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Phylip's extra ouputs are now stored in the job working directory
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 20 Nov 2013 16:32:01 -0500
parents 8997f2ca8c7a
children
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1 <tool id="gd_make_gd_file" name="Make File" version="1.0.0">
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2 <description>: Build a gd_snp or gd_genotype file</description>
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3
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4 <command interpreter="python">
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5 #import base64
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6 #set $preamble_arg = base64.b64encode(str($preamble_names))
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7 #set $species_arg = base64.b64encode(str($species))
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8 make_gd_file.py '$input' '$scaffold_col' '$pos_col' '$ref_col' '$rPos_col' '$preamble_arg' '$names' '$species_arg' '$dbkey' '$output_type' '$output'
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9 </command>
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10
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11 <inputs>
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12 <param name="input" type="data" format="tabular" label="Input dataset" />
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13 <param name="scaffold_col" type="data_column" data_ref="input" label="Column with scaffold/contig" />
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14 <param name="pos_col" type="data_column" numerical="true" data_ref="input" label="Column with position" />
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15 <param name="ref_col" type="data_column" data_ref="input" label="Column with reference species chromosome" />
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16 <param name="rPos_col" type="data_column" numerical="true" data_ref="input" label="Column with reference species position" />
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17
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18 <param name="preamble_names" type="text" area="true" size="5x40" label="Preamble column names">
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19 <sanitizer>
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20 <valid initial="string.printable"/>
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21 </sanitizer>
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22 </param>
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23 <param name="names" type="data" format="txt" label="Names dataset" />
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24
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25 <param name="species" type="text" label="Focus species">
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26 <sanitizer>
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27 <valid initial="string.printable"/>
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28 </sanitizer>
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29 </param>
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30 <param name="dbkey" type="genomebuild" label="Reference species" />
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31
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32 <param name="output_type" type="select" label="Output format">
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33 <option value="gd_snp" selected="true">gd_snp</option>
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34 <option value="gd_genotype">gd_genotype</option>
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35 </param>
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36 </inputs>
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37
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38 <outputs>
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39 <data name="output" format="gd_snp">
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40 <change_format>
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41 <when input="output_type" value="gd_genotype" format="gd_genotype" />
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42 </change_format>
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43 </data>
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44 </outputs>
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45
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46 <!--
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47 <tests>
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48 <test>
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49 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
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50 <param name="p1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" />
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51 <param name="lo_coverage" value="0" />
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52 <param name="hi_coverage" value="1000" />
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53 <param name="low_ind_cov" value="3" />
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54 <param name="lo_quality" value="30" />
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55 <output name="output" file="test_out/modify_snp_table/modify.gd_snp" />
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56 </test>
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57 </tests>
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58 -->
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59
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60 <help>
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61 **Dataset formats**
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62
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63 The input datasets are in tabular_ and text_ formats.
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64 The output dataset is in gd_snp_ or gd_genotype_ format. (`Dataset missing?`_)
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65
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66 .. _tabular: ./static/formatHelp.html#tab
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67 .. _text: ./static/formatHelp.html#text
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68 .. _gd_snp: ./static/formatHelp.html#gd_snp
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69 .. _gd_genotype: ./static/formatHelp.html#gd_genotype
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70 .. _Dataset missing?: ./static/formatHelp.html
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71
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72 -----
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73
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74 **What it does**
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75
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76 This tool simplifies the job of creating a Galaxy file with format gd_snp
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77 or gd_genotype. Often, the most complex part of preparing one of these
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78 files is to specify how individuals are related to columns of the table,
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79 a task facilitated by this command. Each gd_snp or gd_genotype file
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80 typically has columnns giving:
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81
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82 1. scaffold/contig name
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83 2. zero-based position in the scaffold/contig
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84 3. reference species chromosome
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85 4. zero-based position in the reference species chromosome
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86
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87 The user needs to specify the columns containing these data. Columns are
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88 numbered starting with 1. The user also specifies brief column names for
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89 these columns. When the focus species and the reference species are the
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90 same, the scaffold/contig name and reference species chromosome columns
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91 will be identical, as will the position in the scaffold/contig and
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92 position in the reference species chromosome columns.
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93
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94 To inform Galaxy about the correpondence between individuals and columns
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95 of the table, the user directs the tool to a history item that lists
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96 the individuals in order. Each line starts with unique name for the
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97 individuals (no embedded space or tab character), followed by an arbitrary
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98 (possibly empty) set of words that are helpful for specifying groups
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99 of individuals.
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100 </help>
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101 </tool>