Mercurial > repos > iuc > reprof

annotate reprof.xml @ 14:8c83f1fb30f6 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reprof commit 98288bb0ee8760018924574b81c8759bac55b529
author iuc
date Fri, 11 Dec 2015 14:26:29 -0500
parents d167e711cf32
children
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1 <?xml version="1.0"?>
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2 <tool id="rost_reprof" name="reprof" version="@WRAPPER_VERSION@-gx1">
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3 <description>protein secondary structure and accessibility prediction</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 ln -s $query query.fa;
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10 python $__tool_directory__/reprof.py query.fa \$REPROF_MODEL_DIR
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11 ]]></command>
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12 <inputs>
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13 <param name="query" label="Protein sequences" type="data" format="fasta" />
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14 <param name="outputs" type="select" multiple="true" label="Additional Outputs">
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15 <option value="pE">Probability of Extended/Sheet</option>
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16 <option value="pH">Probability of Helix</option>
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17 <option value="pL">Probability of Loop</option>
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18 <option value="RI_S">Secondary Structure Reliability Index</option>
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20 <option value="PACC">Absolute Solvent Accessibility</option>
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21 <option value="PREL">Relative Solvent Accessibility</option>
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22 <option value="P10">Relative Solvent Accessibility</option>
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23 <option value="RI_A">Solvent Accessibility Reliability Index</option>
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24 </param>
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25 </inputs>
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26 <outputs>
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27 <data format="gff3" name="secondary_structure" from_work_dir="secondary_structure.gff3" label="Secondary Structure of ${on_string}"/>
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28 <data format="wig" name="pE" from_work_dir="pE.wig" label="Probability of Extended/Sheet (${on_string})">
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29 <filter>outputs is not None and 'pE' in outputs</filter>
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30 </data>
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31 <data format="wig" name="pH" from_work_dir="pH.wig" label="Probability of Helix (${on_string})">
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32 <filter>outputs is not None and 'pH' in outputs</filter>
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33 </data>
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34 <data format="wig" name="pL" from_work_dir="pL.wig" label="Probability of Loop (${on_string})" >
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35 <filter>outputs is not None and 'pL' in outputs</filter>
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36 </data>
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37 <data format="wig" name="RI_S" from_work_dir="RI_S.wig" label="Secondary Structure Reliability Index (${on_string})">
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38 <filter>outputs is not None and 'RI_S' in outputs</filter>
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39 </data>
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41 <data format="gff3" name="solvent_accessibility" from_work_dir="solvent_accessibility.gff3" label="Solvent Accessibile Regions of ${on_string}" />
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42 <data format="wig" name="PACC" from_work_dir="PACC.wig" label="Absolute Solvent Accessibility of ${on_string}">
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43 <filter>outputs is not None and 'PACC' in outputs</filter>
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44 </data>
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45 <data format="wig" name="PREL" from_work_dir="PREL.wig" label="Relative Solvent Accessibility of ${on_string}">
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46 <filter>outputs is not None and 'PREL' in outputs</filter>
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47 </data>
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48 <data format="wig" name="P10" from_work_dir="P10.wig" label="Relative Solvent Accessibility (0-9) of ${on_string}">
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49 <filter>outputs is not None and 'P10' in outputs</filter>
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50 </data>
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51 <data format="wig" name="RI_A" from_work_dir="RI_A.wig" label="Solvent Accessibility Reliability Index (${on_string})">
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52 <filter>outputs is not None and 'RI_A' in outputs</filter>
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53 </data>
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55 <data format="tabular" name="report" from_work_dir="report.tsv" label="Report on Protein Composition of ${on_string}" />
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56 </outputs>
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57 <tests>
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58 <test>
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59 <param name="query" value="test.fa" />
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61 <output name="secondary_structure" file="secondary_structure.gff3" />
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62 <output name="solvent_accessibility" file="solvent_accessibility.gff3" />
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63 <output name="pE" file="pE.wig" />
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64 <output name="pH" file="pH.wig" />
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65 <output name="pL" file="pL.wig" />
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66 <output name="RI_S" file="RI_S.wig" />
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67 <output name="PACC" file="PACC.wig" />
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68 <output name="PREL" file="PREL.wig" />
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69 <output name="P10" file="P10.wig" />
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70 <output name="RI_A" file="RI_A.wig" />
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71 </test>
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72 </tests>
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73 <help><![CDATA[
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74 reprof
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75 ======
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76
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77 Reprof is a protein secondary structure and accessibility predictor from the
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78 Rost Lab. Prediction is done from protein sequences.
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79
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80 Three states of secondary structure are predicted: helix (H; includes alpha-,
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81 pi- and 3_10-helix), (beta-)strand (E = extended strand in beta-sheet
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82 conformation of at least two residues length) and loop (L).
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84 Protein Classification
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85 ----------------------
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86
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87 Proteins can be classified as mixed given the following classes:
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88
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89 - 'all-alpha': %H > 45% AND %E < 5%
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90 - 'all-beta': %H < 5% AND %E > 45%
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91 - 'alpha-beta': %H > 30% AND %E > 20%
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92 - 'mixed': All others
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93
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94 Gff3 Data and Evidence Codes
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95 ----------------------------
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96
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97 In order to facilitate interoperability with other downstream analyses, and to
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98 document provenance, the Galaxy tool author has opted to apply ECO:0000255 to
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99 all annotated features in the GFF3 file. Per the `UniPro Evidence page <http://www.uniprot.org/help/evidences#ECO:0000255>`__
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100
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101 The ECO code ECO:0000255 is also used for information which has been
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102 generated by various sequence analysis programs that are used during the
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103 manual curation process and which has been verified by a curator.
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104
0
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105 ]]></help>
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106 <citations>
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107 <citation type="doi">10.1186/1471-2105-10-S13-O3</citation>
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108 <citation type="doi">10.1002/pro.5560050824</citation>
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109 </citations>
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110 </tool>