PageRenderTime 27ms CodeModel.GetById 3ms RepoModel.GetById 0ms app.codeStats 0ms

/tools/emboss_5/emboss_syco.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 203 lines | 187 code | 5 blank | 11 comment | 0 complexity | de0709dc84a841d995612766f7fdb191 MD5 | raw file
    

  1. <tool id="EMBOSS: syco96" name="syco" version="5.0.0">

    2. 

  2.   <!-- graphics output -->
    3. 

  3.   <description>Synonymous codon usage Gribskov statistic plot</description>

    4. 

  4.   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>

    5. 

  5.   <command interpreter="perl">emboss_single_outputfile_wrapper.pl syco -sequence $input1 -graph png -goutfile $ofile1 -outfile $ofile2 -cfile $cfile -window "$window" -uncommon $uncommon -minimum "$minimum"

    6. 

  6.   -auto</command>

    7. 

  7.   <inputs>

    8. 

  8.     <param format="fasta" name="input1" type="data">

    9. 

  9.       <label>Sequence</label>

    10. 

  10.     </param>

    11. 

  11.     <param name="cfile" type="select">

    12. 

  12.       <label>Codon Usage File</label>

    13. 

  13.       <option value="Ehum.cut">Ehum.cut</option>

    14. 

  14.       <option value="Eyeastcai.cut">Eyeastcai.cut</option>

    15. 

  15.       <option value="Eacc.cut">Eacc.cut</option>

    16. 

  16.       <option value="Eadenovirus5.cut">Eadenovirus5.cut</option>

    17. 

  17.       <option value="Eadenovirus7.cut">Eadenovirus7.cut</option>

    18. 

  18.       <option value="Eaidlav.cut">Eaidlav.cut</option>

    19. 

  19.       <option value="Eanasp.cut">Eanasp.cut</option>

    20. 

  20.       <option value="Eani.cut">Eani.cut</option>

    21. 

  21.       <option value="Eani_h.cut">Eani_h.cut</option>

    22. 

  22.       <option value="Eanidmit.cut">Eanidmit.cut</option>

    23. 

  23.       <option value="Easn.cut">Easn.cut</option>

    24. 

  24.       <option value="Eath.cut">Eath.cut</option>

    25. 

  25.       <option value="Eatu.cut">Eatu.cut</option>

    26. 

  26.       <option value="Eavi.cut">Eavi.cut</option>

    27. 

  27.       <option value="Ebja.cut">Ebja.cut</option>

    28. 

  28.       <option value="Ebly.cut">Ebly.cut</option>

    29. 

  29.       <option value="Ebme.cut">Ebme.cut</option>

    30. 

  30.       <option value="Ebmo.cut">Ebmo.cut</option>

    31. 

  31.       <option value="Ebna.cut">Ebna.cut</option>

    32. 

  32.       <option value="Ebov.cut">Ebov.cut</option>

    33. 

  33.       <option value="Ebovsp.cut">Ebovsp.cut</option>

    34. 

  34.       <option value="Ebst.cut">Ebst.cut</option>

    35. 

  35.       <option value="Ebsu.cut">Ebsu.cut</option>

    36. 

  36.       <option value="Ebsu_h.cut">Ebsu_h.cut</option>

    37. 

  37.       <option value="Ecac.cut">Ecac.cut</option>

    38. 

  38.       <option value="Ecal.cut">Ecal.cut</option>

    39. 

  39.       <option value="Eccr.cut">Eccr.cut</option>

    40. 

  40.       <option value="Ecel.cut">Ecel.cut</option>

    41. 

  41.       <option value="Echi.cut">Echi.cut</option>

    42. 

  42.       <option value="Echicken.cut">Echicken.cut</option>

    43. 

  43.       <option value="Echisp.cut">Echisp.cut</option>

    44. 

  44.       <option value="Echk.cut">Echk.cut</option>

    45. 

  45.       <option value="Echmp.cut">Echmp.cut</option>

    46. 

  46.       <option value="Echnt.cut">Echnt.cut</option>

    47. 

  47.       <option value="Echos.cut">Echos.cut</option>

    48. 

  48.       <option value="Echzm.cut">Echzm.cut</option>

    49. 

  49.       <option value="Echzmrubp.cut">Echzmrubp.cut</option>

    50. 

  50.       <option value="Ecpx.cut">Ecpx.cut</option>

    51. 

  51.       <option value="Ecre.cut">Ecre.cut</option>

    52. 

  52.       <option value="Ecrisp.cut">Ecrisp.cut</option>

    53. 

  53.       <option value="Ectr.cut">Ectr.cut</option>

    54. 

  54.       <option value="Edayhoff.cut">Edayhoff.cut</option>

    55. 

  55.       <option value="Eddi.cut">Eddi.cut</option>

    56. 

  56.       <option value="Eddi_h.cut">Eddi_h.cut</option>

    57. 

  57.       <option value="Edog.cut">Edog.cut</option>

    58. 

  58.       <option value="Edro.cut">Edro.cut</option>

    59. 

  59.       <option value="Edro_h.cut">Edro_h.cut</option>

    60. 

  60.       <option value="Edrosophila.cut">Edrosophila.cut</option>

    61. 

  61.       <option value="Eeca.cut">Eeca.cut</option>

    62. 

  62.       <option value="Eeco.cut">Eeco.cut</option>

    63. 

  63.       <option value="Eeco_h.cut">Eeco_h.cut</option>

    64. 

  64.       <option value="Eecoli.cut">Eecoli.cut</option>

    65. 

  65.       <option value="Ef1.cut">Ef1.cut</option>

    66. 

  66.       <option value="Efish.cut">Efish.cut</option>

    67. 

  67.       <option value="Efmdvpolyp.cut">Efmdvpolyp.cut</option>

    68. 

  68.       <option value="Eham.cut">Eham.cut</option>

    69. 

  69.       <option value="Ehha.cut">Ehha.cut</option>

    70. 

  70.       <option value="Ehin.cut">Ehin.cut</option>

    71. 

  71.       <option value="Ehma.cut">Ehma.cut</option>

    72. 

  72.       <option value="Ehuman.cut">Ehuman.cut</option>

    73. 

  73.       <option value="Ekla.cut">Ekla.cut</option>

    74. 

  74.       <option value="Ekpn.cut">Ekpn.cut</option>

    75. 

  75.       <option value="Ella.cut">Ella.cut</option>

    76. 

  76.       <option value="Emac.cut">Emac.cut</option>

    77. 

  77.       <option value="Emaize.cut">Emaize.cut</option>

    78. 

  78.       <option value="Emam_h.cut">Emam_h.cut</option>

    79. 

  79.       <option value="Emixlg.cut">Emixlg.cut</option>

    80. 

  80.       <option value="Emouse.cut">Emouse.cut</option>

    81. 

  81.       <option value="Emsa.cut">Emsa.cut</option>

    82. 

  82.       <option value="Emse.cut">Emse.cut</option>

    83. 

  83.       <option value="Emta.cut">Emta.cut</option>

    84. 

  84.       <option value="Emtu.cut">Emtu.cut</option>

    85. 

  85.       <option value="Emus.cut">Emus.cut</option>

    86. 

  86.       <option value="Emussp.cut">Emussp.cut</option>

    87. 

  87.       <option value="Emva.cut">Emva.cut</option>

    88. 

  88.       <option value="Emze.cut">Emze.cut</option>

    89. 

  89.       <option value="Emzecp.cut">Emzecp.cut</option>

    90. 

  90.       <option value="Encr.cut">Encr.cut</option>

    91. 

  91.       <option value="Eneu.cut">Eneu.cut</option>

    92. 

  92.       <option value="Engo.cut">Engo.cut</option>

    93. 

  93.       <option value="Eoncsp.cut">Eoncsp.cut</option>

    94. 

  94.       <option value="Epae.cut">Epae.cut</option>

    95. 

  95.       <option value="Epea.cut">Epea.cut</option>

    96. 

  96.       <option value="Epet.cut">Epet.cut</option>

    97. 

  97.       <option value="Epfa.cut">Epfa.cut</option>

    98. 

  98.       <option value="Ephix174.cut">Ephix174.cut</option>

    99. 

  99.       <option value="Ephv.cut">Ephv.cut</option>

    100. 

  100.       <option value="Ephy.cut">Ephy.cut</option>

    101. 

  101.       <option value="Epig.cut">Epig.cut</option>

    102. 

  102.       <option value="Epolyomaa2.cut">Epolyomaa2.cut</option>

    103. 

  103.       <option value="Epombe.cut">Epombe.cut</option>

    104. 

  104.       <option value="Epombecai.cut">Epombecai.cut</option>

    105. 

  105.       <option value="Epot.cut">Epot.cut</option>

    106. 

  106.       <option value="Eppu.cut">Eppu.cut</option>

    107. 

  107.       <option value="Epse.cut">Epse.cut</option>

    108. 

  108.       <option value="Epsy.cut">Epsy.cut</option>

    109. 

  109.       <option value="Epvu.cut">Epvu.cut</option>

    110. 

  110.       <option value="Erab.cut">Erab.cut</option>

    111. 

  111.       <option value="Erabbit.cut">Erabbit.cut</option>

    112. 

  112.       <option value="Erabsp.cut">Erabsp.cut</option>

    113. 

  113.       <option value="Erat.cut">Erat.cut</option>

    114. 

  114.       <option value="Eratsp.cut">Eratsp.cut</option>

    115. 

  115.       <option value="Erca.cut">Erca.cut</option>

    116. 

  116.       <option value="Erhm.cut">Erhm.cut</option>

    117. 

  117.       <option value="Eric.cut">Eric.cut</option>

    118. 

  118.       <option value="Erle.cut">Erle.cut</option>

    119. 

  119.       <option value="Erme.cut">Erme.cut</option>

    120. 

  120.       <option value="Ersp.cut">Ersp.cut</option>

    121. 

  121.       <option value="Esalsp.cut">Esalsp.cut</option>

    122. 

  122.       <option value="Esau.cut">Esau.cut</option>

    123. 

  123.       <option value="Esco.cut">Esco.cut</option>

    124. 

  124.       <option value="Esgi.cut">Esgi.cut</option>

    125. 

  125.       <option value="Eshp.cut">Eshp.cut</option>

    126. 

  126.       <option value="Eshpsp.cut">Eshpsp.cut</option>

    127. 

  127.       <option value="Esli.cut">Esli.cut</option>

    128. 

  128.       <option value="Eslm.cut">Eslm.cut</option>

    129. 

  129.       <option value="Esma.cut">Esma.cut</option>

    130. 

  130.       <option value="Esmi.cut">Esmi.cut</option>

    131. 

  131.       <option value="Esmu.cut">Esmu.cut</option>

    132. 

  132.       <option value="Esoy.cut">Esoy.cut</option>

    133. 

  133.       <option value="Espi.cut">Espi.cut</option>

    134. 

  134.       <option value="Espn.cut">Espn.cut</option>

    135. 

  135.       <option value="Espo.cut">Espo.cut</option>

    136. 

  136.       <option value="Espo_h.cut">Espo_h.cut</option>

    137. 

  137.       <option value="Espu.cut">Espu.cut</option>

    138. 

  138.       <option value="Esta.cut">Esta.cut</option>

    139. 

  139.       <option value="Esty.cut">Esty.cut</option>

    140. 

  140.       <option value="Esus.cut">Esus.cut</option>

    141. 

  141.       <option value="Esv40.cut">Esv40.cut</option>

    142. 

  142.       <option value="Esyhsp.cut">Esyhsp.cut</option>

    143. 

  143.       <option value="Esynsp.cut">Esynsp.cut</option>

    144. 

  144.       <option value="Etbr.cut">Etbr.cut</option>

    145. 

  145.       <option value="Etcr.cut">Etcr.cut</option>

    146. 

  146.       <option value="Eter.cut">Eter.cut</option>

    147. 

  147.       <option value="Etetsp.cut">Etetsp.cut</option>

    148. 

  148.       <option value="Etob.cut">Etob.cut</option>

    149. 

  149.       <option value="Etobcp.cut">Etobcp.cut</option>

    150. 

  150.       <option value="Etom.cut">Etom.cut</option>

    151. 

  151.       <option value="Etrb.cut">Etrb.cut</option>

    152. 

  152.       <option value="Evco.cut">Evco.cut</option>

    153. 

  153.       <option value="Ewht.cut">Ewht.cut</option>

    154. 

  154.       <option value="Exel.cut">Exel.cut</option>

    155. 

  155.       <option value="Exenopus.cut">Exenopus.cut</option>

    156. 

  156.       <option value="Eyeast.cut">Eyeast.cut</option>

    157. 

  157.       <option value="Eyen.cut">Eyen.cut</option>

    158. 

  158.       <option value="Eysc.cut">Eysc.cut</option>

    159. 

  159.       <option value="Eysc_h.cut">Eysc_h.cut</option>

    160. 

  160.       <option value="Eyscmt.cut">Eyscmt.cut</option>

    161. 

  161.       <option value="Eysp.cut">Eysp.cut</option>

    162. 

  162.       <option value="Ezebrafish.cut">Ezebrafish.cut</option>

    163. 

  163.       <option value="Ezma.cut">Ezma.cut</option>

    164. 

  164.     </param>

    165. 

  165.     <param name="window" size="4" type="text" value="30">

    166. 

  166.       <label>Averaging window</label>

    167. 

  167.     </param>

    168. 

  168.     <param name="uncommon" type="select">

    169. 

  169.       <label>Show common codon usage</label>

    170. 

  170.       <option value="no">No</option>

    171. 

  171.       <option value="yes">Yes</option>

    172. 

  172.     </param>

    173. 

  173.     <param name="minimum" size="4" type="text" value="0.15">

    174. 

  174.       <label>Minimum value for a common codon</label>

    175. 

  175.     </param>

    176. 

  176.   </inputs>

    177. 

  177.   <outputs>

    178. 

  178.     <data format="png" name="ofile1" />
    179. 

  179.     <data format="syco" name="ofile2" />

    180. 

  180.   </outputs>
    181. 

  181.  <!--   <tests>
    182. 

  182.     <test>
    183. 

  183.       <param name="input1" value="2.fasta"/>
    184. 

  184.       <param name="cfile" value="Ehum.cut"/>
    185. 

  185.       <param name="window" value="30"/>
    186. 

  186.       <param name="uncommon" value="no"/>
    187. 

  187.       <param name="minimum" value="0.15"/>
    188. 

  188.       <output name="ofile2" file="emboss_syco_out.syco"/>
    189. 

  189.     </test>
    190. 

  190.   </tests> -->

    191. 

  191.   <help>
    192. 

  192. 

  193.     You can view the original documentation here_.
    194. 

  194.     
    195. 

  195.     .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/syco.html

    196. 

  196. 

    197. 

  197. ------

    198. 

  198. 

    199. 

  199. **Citation**

    200. 

  200. 

    201. 

  201. If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
    202. 

  202.   </help>
    203. 

  203. </tool>
    204. 

  204.