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1 <?xml version="1.0"?>
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2 <tool id="find_in_reference" name="find in reference" version="0.0.1">
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3 <description>filter peptides that are present in proteins</description>
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4 <command interpreter="python">find_in_reference.py --input "$input"
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5 --reference "$reference"
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6 #if $column.set == 'yes':
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7 --input_column $column.input_column
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8 --reference_column $column.reference_column
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9 #end if
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10 $case_insensitive
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11 #if 'novel' in $outputs.__str__ or not 'found' in $outputs.__str__:
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12 --output "$novel"
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13 #end if
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14 #if 'found' in $outputs.__str__:
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15 --filtered "$found"
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16 #if $annotate.from_ref == 'yes' and str($annotate.annotation_columns) != 'None':
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17 --annotation_columns $annotate.annotation_columns
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18 #if $annotate.annotation_separator != '':
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19 --annotation_separator '$annotate.annotation_separator'
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20 #end if
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21 #if $annotate.annotation_col_sep != '':
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22 --annotation_col_sep '$annotate.annotation_col_sep'
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23 #end if
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24 #end if
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25 #end if
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26 </command>
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27 <inputs>
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28 <param name="input" type="data" format="tabular" label="Input file to be filtered"
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29 help="e.g. a peptide fasta converted to tabular"/>
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30 <param name="reference" type="data" format="tabular" label="reference file to search"
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31 help="e.g. a protein fasta converted to tabular"/>
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32 <conditional name="column">
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33 <param name="set" type="select" label="select columns to compare">
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34 <option value="no" selected="true">Use last column of input and reference</option>
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35 <option value="yes">Choose the column of input and reference to compare</option>
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36 </param>
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37 <when value="no"/>
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38 <when value="yes">
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39 <param name="input_column" type="data_column" data_ref="input" label="column in input (defaults to last column)"
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40 help=""/>
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41 <param name="reference_column" type="data_column" data_ref="reference" label="column in reference (defaults to last column)"
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42 help=""/>
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43 </when>
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44 </conditional>
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45 <param name="case_insensitive" type="boolean" truevalue="--case_insensitive" falsevalue="" checked="false" label="Ignore case when comparing"/>
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46 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
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47 <option value="novel" selected="true">lines with no match in reference</option>
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48 <option value="found">lines with match in reference</option>
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49 </param>
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50 <conditional name="annotate">
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51 <param name="from_ref" type="select" label="Annotate found input entries with columns from reference">
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52 <option value="no" selected="true">No</option>
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53 <option value="yes">Yes</option>
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54 </param>
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55 <when value="no"/>
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56 <when value="yes">
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57 <param name="annotation_columns" type="data_column" data_ref="reference" multiple="true" label="columns from reference to append to found input lines"
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58 help=""/>
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59 <param name="annotation_separator" type="text" value=";" optional="true" label="separator to place between annotations from different reference lines"
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60 help="defaults to ;">
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61 <validator type="regex" message="Single quote character is not allowed">^[^']*$</validator>
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62 <sanitizer>
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63 <valid initial="string.printable">
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64 <remove value="'"/>
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65 </valid>
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66 <mapping initial="none">
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67 <add source="'" target=""/>
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68 </mapping>
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69 </sanitizer>
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70 </param>
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71 <param name="annotation_col_sep" type="text" value="," optional="true" label="separator to place between annotation columns from the same reference line"
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72 help="defaults to ,">
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73 <validator type="regex" message="Single quote character is not allowed">^[^']*$</validator>
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74 <sanitizer>
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75 <valid initial="string.printable">
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76 <remove value="'"/>
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77 </valid>
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78 <mapping initial="none">
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79 <add source="'" target=""/>
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80 </mapping>
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81 </sanitizer>
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82 </param>
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83 </when>
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84 </conditional>
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85 </inputs>
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86 <stdio>
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87 <exit_code range="1:" level="fatal" description="Error" />
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88 </stdio>
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89 <outputs>
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90 <data name="found" metadata_source="input" format_source="input" label="${tool.name} on ${on_string}: found">
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91 <filter>'found' in str(outputs)</filter>
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92 </data>
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93 <data name="novel" metadata_source="input" format_source="input" label="${tool.name} on ${on_string}: novel">
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94 <filter>'novel' in str(outputs) or not 'found' in str(outputs)</filter>
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95 </data>
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96 </outputs>
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97 <tests>
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98 <test>
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99 <param name="input" value="human_peptides.tabular" ftype="tabular" dbkey="hg19"/>
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100 <param name="reference" value="human_proteins.tabular" ftype="tabular" dbkey="hg19"/>
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101 <output name="novel" file="novel_peptides.tabular"/>
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102 </test>
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103 </tests>
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104 <help>
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105 **Find in Reference**
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106
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107 Filters lines of a tabular input file by checking if the selected input column value
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108 is a substring of the selected column of any line in the reference file.
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109
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110 This can be used to check if peptides sequences are present in a set of reference proteins,
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111 as a means of filtering out uninteresting peptide sequences.
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112
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113 For Example with::
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114
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115 Input
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116 >pep1 LIL
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117 >pep2 WTF
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118 >pep3 ISK
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119
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120 Reference
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121 >prot1 RLET
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122 >prot2 LLIL
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123 >prot3 LAPSE
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124 >prot3 RISKY
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125
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126 The outputs
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127
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128 Not found in reference
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129 >pep2 WTF
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130
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131 Found in reference
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132 >pep1 LIL
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133 >pep3 ISK
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134
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135
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136 </help>
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137 </tool>
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