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