Mercurial > repos > iuc > meme_fimo

annotate fimo.xml @ 8:53846f74a019 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit ef11594cf3ca79e444ab4e30d83de5951a636faf
author iuc
date Sun, 10 Jul 2016 09:02:14 -0400
parents b3f7ff168b9a
children 307b2f3559bf
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8
53846f74a019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit ef11594cf3ca79e444ab4e30d83de5951a636faf
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1 <tool id="meme_fimo" name="FIMO" version="4.11.1.0">
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2 <description>- Scan a set of sequences for motifs.</description>
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3 <requirements>
8
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4 <requirement type="package" version="1.3.20">graphicsmagick</requirement>
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5 <requirement type="package" version="4.11.1">meme</requirement>
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6 </requirements>
8
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7 <stdio>
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8 <!-- Anything other than zero is an error -->
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9 <exit_code range="1:" />
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10 <!-- In case the return code has not been set propery check stderr too -->
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11 <regex match="Error:" />
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12 <regex match="Exception:" />
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13 </stdio>
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14 <command>
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15 <![CDATA[
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16 mkdir -p output &&
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17 python $__tool_directory__/fimo_wrapper.py
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18 --input_motifs "${input_motifs}"
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19 #if str($fasta_type.fasta_type_selector) == 'history':
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20 --input_fasta "${fasta_type.input_database}"
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21 #else:
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22 --input_fasta "${fasta_type.input_database.fields.path}"
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23 #end if
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24 --options_type $options_type.options_type_selector
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25 #if str($options_type.options_type_selector) == 'advanced':
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26 --alpha "${options_type.alpha}"
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27 #if str($options_type.bgfile_type.bgfile_type_selector) == 'motif_file':
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28 --bgfile "motif-file"
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29 #elif str($options_type.bgfile_type.bgfile_type_selector) == 'bgfile':
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30 --bgfile "${options_type.bgfile_type.bgfile}"
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31 #end if
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32 ${options_type.max_strand}
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33 --max_stored_scores "${options_type.max_stored_scores}"
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34 #if str($options_type.motifs_cond.motifs_selector) == 'no':
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35 #for $motif in $options_type.motifs:
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36 --motif "${motif.motif}"
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37 #end for
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38 #end if
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39 --output_separate_motifs ${options_type.output_separate_motifs}
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40 --motif_pseudo "${options_type.motif_pseudo}"
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41 ${options_type.no_qvalue}
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42 ${options_type.norc}
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43 #if str($options_type.parse_genomic_coord_cond.parse_genomic_coord) == 'yes':
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44 --parse_genomic_coord 'yes'
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45 --remove_duplicate_coords ${options_type.parse_genomic_coord_cond.remove_duplicate_coords}
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46 #end if
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47 #if str($options_type.psp_cond.psp_selector) == 'yes':
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48 --input_psp "${input_psp}"
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49 #end if
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50 #if str($options_type.prior_dist_cond.prior_dist_selector) == 'yes':
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51 --input_prior_dist "${input_prior_dist}"
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52 #end if
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53 ${options_type.qv_thresh}
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54 --thresh ${options_type.thresh}
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55 #end if
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56 --output_path '${html_outfile.files_path}'
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57 --html_output "${html_outfile}"
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58 --interval_output '${interval_outfile}'
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59 --txt_output "${txt_outfile}"
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60 --xml_output "${xml_outfile}"
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61 --gff_output "${gff_outfile}"
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62 ]]>
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63 </command>
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64 <inputs>
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65 <param name="input_motifs" type="data" format="memexml" label="'MEME output' formatted file"/>
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66 <conditional name="fasta_type">
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67 <param name="fasta_type_selector" type="select" label="Source for sequence to search">
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68 <option value="cached">Locally Cached sequences</option>
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69 <option value="history" selected="true">Sequences from your history</option>
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70 </param>
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71 <when value="cached">
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72 <param name="input_database" type="select" label="Genome to search">
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73 <options from_data_table="all_fasta" />
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74 </param>
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75 </when>
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76 <when value="history">
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77 <param format="fasta" name="input_database" type="data" label="Sequences"/>
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78 </when>
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79 </conditional>
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80 <conditional name="options_type">
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81 <param name="options_type_selector" type="select" label="Options configuration">
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82 <option value="basic" selected="true">Basic</option>
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83 <option value="advanced">Advanced</option>
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84 </param>
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85 <when value="basic" />
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86 <when value="advanced">
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87 <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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88 <conditional name="bgfile_type">
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89 <param name="bgfile_type_selector" type="select" label="Background file type">
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90 <option value="default" selected="true">Use frequencies embedded in the application from the non-redundant database</option>
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91 <option value="motif_file">Use frequencies from motif file</option>
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92 <option value="bgfile">Use frequencies from background file</option>
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93 </param>
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parents:
diff changeset
94 <when value="motif_file" />
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
95 <when value="default" />
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
96 <when value="bgfile">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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97 <param name="bgfile" type="data" format="txt" optional="True" label="Background Model" help="File must be in MEME background file format."/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
98 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
99 </conditional>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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100 <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
101 <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
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parents:
diff changeset
102 <conditional name="motifs_cond">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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103 <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
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diff changeset
104 <option value="yes" selected="true">Yes</option>
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parents:
diff changeset
105 <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
106 </param>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
107 <when value="yes"/>
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parents:
diff changeset
108 <when value="no">
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109 <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
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110 <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
111 </repeat>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
112 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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diff changeset
113 </conditional>
5
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parents: 2
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114 <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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115 <option value="no" selected="true">No</option>
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parents: 2
diff changeset
116 <option value="yes">Yes</option>
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parents: 2
diff changeset
117 </param>
0
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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118 <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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119 <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
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120 <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
diff changeset
121 <conditional name="parse_genomic_coord_cond">
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parents: 2
diff changeset
122 <param name="parse_genomic_coord" label="Check each sequence header for UCSC style genomic coordinates" type="select">
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iuc
parents: 2
diff changeset
123 <option value="no" selected="true">No</option>
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parents: 2
diff changeset
124 <option value="yes">Yes</option>
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parents: 2
diff changeset
125 </param>
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parents: 2
diff changeset
126 <when value="yes">
6
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parents: 5
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127 <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
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128 <option value="no" selected="true">No</option>
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parents: 5
diff changeset
129 <option value="yes">Yes</option>
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parents: 5
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130 </param>
5
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parents: 2
diff changeset
131 </when>
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parents: 2
diff changeset
132 <when value="no"/>
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parents: 2
diff changeset
133 </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
134 <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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135 <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
136 <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
137 <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
138 </param>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
139 <when value="no"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
140 <when value="yes">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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parents:
diff changeset
141 <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
142 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
143 </conditional>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
144 <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
145 <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
146 <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
147 <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
148 </param>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
149 <when value="no"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
150 <when value="yes">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
151 <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
152 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
153 </conditional>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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154 <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:
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155 <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
156 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
157 </conditional>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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158 <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:
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159 <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
160 </param>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
161 </inputs>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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diff changeset
162 <outputs>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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163 <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
164 <actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
165 <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
166 <when value="cached">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
167 <action type="metadata" name="dbkey">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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168 <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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parents:
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169 <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
170 <filter type="param_value" ref="fasta_type.input_database" column="1"/>
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diff changeset
171 </option>
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iuc
parents:
diff changeset
172 </action>
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>
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174 </conditional>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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parents:
diff changeset
175 </actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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parents:
diff changeset
176 </data>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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177 <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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parents:
diff changeset
178 <actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
179 <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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parents:
diff changeset
180 <when value="cached">
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parents:
diff changeset
181 <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
182 <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
183 <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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diff changeset
184 </option>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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diff changeset
185 </action>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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parents:
diff changeset
186 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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187 </conditional>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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188 </actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
189 </data>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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190 <data format="tabular" name="gff_outfile" label="${tool.name} on ${on_string} (almost-gff)">
7
b3f7ff168b9a Uploaded
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191 <filter>options_type['options_type_selector'] == 'basic' or (options_type['options_type_selector'] == 'advanced' and 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
iuc
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192 <actions>
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193 <conditional name="fasta_type.fasta_type_selector">
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194 <when value="cached">
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195 <action type="metadata" name="dbkey">
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196 <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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197 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
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198 </option>
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199 </action>
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200 </when>
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201 </conditional>
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202 </actions>
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203 </data>
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204 <collection name="motifs" type="list" label="Motifs: ${tool.name} on ${on_string}">
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205 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output" ext="gff" visible="false" />
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206 <filter>options_type['options_type_selector'] == 'advanced' and options_type['output_separate_motifs'] == 'yes'</filter>
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207 </collection>
0
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208 <data format="cisml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)">
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209 <actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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210 <conditional name="fasta_type.fasta_type_selector">
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211 <when value="cached">
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iuc
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212 <action type="metadata" name="dbkey">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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213 <option type="from_data_table" name="all_fasta" column="1" offset="0">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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214 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
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215 </option>
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216 </action>
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217 </when>
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218 </conditional>
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219 </actions>
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220 </data>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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221 <data format="interval" name="interval_outfile" label="${tool.name} on ${on_string} (interval)">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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222 <actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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223 <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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224 <when value="cached">
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225 <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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226 <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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227 <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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228 </option>
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229 </action>
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230 </when>
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231 </conditional>
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232 </actions>
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233 </data>
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234 </outputs>
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235 <tests>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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236 <test>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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237 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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238 <param name="fasta_type_selector" value="history"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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239 <param name="input_database" value="phiX.fasta" ftype="fasta"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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240 <param name="options_type_selector" value="basic"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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241 <param name="non_commercial_use" value="True"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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242 <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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243 <output name="txt_outfile" file="fimo_output_txt_1.txt" compare="contains"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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244 <output name="gff_outfile" file="fimo_output_almost-gff_1.txt" compare="contains"/>
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245 <output name="xml_outfile" file="fimo_output_xml_1.xml" compare="contains"/>
0
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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246 <output name="interval_outfile" file="fimo_output_interval_1.txt" compare="contains"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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247 </test>
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248 <test>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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249 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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250 <param name="fasta_type_selector" value="history"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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251 <param name="input_database" value="phiX.fasta" ftype="fasta"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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252 <param name="options_type_selector" value="advanced"/>
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253 <param name="non_commercial_use" value="True"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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254 <output name="html_outfile" file="fimo_output_html_2.html" compare="contains"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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255 <output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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256 <output name="gff_outfile" file="fimo_output_almost-gff_2.txt" compare="contains"/>
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257 <output name="xml_outfile" file="fimo_output_xml_2.xml" compare="contains"/>
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258 <output name="interval_outfile" file="fimo_output_interval_2.txt" compare="contains"/>
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259 </test>
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260 <test>
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261 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/>
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262 <param name="fasta_type_selector" value="history"/>
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263 <param name="input_database" value="phiX.fasta" ftype="fasta"/>
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264 <param name="options_type_selector" value="advanced"/>
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265 <param name="parse_genomic_coord" value="yes"/>
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266 <param name="remove_duplicate_coords" value="yes"/>
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267 <param name="output_separate_motifs" value="yes"/>
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268 <param name="non_commercial_use" value="True"/>
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269 <output name="html_outfile" file="fimo_output_html_2.html" compare="contains"/>
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270 <output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/>
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271 <output_collection name="motifs" type="list">
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272 <element name="MOTIF1.gff" file="motif1.gff" ftype="gff" compare="contains"/>
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273 </output_collection>
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274 <output name="xml_outfile" file="fimo_output_xml_2.xml" compare="contains"/>
0
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275 <output name="interval_outfile" file="fimo_output_interval_2.txt" compare="contains"/>
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276 </test>
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277 </tests>
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278 <help>
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279
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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280 .. class:: warningmark
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281
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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282 **WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted.
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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283 Before using, be sure to review, agree, and comply with the license.**
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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284
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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285 FIMO scans a sequence database for individual matches to each of the motifs you provide (sample output for motifs and sequences).
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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286 The name FIMO stands for 'Find Individual Motif Occurrences'. The program searches a database of sequences for occurrences of
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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287 known motifs, treating each motif independently. Motifs must be in MEME Motif Format. You can define the statistical threshold
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288 (p-value) for motifs and whether FIMO scans just the given sequences or their reverse complements (where applicable).
0
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289
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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290 .. class:: infomark
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291
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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292 For detailed information on FIMO, click here_, or view the license_.
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293
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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294 .. _here: http://meme-suite.org/doc/fimo.html?man_type=web
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295 .. _license: http://meme-suite.org/doc/copyright.html?man_type=web
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296
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297 </help>
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298 <citations>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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299 <citation type="doi">10.1093/bioinformatics/btr064</citation>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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300 </citations>
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301 </tool>