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/tools/meme/fimo.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 238 lines | 198 code | 36 blank | 4 comment | 0 complexity | f6615e228480ced549e7a90313c6475f MD5 | raw file
  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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21330290&gt;`_
223
224
225For detailed information on FIMO, click here_. To view the license_.
226
227------
228
229**Citation**
230
231If 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>