"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
101 <when value="no">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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102 <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
103 <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
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parents:
diff changeset
104 </repeat>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
105 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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diff changeset
106 </conditional>
5
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parents: 2
diff changeset
107 <param name="output_separate_motifs" type="select" label="Output a dataset per motif?" help="Output a collection consisting of a separate dataset for each motif in the input">
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parents: 2
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108 <option value="no" selected="true">No</option>
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parents: 2
diff changeset
109 <option value="yes">Yes</option>
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parents: 2
diff changeset
110 </param>
0
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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111 <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
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112 <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:
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113 <param name="norc" label="Do not score the reverse complement DNA strand" type="boolean" truevalue="--norc" falsevalue="" checked="False" />
5
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parents: 2
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114 <conditional name="parse_genomic_coord_cond">
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parents: 2
diff changeset
115 <param name="parse_genomic_coord" label="Check each sequence header for UCSC style genomic coordinates" type="select">
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parents: 2
diff changeset
116 <option value="no" selected="true">No</option>
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parents: 2
diff changeset
117 <option value="yes">Yes</option>
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parents: 2
diff changeset
118 </param>
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parents: 2
diff changeset
119 <when value="yes">
6
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parents: 5
diff changeset
120 <param name="remove_duplicate_coords" type="select" label="Remove duplicate entries in unique GFF coordinates?" help="Remove duplicate entries as defined by the unique GFF coordinates">
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parents: 5
diff changeset
121 <option value="no" selected="true">No</option>
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parents: 5
diff changeset
122 <option value="yes">Yes</option>
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parents: 5
diff changeset
123 </param>
5
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parents: 2
diff changeset
124 </when>
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parents: 2
diff changeset
125 <when value="no"/>
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parents: 2
diff changeset
126 </conditional>
0
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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diff changeset
127 <conditional name="psp_cond">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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diff changeset
128 <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
129 <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
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diff changeset
130 <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
131 </param>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
132 <when value="no"/>
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iuc
parents:
diff changeset
133 <when value="yes">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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134 <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
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diff changeset
135 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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parents:
diff changeset
136 </conditional>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
137 <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
138 <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
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diff changeset
139 <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
140 <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
141 </param>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
142 <when value="no"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
143 <when value="yes">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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144 <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
145 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
146 </conditional>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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147 <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
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148 <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
149 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
150 </conditional>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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parents:
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151 <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
152 <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
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diff changeset
153 </param>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
154 </inputs>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
155 <outputs>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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156 <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
157 <actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
158 <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
159 <when value="cached">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
160 <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
161 <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
162 <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
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parents:
diff changeset
163 <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
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diff changeset
164 </option>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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diff changeset
165 </action>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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diff changeset
166 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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167 </conditional>
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diff changeset
168 </actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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diff changeset
169 </data>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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170 <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
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diff changeset
171 <actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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diff changeset
172 <conditional name="fasta_type.fasta_type_selector">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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diff changeset
173 <when value="cached">
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diff changeset
174 <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
175 <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
176 <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
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177 </option>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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178 </action>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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diff changeset
179 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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180 </conditional>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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diff changeset
181 </actions>
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diff changeset
182 </data>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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183 <data format="tabular" name="gff_outfile" label="${tool.name} on ${on_string} (almost-gff)">
5
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parents: 2
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184 <filter>options_type['output_separate_motifs'] == 'no'</filter>
0
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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diff changeset
185 <actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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diff changeset
186 <conditional name="fasta_type.fasta_type_selector">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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187 <when value="cached">
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diff changeset
188 <action type="metadata" name="dbkey">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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189 <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
190 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
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191 </option>
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192 </action>
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193 </when>
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194 </conditional>
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195 </actions>
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196 </data>
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197 <collection name="motifs" type="list" label="Motifs: ${tool.name} on ${on_string}">
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198 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output" ext="gff" visible="false" />
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199 <filter>options_type['output_separate_motifs'] == 'yes'</filter>
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200 </collection>
0
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201 <data format="cisml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)">
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202 <actions>
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203 <conditional name="fasta_type.fasta_type_selector">
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204 <when value="cached">
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205 <action type="metadata" name="dbkey">
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206 <option type="from_data_table" name="all_fasta" column="1" offset="0">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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207 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
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208 </option>
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209 </action>
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210 </when>
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211 </conditional>
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212 </actions>
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213 </data>
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214 <data format="interval" name="interval_outfile" label="${tool.name} on ${on_string} (interval)">
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215 <actions>
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216 <conditional name="fasta_type.fasta_type_selector">
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217 <when value="cached">
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218 <action type="metadata" name="dbkey">
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219 <option type="from_data_table" name="all_fasta" column="1" offset="0">
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220 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
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221 </option>
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222 </action>
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223 </when>
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224 </conditional>
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225 </actions>
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226 </data>
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227 </outputs>
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228 <tests>
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229 <test>
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230 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/>
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231 <param name="fasta_type_selector" value="history"/>
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232 <param name="input_database" value="phiX.fasta" ftype="fasta"/>
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233 <param name="options_type_selector" value="basic"/>
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234 <param name="non_commercial_use" value="True"/>
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235 <output name="html_outfile" file="fimo_output_html_1.html" compare="contains"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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236 <output name="txt_outfile" file="fimo_output_txt_1.txt" compare="contains"/>
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237 <output name="gff_outfile" file="fimo_output_almost-gff_1.txt" compare="contains"/>
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238 <output name="xml_outfile" file="fimo_output_xml_1.xml" compare="contains"/>
0
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239 <output name="interval_outfile" file="fimo_output_interval_1.txt" compare="contains"/>
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240 </test>
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241 <test>
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242 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/>
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243 <param name="fasta_type_selector" value="history"/>
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244 <param name="input_database" value="phiX.fasta" ftype="fasta"/>
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245 <param name="options_type_selector" value="advanced"/>
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246 <param name="non_commercial_use" value="True"/>
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247 <output name="html_outfile" file="fimo_output_html_2.html" compare="contains"/>
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248 <output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/>
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249 <output name="gff_outfile" file="fimo_output_almost-gff_2.txt" compare="contains"/>
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250 <output name="xml_outfile" file="fimo_output_xml_2.xml" compare="contains"/>
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251 <output name="interval_outfile" file="fimo_output_interval_2.txt" compare="contains"/>
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252 </test>
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253 <test>
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254 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/>
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255 <param name="fasta_type_selector" value="history"/>
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256 <param name="input_database" value="phiX.fasta" ftype="fasta"/>
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257 <param name="options_type_selector" value="advanced"/>
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258 <param name="parse_genomic_coord" value="--parse_genomic_coord"/>
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259 <param name="remove_duplicate_coords" value="yes"/>
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260 <param name="output_separate_motifs" value="yes"/>
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261 <param name="non_commercial_use" value="True"/>
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262 <output name="html_outfile" file="fimo_output_html_2.html" compare="contains"/>
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263 <output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/>
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264 <output_collection name="motifs" type="list">
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265 <element name="MOTIF1.gff" file="motif1.gff" ftype="gff" compare="contains"/>
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266 </output_collection>
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267 <output name="xml_outfile" file="fimo_output_xml_2.xml" compare="contains"/>
0
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268 <output name="interval_outfile" file="fimo_output_interval_2.txt" compare="contains"/>
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269 </test>
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270 </tests>
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271 <help>
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272
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273 .. class:: warningmark
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274
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275 **WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted.
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276 Before using, be sure to review, agree, and comply with the license.**
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277
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278 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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279 The name FIMO stands for 'Find Individual Motif Occurrences'. The program searches a database of sequences for occurrences of
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280 known motifs, treating each motif independently. Motifs must be in MEME Motif Format. You can define the statistical threshold
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281 (p-value) for motifs and whether FIMO scans just the given sequences or their reverse complements (where applicable).
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282
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283 .. class:: infomark
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284
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285 For detailed information on FIMO, click here_, or view the license_.
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286
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287 .. _here: http://meme-suite.org/doc/fimo.html?man_type=web
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288 .. _license: http://meme-suite.org/doc/copyright.html?man_type=web
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289
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290 </help>
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291 <citations>
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292 <citation type="doi">10.1093/bioinformatics/btr064</citation>
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293 </citations>
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294 </tool>