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annotate validate_mapping_file.xml @ 0:c1bd0c560018 draft default tip

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author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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1 <tool id="qiime_validate_mapping_file" name="Validate mapping file" version="1.9.1">
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2 <description>to check for required data and format</description>
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3
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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
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8 <expand macro="requirements" />
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9
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10 <version_command><![CDATA[
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11 validate_mapping_file.py --version
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12 ]]></version_command>
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13
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14 <command><![CDATA[
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15 validate_mapping_file.py
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16 -m $mapping_fp
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17 -o validate_mapping_file_output
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18 $verbose
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19 -c $char_replace
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20 $not_barcoded
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21 $variable_len_barcodes
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22 $disable_primer_check
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23
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24 #if str($added_demultiplex_field):
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25 -j $added_demultiplex_field
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26 #end if
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27
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28 $suppress_html
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29
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30 #if not $suppress_html:
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31 &&
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32 mkdir -p $html_report.files_path
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33 &&
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34 cp validate_mapping_file_output/*.html $html_report.files_path
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35 &&
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36 cp "validate_mapping_file_output/overlib.js" "$html_report.extra_files_path"
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37 &&
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38 mv $html_report.files_path/*.html $html_report
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39 #end if
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40 ]]>
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41 </command>
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42
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43 <inputs>
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44 <param name="mapping_fp" label="Metadata mapping filepath" type="data"
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45 format="tabular,csv,txt,tsv" help="(-m/--mapping_fp)"/>
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46
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47 <param name="verbose" type="boolean" label="Enable printing information
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48 to standard out?" truevalue="-v" falsevalue="" checked="False"
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49 help="(-v/--verbose)" />
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50
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51 <param name="char_replace" type="text" value="_" label="Default character
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52 used to replace invalid characters found in the mapping file"
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53 help="Must be a valid character (alphanumeric, period, or underscore).
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54 (-c/--char_replace)"/>
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55
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56 <param name="not_barcoded" type="boolean" label="Are barcodes present?"
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57 truevalue="" falsevalue="--not_barcoded" checked="True"
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58 help="BarcodeSequence header is still required in mapping file
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59 (-b/--not_barcoded)"/>
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60
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61 <param name="variable_len_barcodes" type="boolean" label="Are barcodes with
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62 variable length?" truevalue="" falsevalue="--variable_len_barcodes"
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63 checked="True" help="(-B/--variable_len_barcodes)"/>
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64
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65 <param name="disable_primer_check" type="boolean" label="Disable checks
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66 for primers?" truevalue="-disable_primer_check" falsevalue=""
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67 checked="False" help="LinkerPrimerSequence header is still required
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68 in mapping file (-p/--disable_primer_check)"/>
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69
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70 <param name="added_demultiplex_field" type="text" label="Field
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71 to use in the mapping file as additional demultiplexing (optional)"
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72 help="It can be used with or without barcodes. All combinations of
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73 barcodes/primers and these fields must be unique. The fields must contain
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74 values that can be parsed from the fasta labels such as 'plate=R_2008_12_09'.
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75 In this case, 'plate' would be the column header and 'R_2008_12_09'
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76 would be the field data (minus quotes) in the mapping file.
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77 To use the run prefix from the fasta label, such as 'FLP3FBN01ELBSX',
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78 where 'FLP3FBN01' is generated from the run ID, use 'run_prefix' and
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79 set the run prefix to be used as the data under the column header
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80 'run_prefix' (-j/--added_demultiplex_field)" optional="True"/>
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81
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82 <param name="suppress_html" type="boolean" label="Disable html file
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83 generation?" truevalue="-s" falsevalue="" checked="False"
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84 help="It can be useful for extremely large mapping files
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85 (-s/--suppress_html)"/>
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86 </inputs>
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87
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88 <outputs>
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89 <data name="html_report" format="html"
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90 label="${tool.name} on ${on_string}: html report">
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91 <filter>suppress_html is False</filter>
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92 </data>
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93 <data name="log" format="txt"
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94 from_work_dir="validate_mapping_file_output/*.log"
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95 label="${tool.name} on ${on_string}: log"/>
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96 <data format="tabular" name="mapping_fp_corrected"
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97 from_work_dir="validate_mapping_file_output/*corrected.txt"
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98 label="${tool.name} on ${on_string}: corrected map" />
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99 </outputs>
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100
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101 <tests>
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102 <test>
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103 <param name="mapping_fp" value="map.tsv"/>
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104 <param name="verbose" value="" />
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105 <param name="char_replace" value="_" />
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106 <param name="not_barcoded" value="" />
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107 <param name="variable_len_barcodes" value="" />
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108 <param name="disable_primer_check" value="" />
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109 <param name="suppress_html" value="" />
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110
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111 <output name="log" file="validate_mapping_file_log.txt"/>
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112 <output name="mapping_fp_corrected"
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113 file="validate_mapping_file_corrected_map.tabular"/>
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114 </test>
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115 </tests>
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116
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117 <help><![CDATA[
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118 **What it does?**
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119
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120 This tool checks user’s metadata mapping file for required data, valid format
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121
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122 Specifically, it checks that:
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123
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124 - The BarcodeSequence, LinkerPrimerSequences, and ReversePrimer fields have valid IUPAC DNA characters, and BarcodeSequence characters are non-degenerate (error)
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125 - The SampleID, BarcodeSequence, LinkerPrimerSequence, and Description headers are present. (error)
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126 - There are not duplicate header fields (error)
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127 - There are not duplicate barcodes (error)
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128 - Barcodes are of the same length. Suppressed when variable_len_barcode flag is passed (warning)
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129 - The headers do not contain invalid characters (alphanumeric and underscore only) (warning)
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130 - The data fields do not contain invalid characters (alphanumeric, underscore, space, and +-%./:,; characters) (warning)
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131 - SampleID fields are MIENS compliant (only alphanumeric and . characters). (warning)
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132 - There are no duplicates when the primer and variable length barcodes are appended (error)
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133 - There are no duplicates when barcodes and added demultiplex fields (-j option) are combined (error)
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134 - Data fields are not found beyond the Description column (warning)
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135
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136 More information about this tool is available on
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137 `QIIME documentation <http://qiime.org/scripts/validate_mapping_file.html>`_.
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138 ]]>
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139 </help>
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140
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141 <citations>
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142 <expand macro="citations" />
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143 </citations>
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144
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145 </tool>