Mercurial > repos > iuc > meme_fimo

annotate fimo.xml @ 15:0c5239d1aa65 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
author iuc
date Wed, 11 Dec 2019 18:05:35 -0500
parents c1a9a297ba8b
children be146697a083
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c470b36b592d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
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1 <tool id="meme_fimo" name="FIMO" version="@WRAPPER_VERSION@.0">
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2 <description>- Scan a set of sequences for motifs</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 fimo
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9 -o ./out/
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10 $scanrc
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11 #if str( $options_type.options_type_selector ) == 'advanced':
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12 --thresh $options_type.thresh
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13 $options_type.qv_thresh
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14 #if str( $options_type.bgfile_type.bgfile_type_selector ) == 'motif_file':
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15 --bgfile --motif--
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16 #elif str( $options_type.bgfile_type.bgfile_type_selector ) == 'bgfile':
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17 --bgfile $options_type.bgfile_type.bgfile
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18 #elif str( $options_type.bgfile_type.bgfile_type_selector ) == 'uniform_distr':
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19 --bgfile --uniform--
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20 #end if
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21 $options_type.max_strand
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22 --max-stored-scores $options_type.max_stored_scores
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24 #if str( $options_type.motifs_cond.motif_selector) == 'yes':
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25 #for $motif in $options_type.motifs_cond.motifs:
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26 --motif '$motif.motif'
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27 #end for
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28 #end if
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29
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30 --motif-pseudo $options_type.motif_pseudo
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31 $options_type.no_qvalue
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32 $options_type.parse_genomic_coords
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34 #if str( $options_type.psp_cond.psp_selector ) == 'yes':
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35 --psp $options_type.psp_cond.input_psp
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36 --alpha $options_type.psp_cond.alpha
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37 #end if
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38
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39 #if str( $options_type.prior_dist_cond.prior_dist_selector ) == 'yes':
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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40 --prior-dist $options_type.prior_dist_cond.input_prior_dist
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41 #end if
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42 #end if
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43 '$input_motifs'
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44 #if str($fasta_type.fasta_type_selector) == 'history':
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45 '${fasta_type.input_database}'
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46 #else:
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47 '${fasta_type.input_database.fields.path}'
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48 #end if
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49 && mv ./out/fimo.html '${html_outfile}'
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0c5239d1aa65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
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50 && mv ./out/fimo.tsv '${txt_outfile}'
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51 && mv ./out/fimo.xml '${xml_outfile}'
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52 && mv ./out/fimo.gff '${gff_outfile}'
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53 ]]></command>
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54 <inputs>
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55 <param name="input_motifs" type="data" format="memexml" label="DREME or MEME output XML file"
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56 help="DREME or MEME output XML file containing found motifs"/>
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57 <conditional name="fasta_type">
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58 <param name="fasta_type_selector" type="select" label="Source for sequence to search">
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59 <option value="cached">Locally Cached sequences</option>
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60 <option value="history" selected="true">Sequences from your history</option>
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61 </param>
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62 <when value="cached">
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63 <param name="input_database" type="select" label="Genome to search">
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64 <options from_data_table="all_fasta" />
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65 </param>
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66 </when>
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67 <when value="history">
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68 <param format="fasta" name="input_database" type="data" label="Sequences"/>
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69 </when>
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70 </conditional>
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71 <param name="scanrc" label="Check reverse complement strand" type="boolean"
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72 truevalue="" falsevalue="--norc" checked="False"
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73 help="Search for motifs also on reverse complement strand"/>
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74 <conditional name="options_type">
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75 <param name="options_type_selector" type="select" label="Options configuration">
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76 <option value="basic" selected="true">Basic</option>
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77 <option value="advanced">Advanced</option>
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78 </param>
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79 <when value="basic"/>
0
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80 <when value="advanced">
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81 <param name="thresh" type="float" value="1e-4" argument="--thresh"
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82 label="Output threshold for displaying search results"
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83 help="Only output results with a p-value less than the given threshold. To apply set threshold to q-values rather than p-values, set --qv-thresh."/>
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84 <param name="qv_thresh" label="Apply output threshold to q-values?" argument="--qv-thresh"
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85 type="boolean" truevalue="--qv_thresh" falsevalue="" checked="False"
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86 help="Default: apply set threshold on p-values"/>
0
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87 <conditional name="bgfile_type">
13
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88 <param name="bgfile_type_selector" type="select" label="Background model selection">
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89 <option value="default" selected="true">Use embedded letter frequencies from non-redundant DNA/protein database</option>
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90 <option value="motif_file">Use 0-order letter frequencies from motif file</option>
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91 <option value="bgfile">Use 0-order letter frequencies from background file</option>
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92 <option value="uniform_distr">Use uniform letter frequencies</option>
0
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93 </param>
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94 <when value="motif_file" />
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95 <when value="default" />
13
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parents: 11
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96 <when value="uniform_distr" />
0
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97 <when value="bgfile">
13
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98 <param name="bgfile" type="data" format="txt" optional="True" label="Background model file" help="File must be in Markov background model format (see MEME suite tool fasta-get-markov for details)"/>
0
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diff changeset
99 </when>
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100 </conditional>
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101 <param name="max_strand" label="Report best match in case of overlapping matches on both strands?" argument="--max-strand"
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102 type="boolean" truevalue="--max-strand" falsevalue="" checked="False"
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103 help="If matches on both strands at a given position satisfy the output threshold, only report the match for the strand with the higher score. If the scores are tied, the matching strand is chosen at random (default: report both matches)."/>
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104 <param name="max_stored_scores" type="integer" value="100000" argument="--max-stored-scores"
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105 label="Maximum number of scores that will be stored"
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106 help="Keeping a complete list of scores may exceed available memory. Once the number of stored scores reaches the maximum allowed, the least significant 50% of scores will be dropped. In this case, the list of reported motifs may be incomplete and the q-value calculation will be approximate."/>
0
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107 <conditional name="motifs_cond">
13
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108 <param name="motif_selector" type="select" label="Specify single input motifs for scanning?">
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109 <option value="no" selected="true">No</option>
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110 <option value="yes">Yes</option>
0
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111 </param>
13
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parents: 11
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112 <when value="no"/>
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113 <when value="yes">
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114 <repeat name="motifs" title="Supply input motif ID">
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115 <param name="motif" type="text" value="" label="Specify motif by id">
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116 <validator type="empty_field" />
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117 <validator type="regex" message="Value may include alphanumeric characters.">[A-Za-z]+</validator>
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118 </param>
0
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119 </repeat>
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120 </when>
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121 </conditional>
13
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122 <param name="motif_pseudo" type="float" value="0.1" argument="--motif-pseudo"
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123 label="Pseudocount to add to counts in motif matrix"
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124 help="A pseudocount to be added to each count in the motif matrix, after first multiplying by the corresponding background frequency"/>
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125 <param name="no_qvalue" label="Disable q-value calculation?"
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126 type="boolean" truevalue="--no-qvalue" falsevalue="" checked="False" argument="--no-qvalue"
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127 help="The q-value calculation is that of Benjamini and Hochberg (1995) (default: calculate q-value for each p-value)"/>
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128 <param name="parse_genomic_coords" label="Check each sequence header for UCSC-style genomic coordinates?"
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129 type="boolean" truevalue="--parse-genomic-coord" falsevalue="" checked="False" argument="--parse-genomic-coord"
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130 help=" If genomic coordinates are found they will be used as the coordinates in the output."/>
0
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131 <conditional name="psp_cond">
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132 <param name="psp_selector" type="select" label="Use position-specific priors?">
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133 <option value="no" selected="true">No</option>
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134 <option value="yes">Yes</option>
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135 </param>
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diff changeset
136 <when value="no"/>
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137 <when value="yes">
13
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138 <param name="input_psp" type="data" format="txt" argument="--psp"
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139 label="Select file containing position-specific priors"
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140 help="File should be in MEME PSP format or wiggle format (can be generated by MEME suite tool create-priors)"/>
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141 <param name="alpha" type="float" value="1.0" min="0" max="1.0" argument="--alpha"
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142 label="Alpha parameter for calculating position-specific priors"
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143 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)"/>
0
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144 </when>
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145 </conditional>
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146 <conditional name="prior_dist_cond">
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147 <param name="prior_dist_selector" type="select" label="Use binned distribution of priors?">
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148 <option value="no" selected="true">No</option>
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149 <option value="yes">Yes</option>
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150 </param>
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151 <when value="no"/>
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152 <when value="yes">
13
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153 <param name="input_prior_dist" type="data" format="txt" argument="--prior-dist"
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154 label="Select dataset containing binned distribution of priors"
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155 help="This file can be generated using the MEME suite tool create-priors"/>
0
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156 </when>
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157 </conditional>
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158 </when>
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159 </conditional>
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160 <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">
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161 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
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162 </param>
13
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163 <section name="output_options" title="Additional output options">
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164 <param name="html_outfile" type="boolean" value="False" label="Output HTML file" help="FIMO HTML output file"/>
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165 <param name="xml_outfile" type="boolean" value="False" label="Output XML file" help="FIMO XML output file"/>
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166 <param name="gff_outfile" type="boolean" value="False" label="Output GFF file" help="FIMO GFF output file"/>
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167 </section>
0
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168 </inputs>
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169 <outputs>
13
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170 <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (text)">
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171 <actions>
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diff changeset
172 <conditional name="fasta_type.fasta_type_selector">
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
173 <when value="cached">
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
174 <action type="metadata" name="dbkey">
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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parents: 11
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175 <option type="from_data_table" name="all_fasta" column="1" offset="0">
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
176 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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parents: 11
diff changeset
177 </option>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
178 </action>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
179 </when>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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parents: 11
diff changeset
180 </conditional>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
181 </actions>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
182 </data>
0
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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183 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)">
13
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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184 <filter>(output_options['html_outfile'] is True)</filter>
0
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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185 <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
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
iuc
parents:
diff changeset
187 <when value="cached">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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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
parents:
diff changeset
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
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diff changeset
190 <filter type="param_value" column="0" value="seq" keep="True"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
191 <filter type="param_value" ref="fasta_type.input_database" column="1"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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diff changeset
192 </option>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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193 </action>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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diff changeset
194 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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195 </conditional>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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196 </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
197 </data>
13
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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parents: 11
diff changeset
198 <data format="txt" name="gff_outfile" label="${tool.name} on ${on_string} (gff)">
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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diff changeset
199 <filter>(output_options['gff_outfile'] is True)</filter>
0
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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diff changeset
200 <actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
201 <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
202 <when value="cached">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
203 <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
204 <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
205 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
206 </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
207 </action>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
208 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
209 </conditional>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
210 </actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
211 </data>
13
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
212 <data format="memexml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)">
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
213 <filter>(output_options['xml_outfile'] is True)</filter>
0
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
214 <actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
215 <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
216 <when value="cached">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
217 <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
218 <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
219 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
220 </option>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
221 </action>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
222 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
223 </conditional>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
224 </actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
225 </data>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
226 </outputs>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
227 <tests>
13
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
228 <test expect_num_outputs="4">
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
229 <param name="input_motifs" value="meme_fimo_input_1.xml" ftype="memexml"/>
0
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
230 <param name="fasta_type_selector" value="history"/>
13
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
231 <param name="input_database" value="hsa_chrM.fa" ftype="fasta"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
232 <param name="scanrc" value="true"/>
0
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
233 <param name="options_type_selector" value="basic"/>
13
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
234 <param name="html_outfile" value="True"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
235 <param name="xml_outfile" value="True"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
236 <param name="gff_outfile" value="True"/>
0
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
237 <param name="non_commercial_use" value="True"/>
15
0c5239d1aa65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
iuc
parents: 14
diff changeset
238 <output name="html_outfile" file="fimo_output_test1.html" compare="contains"/>
0c5239d1aa65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
iuc
parents: 14
diff changeset
239 <output name="txt_outfile" file="fimo_output_test1.txt" compare="contains"/>
0c5239d1aa65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
iuc
parents: 14
diff changeset
240 <output name="xml_outfile" file="fimo_output_test1.xml" compare="contains"/>
0c5239d1aa65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
iuc
parents: 14
diff changeset
241 <output name="gff_outfile" file="fimo_output_test1.gff" compare="contains"/>
5
eca84de658b0 Uploaded
iuc
parents: 2
diff changeset
242 </test>
13
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
243 <test expect_num_outputs="4">
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
244 <param name="input_motifs" value="dreme_fimo_input_1.xml" ftype="memexml"/>
5
eca84de658b0 Uploaded
iuc
parents: 2
diff changeset
245 <param name="fasta_type_selector" value="history"/>
13
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
246 <param name="input_database" value="hsa_chrM.fa" ftype="fasta"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
247 <param name="scanrc" value="true"/>
5
eca84de658b0 Uploaded
iuc
parents: 2
diff changeset
248 <param name="options_type_selector" value="advanced"/>
13
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
249 <param name="bgfile_type_selector" value="bgfile"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
250 <param name="bgfile" value="fimo_background_probs_hsa_chrM.txt"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
251 <param name="html_outfile" value="True"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
252 <param name="xml_outfile" value="True"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
253 <param name="gff_outfile" value="True"/>
5
eca84de658b0 Uploaded
iuc
parents: 2
diff changeset
254 <param name="non_commercial_use" value="True"/>
15
0c5239d1aa65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
iuc
parents: 14
diff changeset
255 <output name="html_outfile" file="fimo_output_test2.html" compare="contains"/>
0c5239d1aa65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
iuc
parents: 14
diff changeset
256 <output name="txt_outfile" file="fimo_output_test2.txt" compare="contains"/>
0c5239d1aa65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
iuc
parents: 14
diff changeset
257 <output name="xml_outfile" file="fimo_output_test2.xml" compare="contains"/>
0c5239d1aa65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
iuc
parents: 14
diff changeset
258 <output name="gff_outfile" file="fimo_output_test2.gff" compare="contains"/>
13
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
259 </test>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
260 <test expect_num_outputs="3">
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
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261 <param name="input_motifs" value="dreme_fimo_input_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="hsa_chrM.fa" ftype="fasta"/>
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264 <param name="scanrc" value="true"/>
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265 <param name="options_type_selector" value="advanced"/>
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266 <param name="thresh" value="0.01"/>
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267 <param name="bgfile_type_selector" value="uniform_distr"/>
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268 <param name="motif_selector" value="yes"/>
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269 <repeat name="motifs">
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270 <param name="motif" value="ACTAAYH"/>
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271 </repeat>
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272 <param name="html_outfile" value="True"/>
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273 <param name="xml_outfile" value="True"/>
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274 <param name="gff_outfile" value="False"/>
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275 <param name="non_commercial_use" value="True"/>
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276 <output name="html_outfile" file="fimo_output_test3.html" compare="contains"/>
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277 <output name="txt_outfile" file="fimo_output_test3.txt" compare="contains"/>
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278 <output name="xml_outfile" file="fimo_output_test3.xml" compare="contains"/>
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279 </test>
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280 </tests>
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281 <help>
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282
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283 .. class:: warningmark
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284
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285 **WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted.
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286 Before using, be sure to review, agree, and comply with the license.**
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287
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288 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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289 The name FIMO stands for 'Find Individual Motif Occurrences'. The program searches a database of sequences for occurrences of
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290 known motifs, treating each motif independently. Motifs must be in MEME Motif Format. You can define the statistical threshold
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291 (p-value) for motifs and whether FIMO scans just the given sequences or their reverse complements (where applicable).
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292
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293 .. class:: infomark
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294
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295 For detailed information on FIMO, click here_, or view the license_.
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296
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297 .. _here: http://meme-suite.org/doc/fimo.html?man_type=web
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298 .. _license: http://meme-suite.org/doc/copyright.html?man_type=web
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299
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300 </help>
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301 <citations>
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302 <citation type="doi">10.1093/bioinformatics/btr064</citation>
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303 </citations>
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304 </tool>