1
+ − 1 <tool id="meme_fimo" name="FIMO" version="0.0.1">
+ − 2 <requirements><requirement type="package">meme</requirement></requirements>
+ − 3 <description>- Find Individual Motif Occurrences</description>
+ − 4 <command interpreter="python">fimo_wrapper.py 'fimo --o "${$html_outfile.files_path}" --verbosity "1"
+ − 5
+ − 6 #if str( $options_type.options_type_selector ) == 'advanced':
+ − 7 --max-seq-length "${options_type.max_seq_length}"
+ − 8 --max-stored-scores "${options_type.max_stored_scores }"
+ − 9 --motif-pseudo "${options_type.motif_pseudo}"
+ − 10 ${options_type.norc}
+ − 11 --output-pthresh "${options_type.output_pthresh}"
+ − 12
+ − 13
+ − 14 #for $motif in $options_type.motifs:
+ − 15 --motif "${motif.motif}"
+ − 16 #end for
+ − 17
+ − 18 #if str( $options_type.bgfile_type.bgfile_type_selector ) == 'motif-file':
+ − 19 --bgfile "motif-file"
+ − 20 #elif str( $options_type.bgfile_type.bgfile_type_selector ) == 'motif-file':
+ − 21 --bgfile "${options_type.bgfile_type.bgfile}"
+ − 22 #end if
+ − 23
+ − 24 #if str( $options_type.qvalue_type.qvalue_type_selector ) == 'no-qvalue':
+ − 25 --no-qvalue
+ − 26 #else:
+ − 27 --output-qthresh "${options_type.qvalue_type.output_qthresh}"
+ − 28 #end if
+ − 29 #end if
+ − 30
+ − 31 "${input_motifs}"
+ − 32
+ − 33 #if str( $fasta_type.fasta_type_selector ) == 'history':
+ − 34 "${fasta_type.input_database}"
+ − 35 #else:
+ − 36 "${fasta_type.input_database.fields.path}"
+ − 37 #end if
+ − 38
+ − 39 '
+ − 40
+ − 41 '${html_outfile.files_path}'
+ − 42
+ − 43 '${html_outfile}'
+ − 44
+ − 45 '${interval_outfile}'
+ − 46
+ − 47 '${txt_outfile}'
+ − 48
+ − 49 '${xml_outfile}'
+ − 50
+ − 51 '${gff_outfile}'
+ − 52
+ − 53 </command>
+ − 54 <inputs>
+ − 55 <param format="memexml" name="input_motifs" type="data" label="'MEME output' formatted file"/>
+ − 56
+ − 57 <conditional name="fasta_type">
+ − 58 <param name="fasta_type_selector" type="select" label="Source for sequence to search">
+ − 59 <option value="cached">Locally Cached sequences</option>
+ − 60 <option value="history" selected="true">Sequences from your history</option>
+ − 61 </param>
+ − 62 <when value="cached">
+ − 63 <param name="input_database" type="select" label="Genome to search">
+ − 64 <options from_data_table="all_fasta">
+ − 65 </options>
+ − 66 </param>
+ − 67 </when>
+ − 68 <when value="history">
+ − 69 <param format="fasta" name="input_database" type="data" label="Sequences"/>
+ − 70 </when>
+ − 71 </conditional>
+ − 72
+ − 73 <conditional name="options_type">
+ − 74 <param name="options_type_selector" type="select" label="Options Configuration">
+ − 75 <option value="basic" selected="true">Basic</option>
+ − 76 <option value="advanced">Advanced</option>
+ − 77 </param>
+ − 78 <when value="basic">
+ − 79 <!-- do nothing here -->
+ − 80 </when>
+ − 81 <when value="advanced">
+ − 82
+ − 83 <conditional name="bgfile_type">
+ − 84 <param name="bgfile_type_selector" type="select" label="Background file type">
+ − 85 <option value="motif-file">Use Frequencies from Motif File</option>
+ − 86 <option value="default" selected="true">Use frequencies from non-redundant database (default)</option>
+ − 87 <option value="bgfile">Use Frequencies from Background File</option>
+ − 88 </param>
+ − 89 <when value="motif-file">
+ − 90 <!-- do nothing here -->
+ − 91 </when>
+ − 92 <when value="default">
+ − 93 <!-- do nothing here -->
+ − 94 </when>
+ − 95 <when value="bgfile">
+ − 96 <param name="bgfile" type="data" format="txt" optional="True" label="Background Model" />
+ − 97 </when>
+ − 98 </conditional>
+ − 99
+ − 100 <repeat name="motifs" title="Limit to specified motif">
+ − 101 <param name="motif" type="text" value="" label="Specify motif by id" />
+ − 102 </repeat>
+ − 103
+ − 104 <param name="max_seq_length" type="integer" value="250000000" label="Maximum input sequence length" />
+ − 105 <param name="max_stored_scores" type="integer" value="100000" label="Maximum score count to store" />
+ − 106 <param name="motif_pseudo" type="float" value="0.1" label="Pseudocount to add to counts in motif matrix" />
+ − 107 <param name="norc" label="Do not check reverse complement" type="boolean" truevalue="--norc" falsevalue="" checked="False"/>
+ − 108 <param name="output_pthresh" type="float" value="1e-4" label="p-value threshold" />
+ − 109
+ − 110 <conditional name="qvalue_type">
+ − 111 <param name="qvalue_type_selector" type="select" label="q-value options">
+ − 112 <option value="no-qvalue">Do not compute q-value</option>
+ − 113 <option value="q-value" selected="true">Compute q-value</option>
+ − 114 </param>
+ − 115 <when value="no-qvalue">
+ − 116 <!-- do nothing here -->
+ − 117 </when>
+ − 118 <when value="q-value">
+ − 119 <param name="output_qthresh" type="float" value="1.0" label="q-value threshold" />
+ − 120 </when>
+ − 121 </conditional>
+ − 122
+ − 123 </when>
+ − 124 </conditional>
+ − 125
+ − 126 <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">
+ − 127 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
+ − 128 </param>
+ − 129
+ − 130 </inputs>
+ − 131 <outputs>
+ − 132 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)">
+ − 133 <actions>
+ − 134 <conditional name="fasta_type.fasta_type_selector">
+ − 135 <when value="cached">
+ − 136 <action type="metadata" name="dbkey">
+ − 137 <option type="from_data_table" name="all_fasta" column="1" offset="0">
+ − 138 <filter type="param_value" column="0" value="seq" keep="True"/>
+ − 139 <filter type="param_value" ref="fasta_type.input_database" column="1"/>
+ − 140 </option>
+ − 141 </action>
+ − 142 </when>
+ − 143 </conditional>
+ − 144 </actions>
+ − 145 </data>
+ − 146 <data format="tabular" name="txt_outfile" label="${tool.name} on ${on_string} (text)">
+ − 147 <actions>
+ − 148 <conditional name="fasta_type.fasta_type_selector">
+ − 149 <when value="cached">
+ − 150 <action type="metadata" name="dbkey">
+ − 151 <option type="from_data_table" name="all_fasta" column="1" offset="0">
+ − 152 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
+ − 153 </option>
+ − 154 </action>
+ − 155 </when>
+ − 156 </conditional>
+ − 157 </actions>
+ − 158 </data>
+ − 159 <data format="tabular" name="gff_outfile" label="${tool.name} on ${on_string} (almost-gff)">
+ − 160 <actions>
+ − 161 <conditional name="fasta_type.fasta_type_selector">
+ − 162 <when value="cached">
+ − 163 <action type="metadata" name="dbkey">
+ − 164 <option type="from_data_table" name="all_fasta" column="1" offset="0">
+ − 165 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
+ − 166 </option>
+ − 167 </action>
+ − 168 </when>
+ − 169 </conditional>
+ − 170 </actions>
+ − 171 </data>
+ − 172 <data format="cisml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)">
+ − 173 <actions>
+ − 174 <conditional name="fasta_type.fasta_type_selector">
+ − 175 <when value="cached">
+ − 176 <action type="metadata" name="dbkey">
+ − 177 <option type="from_data_table" name="all_fasta" column="1" offset="0">
+ − 178 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
+ − 179 </option>
+ − 180 </action>
+ − 181 </when>
+ − 182 </conditional>
+ − 183 </actions>
+ − 184 </data>
+ − 185 <data format="interval" name="interval_outfile" label="${tool.name} on ${on_string} (interval)">
+ − 186 <actions>
+ − 187 <conditional name="fasta_type.fasta_type_selector">
+ − 188 <when value="cached">
+ − 189 <action type="metadata" name="dbkey">
+ − 190 <option type="from_data_table" name="all_fasta" column="1" offset="0">
+ − 191 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
+ − 192 </option>
+ − 193 </action>
+ − 194 </when>
+ − 195 </conditional>
+ − 196 </actions>
+ − 197 </data>
+ − 198 </outputs>
+ − 199 <tests>
+ − 200 <test>
+ − 201 <param name="input_motifs" value="meme/meme/meme_output_xml_1.xml" ftype="memexml"/>
+ − 202 <param name="fasta_type_selector" value="history"/>
+ − 203 <param name="input_database" value="phiX.fasta" ftype="fasta"/>
+ − 204 <param name="options_type_selector" value="basic"/>
+ − 205 <param name="non_commercial_use" value="True"/>
+ − 206 <output name="html_outfile" file="meme/fimo/fimo_output_html_1.html" lines_diff="12"/>
+ − 207 <output name="txt_outfile" file="meme/fimo/fimo_output_txt_1.txt" lines_diff="0"/>
+ − 208 <output name="gff_outfile" file="meme/fimo/fimo_output_almost-gff_1.txt" lines_diff="0"/>
+ − 209 <output name="xml_outfile" file="meme/fimo/fimo_output_xml_1.xml" lines_diff="8"/>
+ − 210 <output name="interval_outfile" file="meme/fimo/fimo_output_interval_1.txt" lines_diff="0"/>
+ − 211 </test>
+ − 212 </tests>
+ − 213 <help>
+ − 214
+ − 215 .. class:: warningmark
+ − 216
+ − 217 **WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted. Before using, be sure to review, agree, and comply with the license.**
+ − 218
+ − 219 .. class:: infomark
+ − 220
+ − 221 **To cite FIMO:**
+ − 222 `Grant CE, Bailey TL, Noble WS. FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011 Apr 1;27(7):1017-8. <http://www.ncbi.nlm.nih.gov/pubmed/21330290>`_
+ − 223
+ − 224
+ − 225 For detailed information on FIMO, click here_. To view the license_.
+ − 226
+ − 227 ------
+ − 228
+ − 229 **Citation**
+ − 230
+ − 231 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+ − 232
+ − 233
+ − 234 .. _here: http://meme.nbcr.net/meme/fimo-intro.html
+ − 235 .. _license: http://meme.nbcr.net/meme/COPYRIGHT.html
+ − 236
+ − 237 </help>
+ − 238 </tool>