Mercurial > repos > iuc > meme_fimo

annotate fimo.xml @ 19:01f5d04846c4 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
author iuc
date Thu, 29 Aug 2024 10:19:40 +0000
parents c5209f38700d
children
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01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
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1 <tool id="meme_fimo" name="FIMO" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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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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be146697a083 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 8c1eac566cbcc93ceb3d753170bce144d386722c"
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6 <xrefs>
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7 <xref type="bio.tools">meme_fimo</xref>
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8 </xrefs>
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9 <expand macro="requirements"/>
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10 <command detect_errors="exit_code"><![CDATA[
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11 @CHECK_NON_COMMERCIAL_USE@
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12 fimo
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13 -o ./out/
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14 $scanrc
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15 #if str( $options_type.options_type_selector ) == 'advanced':
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16 --thresh $options_type.thresh
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17 $options_type.qv_thresh
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18 #if str( $options_type.bgfile_type.bgfile_type_selector ) == 'motif_file':
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19 --bgfile --motif--
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20 #elif str( $options_type.bgfile_type.bgfile_type_selector ) == 'bgfile':
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21 --bgfile $options_type.bgfile_type.bgfile
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22 #elif str( $options_type.bgfile_type.bgfile_type_selector ) == 'uniform_distr':
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23 --bgfile --uniform--
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24 #end if
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25 $options_type.max_strand
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26 --max-stored-scores $options_type.max_stored_scores
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28 #if str( $options_type.motifs_cond.motif_selector) == 'yes':
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29 #for $motif in $options_type.motifs_cond.motifs:
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30 --motif '$motif.motif'
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31 #end for
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32 #end if
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34 --motif-pseudo $options_type.motif_pseudo
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35 $options_type.no_qvalue
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36 $options_type.parse_genomic_coords
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38 #if str( $options_type.psp_cond.psp_selector ) == 'yes':
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39 --psp $options_type.psp_cond.input_psp
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40 --alpha $options_type.psp_cond.alpha
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41 #end if
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43 #if str( $options_type.prior_dist_cond.prior_dist_selector ) == 'yes':
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44 --prior-dist $options_type.prior_dist_cond.input_prior_dist
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45 #end if
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46 #end if
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47 '$input_motifs'
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48 #if str($fasta_type.fasta_type_selector) == 'history':
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49 '${fasta_type.input_database}'
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50 #else:
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51 '${fasta_type.input_database.fields.path}'
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52 #end if
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53 && mv ./out/fimo.html '${html_outfile}'
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54 && mv ./out/fimo.tsv '${txt_outfile}'
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55 && mv ./out/fimo.xml '${xml_outfile}'
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56 && mv ./out/fimo.gff '${gff_outfile}'
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57 ]]></command>
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58 <inputs>
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59 <param name="input_motifs" type="data" format="memexml" label="DREME or MEME output XML file" help="DREME or MEME output XML file containing found motifs"/>
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60 <conditional name="fasta_type">
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61 <param name="fasta_type_selector" type="select" label="Source for sequence to search">
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62 <option value="cached">Locally Cached sequences</option>
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63 <option value="history" selected="true">Sequences from your history</option>
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64 </param>
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65 <when value="cached">
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66 <param name="input_database" type="select" label="Genome to search">
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67 <options from_data_table="all_fasta"/>
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68 </param>
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69 </when>
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70 <when value="history">
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71 <param name="input_database" type="data" format="fasta" label="Sequences"/>
0
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72 </when>
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73 </conditional>
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74 <param name="scanrc" type="boolean" truevalue="" falsevalue="--norc" checked="False" label="Check reverse complement strand" help="Search for motifs also on reverse complement strand"/>
0
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75 <conditional name="options_type">
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76 <param name="options_type_selector" type="select" label="Options configuration">
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77 <option value="basic" selected="true">Basic</option>
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78 <option value="advanced">Advanced</option>
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79 </param>
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80 <when value="basic"/>
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81 <when value="advanced">
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82 <param argument="--thresh" type="float" value="1e-4" label="Output threshold for displaying search results" 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."/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
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83 <param argument="--qv-thresh" type="boolean" truevalue="--qv_thresh" falsevalue="" checked="False" label="Apply output threshold to q-values?" help="Default: apply set threshold on p-values"/>
0
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84 <conditional name="bgfile_type">
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85 <param name="bgfile_type_selector" type="select" label="Background model selection">
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86 <option value="default" selected="true">Use embedded letter frequencies from non-redundant DNA/protein database</option>
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87 <option value="motif_file">Use 0-order letter frequencies from motif file</option>
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88 <option value="bgfile">Use 0-order letter frequencies from background file</option>
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89 <option value="uniform_distr">Use uniform letter frequencies</option>
0
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90 </param>
19
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91 <when value="motif_file"/>
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92 <when value="default"/>
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93 <when value="uniform_distr"/>
0
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94 <when value="bgfile">
13
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95 <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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96 </when>
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97 </conditional>
19
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98 <param argument="--max-strand" type="boolean" truevalue="--max-strand" falsevalue="" checked="False" label="Report best match in case of overlapping matches on both strands?" 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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99 <param argument="--max-stored-scores" type="integer" value="100000" label="Maximum number of scores that will be stored" 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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100 <conditional name="motifs_cond">
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101 <param name="motif_selector" type="select" label="Specify single input motifs for scanning?">
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102 <option value="no" selected="true">No</option>
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103 <option value="yes">Yes</option>
0
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104 </param>
13
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105 <when value="no"/>
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106 <when value="yes">
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107 <repeat name="motifs" title="Supply input motif ID">
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108 <param name="motif" type="text" value="" label="Specify motif by id">
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109 <validator type="empty_field"/>
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110 <validator type="regex" message="Value may include alphanumeric characters.">[A-Za-z]+</validator>
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111 </param>
0
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112 </repeat>
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113 </when>
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114 </conditional>
19
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115 <param argument="--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"/>
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116 <param argument="--no-qvalue" type="boolean" truevalue="--no-qvalue" falsevalue="" checked="False" label="Disable q-value calculation?" help="The q-value calculation is that of Benjamini and Hochberg (1995) (default: calculate q-value for each p-value)"/>
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117 <param name="parse_genomic_coords" argument="--parse-genomic-coord" type="boolean" truevalue="--parse-genomic-coord" falsevalue="" checked="False" label="Check each sequence header for UCSC-style genomic coordinates?" help=" If genomic coordinates are found they will be used as the coordinates in the output."/>
0
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118 <conditional name="psp_cond">
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119 <param name="psp_selector" type="select" label="Use position-specific priors?">
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120 <option value="no" selected="true">No</option>
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121 <option value="yes">Yes</option>
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122 </param>
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123 <when value="no"/>
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124 <when value="yes">
19
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125 <param name="input_psp" argument="--psp" type="data" format="txt" label="Select file containing position-specific priors" help="File should be in MEME PSP format or wiggle format (can be generated by MEME suite tool create-priors)"/>
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126 <param argument="--alpha" type="float" min="0" max="1.0" value="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)"/>
0
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127 </when>
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128 </conditional>
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129 <conditional name="prior_dist_cond">
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130 <param name="prior_dist_selector" type="select" label="Use binned distribution of priors?">
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131 <option value="no" selected="true">No</option>
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132 <option value="yes">Yes</option>
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133 </param>
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134 <when value="no"/>
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135 <when value="yes">
19
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136 <param name="input_prior_dist" argument="--prior-dist" type="data" format="txt" label="Select dataset containing binned distribution of priors" help="This file can be generated using the MEME suite tool create-priors"/>
0
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137 </when>
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138 </conditional>
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139 </when>
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140 </conditional>
19
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141 <param name="non_commercial_use" type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False" label="I certify that I am not using this tool for commercial purposes.">
0
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142 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
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143 </param>
13
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144 <section name="output_options" title="Additional output options">
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145 <param name="html_outfile" type="boolean" value="False" label="Output HTML file" help="FIMO HTML output file"/>
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146 <param name="xml_outfile" type="boolean" value="False" label="Output XML file" help="FIMO XML output file"/>
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147 <param name="gff_outfile" type="boolean" value="False" label="Output GFF file" help="FIMO GFF output file"/>
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148 </section>
0
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149 </inputs>
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150 <outputs>
13
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151 <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (text)">
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152 <actions>
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153 <conditional name="fasta_type.fasta_type_selector">
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154 <when value="cached">
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155 <action type="metadata" name="dbkey">
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156 <option type="from_data_table" name="all_fasta" column="1" offset="0">
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157 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
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158 </option>
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159 </action>
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160 </when>
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161 </conditional>
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162 </actions>
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163 </data>
0
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164 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)">
13
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165 <filter>(output_options['html_outfile'] is True)</filter>
0
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166 <actions>
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167 <conditional name="fasta_type.fasta_type_selector">
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168 <when value="cached">
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169 <action type="metadata" name="dbkey">
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170 <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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171 <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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172 <filter type="param_value" ref="fasta_type.input_database" column="1"/>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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173 </option>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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174 </action>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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175 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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176 </conditional>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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177 </actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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178 </data>
19
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179 <data format="gff" name="gff_outfile" label="${tool.name} on ${on_string} (gff)">
13
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180 <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
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181 <actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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182 <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
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183 <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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184 <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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185 <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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186 <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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187 </option>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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188 </action>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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189 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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190 </conditional>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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191 </actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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192 </data>
13
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193 <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
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194 <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
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195 <actions>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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196 <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
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197 <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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198 <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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199 <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
200 <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
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201 </option>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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202 </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
203 </when>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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204 </conditional>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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diff changeset
205 </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
206 </data>
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 </outputs>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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diff changeset
208 <tests>
13
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iuc
parents: 11
diff changeset
209 <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
210 <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
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diff changeset
211 <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
212 <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
213 <param name="scanrc" value="true"/>
0
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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214 <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
215 <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
216 <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
217 <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
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diff changeset
218 <param name="non_commercial_use" value="True"/>
19
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
219 <output name="html_outfile" ftype="html">
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
220 <assert_contents>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
221 <has_text text="TACTAAYM"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
222 <has_text text="MEME file name"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
223 </assert_contents>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
224 </output>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
225 <output name="txt_outfile">
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
226 <assert_contents>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
227 <has_text text="motif_id"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
228 <has_text text="sequence_name"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
229 <has_text text="matched_sequence"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
230 <has_text text="TACTAATA"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
231 </assert_contents>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
232 </output>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
233 <output name="xml_outfile" ftype="memexml">
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
234 <assert_contents>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
235 <has_text text="sequence-data num-sequences"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
236 <has_text text="16569"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
237 <has_text text="Cytosine"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
238 <has_text text="TACTAACA"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
239 </assert_contents>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
240 </output>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
241 <output name="gff_outfile" ftype="gff">
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
242 <assert_contents>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
243 <has_text text="gff-version 3"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
244 <has_text text="TACTAAYM_chrM"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
245 <has_text text="qvalue"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
246 <has_text text="nucleotide_motif"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
247 <has_text text="fimo"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
248 <has_text text="chrM"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
249 <has_n_lines n="12"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
250 </assert_contents>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
251 </output>
5
eca84de658b0 Uploaded
iuc
parents: 2
diff changeset
252 </test>
13
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
diff changeset
253 <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
254 <param name="input_motifs" value="dreme_fimo_input_1.xml" ftype="memexml"/>
5
eca84de658b0 Uploaded
iuc
parents: 2
diff changeset
255 <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
256 <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
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diff changeset
257 <param name="scanrc" value="true"/>
5
eca84de658b0 Uploaded
iuc
parents: 2
diff changeset
258 <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
259 <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
260 <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
261 <param name="html_outfile" value="True"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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diff changeset
262 <param name="xml_outfile" value="True"/>
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263 <param name="gff_outfile" value="True"/>
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264 <param name="non_commercial_use" value="True"/>
19
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265 <output name="html_outfile">
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266 <assert_contents>
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267 <has_text text="MOTIF"/>
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268 <has_text text="WIDTH"/>
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269 <has_text text="TTAACA"/>
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270 <has_text text="GAATGT"/>
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271 </assert_contents>
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272 </output>
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273 <output name="txt_outfile">
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274 <assert_contents>
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275 <has_text text="sequence_name"/>
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276 <has_text text="motif_id"/>
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277 <has_text text="matched_sequence"/>
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278 <has_text text="ACTAAYH"/>
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279 <has_text text="chrM"/>
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280 </assert_contents>
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281 </output>
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282 <output name="xml_outfile" ftype="memexml">
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
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283 <assert_contents>
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284 <has_text text="MEME file name"/>
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285 <has_text text="pseudocount"/>
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286 <has_text text="Not G"/>
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287 <has_text text="Keto"/>
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288 </assert_contents>
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289 </output>
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290 <output name="gff_outfile" ftype="gff">
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291 <assert_contents>
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292 <has_text text="gff-version 3"/>
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293 <has_text text="ID=ACTAAYH-DREME-1-4-chrM"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
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294 <has_text text="nucleotide_motif"/>
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295 <has_text text="fimo"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
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296 <has_text text="chrM"/>
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297 <has_n_lines n="12"/>
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298 </assert_contents>
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299 </output>
13
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300 </test>
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301 <test expect_num_outputs="3">
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302 <param name="input_motifs" value="dreme_fimo_input_1.xml" ftype="memexml"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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303 <param name="fasta_type_selector" value="history"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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304 <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
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305 <param name="scanrc" value="true"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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306 <param name="options_type_selector" value="advanced"/>
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307 <param name="thresh" value="0.01"/>
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308 <param name="bgfile_type_selector" value="uniform_distr"/>
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309 <param name="motif_selector" value="yes"/>
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310 <repeat name="motifs">
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311 <param name="motif" value="ACTAAYH"/>
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312 </repeat>
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313 <param name="html_outfile" value="True"/>
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314 <param name="xml_outfile" value="True"/>
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315 <param name="gff_outfile" value="False"/>
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316 <param name="non_commercial_use" value="True"/>
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317 <output name="html_outfile">
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318 <assert_contents>
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319 <has_text text="top_buttons"/>
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320 <has_text text="database_and_motifs"/>
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321 <has_text text="YTAACA"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
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322 <has_text text="ACTAAYH"/>
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323 <has_text text="DREME"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
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324 </assert_contents>
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325 </output>
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326 <output name="txt_outfile">
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327 <assert_contents>
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328 <has_text text="motif_alt_id"/>
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329 <has_text text="matched_sequence"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
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330 <has_text text="ACTAAYH"/>
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331 <has_text text="ACTAACA"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
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332 </assert_contents>
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333 </output>
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334 <output name="xml_outfile" ftype="memexml">
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335 <assert_contents>
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336 <has_text text="complement"/>
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337 <has_text text="letter"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
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338 <has_text text="16569"/>
01f5d04846c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
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339 <has_text text="dna"/>
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340 <has_text text="ACTAAYH"/>
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341 </assert_contents>
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342 </output>
0
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diff changeset
343 </test>
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344 </tests>
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diff changeset
345 <help>
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346
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347 .. class:: warningmark
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348
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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349 **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
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diff changeset
350 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
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351
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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352 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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353 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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354 known motifs, treating each motif independently. Motifs must be in MEME Motif Format. You can define the statistical threshold
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eca84de658b0 Uploaded
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355 (p-value) for motifs and whether FIMO scans just the given sequences or their reverse complements (where applicable).
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fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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357 .. class:: infomark
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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358
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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359 For detailed information on FIMO, click here_, or view the license_.
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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360
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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361 .. _here: http://meme-suite.org/doc/fimo.html?man_type=web
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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362 .. _license: http://meme-suite.org/doc/copyright.html?man_type=web
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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363
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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364 </help>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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365 <citations>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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366 <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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367 </citations>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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368 </tool>