annotate protxml_to_gff.xml @ 2:68d8c9e521d7 draft

planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:34:50 -0400
parents 28067ed4ea0e
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1 <tool id="protxml_to_gff" name="Proteomics to GFF" version="1.1.0">
2
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2 <description>Export Proteomics Data to GFF</description>
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3 <requirements>
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4 <container type="docker">iracooke/protk-1.4.3</container>
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5 <requirement type="package" version="1.4.3">protk</requirement>
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6 <requirement type="package" version="2.2.29">blast+</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1:" level="fatal" description="Failure" />
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10 </stdio>
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11 <command>
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12 protxml_to_gff.rb $protxml_file
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13 #if $database.source_select=="built_in":
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14 -d $database.dbkey
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15 #else
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16 -d $database.fasta_file
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17 #end if
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18 -c $gene_file
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19 #if str( $gffidpattern ):
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20 --gff-idregex='$gffidpattern'
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21 #end if
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22
2
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23 #if str( $genomeidpattern ):
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24 --genome-idregex='$genomeidpattern'
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25 #end if
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26
2
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27 #if str( $ignorepattern ):
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28 --ignore-regex='$ignorepattern'
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29 #end if
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30
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31 --threshold=$peptide_threshold
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32 --prot-threshold=$prot_threshold
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33 $stack_charges
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34 -o $output
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35 </command>
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36 <inputs>
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37 <conditional name="database">
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38 <param name="source_select" type="select" label="Database source used for Proteomics Searches" help="Database should be an amino acid fasta file with entry id's that can be parsed to obtain contig or scaffold ids referenced in your gff file">
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39 <option value="input_ref">Your Upload File</option>
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40 <option value="built_in">Built-In</option>
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41 </param>
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42 <when value="built_in">
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43 <param name="dbkey" type="select" format="text" >
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44 <label>Database</label>
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45 <options from_file="pepxml_databases.loc">
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46 <column name="name" index="0" />
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47 <column name="value" index="2" />
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48 </options>
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49 </param>
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50 </when>
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51 <when value="input_ref">
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52 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
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53 </when>
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54 </conditional>
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55 <param name="protxml_file" type="data" format="protxml" multiple="false" label="Proteomics Search Results" help="A ProtXML file produced by Protein Prophet"/>
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56 <param name="gene_file" type="data" format="gff3" multiple="false" label="Protein coordinates" help="A gff3 file with coordinates for all protein entries used for proteomics searches. Coordinates should correspond to entries in the genome fasta file"/>
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57 <param name="peptide_threshold" label="Peptide Probability Threshold" type="float" value="0.95" min="0" max="1" help="Only peptides within accepted proteins and passing this threshold will appear in the output"/>
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58 <param name="prot_threshold" label="Protein Probability Threshold" type="float" value="0.99" min="0" max="1" help="Only peptides within proteins passing this threshold will appear in the output"/>
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59 <param name="stack_charges" value="false" type="boolean" label="Peptides with different charges get separate gff entries" help="" truevalue="--stack-charge-states" falsevalue="" />
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60 <param name="gffidpattern" size="40" type="text" value="lcl\|([^ ]*)" label="gff id regex" help="Regex with capture group for parsing gff ids from protein ids">
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61 <sanitizer>
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62 <valid initial="string.printable">
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63 <remove value="&apos;"/>
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64 </valid>
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65 <mapping initial="none">
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66 <add source="&apos;" target="__sq__"/>
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67 </mapping>
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68 </sanitizer>
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69 </param>
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70
2
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71 <param name="genomeidpattern" size="40" type="text" label="genome id regex" help="Regex with capture group for parsing genomic ids from protein ids">
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72 <sanitizer>
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73 <valid initial="string.printable">
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74 <remove value="&apos;"/>
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75 </valid>
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76 <mapping initial="none">
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77 <add source="&apos;" target="__sq__"/>
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78 </mapping>
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79 </sanitizer>
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80 </param>
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81
2
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82 <param name="ignorepattern" size="40" type="text" label="ignore regex" help="Regex to match protein ids that we should ignore completely">
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83 <sanitizer>
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84 <valid initial="string.printable">
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85 <remove value="&apos;"/>
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86 </valid>
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87 <mapping initial="none">
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88 <add source="&apos;" target="__sq__"/>
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89 </mapping>
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90 </sanitizer>
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91 </param>
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92
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93
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94
2
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95 </inputs>
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96 <outputs>
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97 <data format="gff3" name="output" />
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98 </outputs>
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99 <tests>
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100 <test>
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101 <param name="source_select" value="input_ref"/>
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102 <param name="fasta_file" value="small_prot.fasta" format="fasta"/>
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103
2
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104 <param name="protxml_file" value="small.prot.xml" format="protxml"/>
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105 <param name="gene_file" value="small_combined.gff" format="gff3"/>
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106 <output name="output" format="gff3">
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107 <assert_contents>
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108 <has_text text="polypeptide" />
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109 </assert_contents>
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110 </output>
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111 </test>
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112 </tests>
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113 <help>
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114
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115 **What it does**
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116
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117 Exports peptides and proteins to gff
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118
2
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119 </help>
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120 </tool>