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annotate metaquantome_filter.xml @ 8:a1df90e6e7d4 draft default tip

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author galaxyp
date Fri, 08 Feb 2019 10:36:53 -0500
parents 80ce9ca55697
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1 <tool id="metaquantome_filter" name="metaQuantome: filter" version="@VERSION@.0">
0
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2 <description>for quality, redundancy, and sample coverage</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 @MAKE_SAMPS_TSV@
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9 metaquantome filter
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10 @COMMON_PARAMS@
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11 --expand_file '$expand_file'
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12 --min_peptides $min_peptides
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13 #if $min_pep_nsamp:
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14 #set $nsamp = max(int($min_peptides),int($min_pep_nsamp))
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15 --min_pep_nsamp $nsamp
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16 #else
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17 --min_pep_nsamp all
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18 #end if
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19 --min_children_non_leaf $min_children_non_leaf
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20 #if $min_child_nsamp:
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21 #set $nsamp = max($min_peptides,$min_child_nsamp)
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22 --min_child_nsamp $nsamp
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23 #else
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24 --min_child_nsamp all
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25 #end if
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26 --qthreshold $qthreshold
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27 --outfile='$outfile'
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28 ]]></command>
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29 <inputs>
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30 <expand macro="common_params"/>
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31 <param argument="--expand_file" type="data" format="tabular" label="metaquantome expand file"
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32 help=""/>
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33 <param argument="--min_peptides" type="integer" value="0" min="0" label="min_peptides">
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34 <help>
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35 Used for filtering to well-supported annotations. The
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36 number of peptides providing evidence for a term is
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37 the number of peptides directly annotated with that
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38 term plus the number of peptides annotated with any of
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39 its descendants. Terms with a number of peptides
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40 greater than or equal to min_peptides are retained.
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41 The default is 0.
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42 </help>
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43 </param>
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44 <param argument="--min_pep_nsamp" type="integer" value="" min="0" optional="true" label="min_pep_nsamp">
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45 <help>
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46 Number of samples per group that must meet or exceed
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47 min_peptides. Default is 'all'.
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48 </help>
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49 </param>
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50 <param argument="--min_children_non_leaf" type="integer" value="0" min="0" label="min_children_non_leaf">
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51 <help>
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52 Used for filtering to informative annotations. A term
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53 is retained if it has a number of children greater
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54 than or equal to min_children_non_leaf. The default is 0.
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55 </help>
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56 </param>
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57 <param argument="--min_child_nsamp" type="integer" value="" min="0" optional="true" label="min_child_nsamp">
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58 <help>
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59 Number of samples per group that must meet or exceed
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60 min_children_nsamp. Default is 'all'.
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61 </help>
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62 </param>
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63 <param argument="--qthreshold" type="integer" value="3" min="0" label="qthreshold">
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64 <help>
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65 Minimum number of intensities in each sample group.
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66 Any functional/taxonomic term with lower number of
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67 per-group intensities will be filtered out. The
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68 default is 3, because this is the minimum number for
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69 t-tests.
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70 </help>
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71 </param>
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72
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73 <expand macro="output_samples_choice"/>
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74 </inputs>
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75 <outputs>
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76 <data format="tabular" name="outfile" label="${tool.name} on ${on_string} filtered"/>
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77 <expand macro="output_samples"/>
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78 </outputs>
3
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79 <tests>
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80 <test>
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81 <param name="expand_file" value="go_expanded.tab" ftype="tabular"/>
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82 <param name="mode" value="f" />
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83 <param name="ontology" value="go" />
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84 <param name="samps_src" value="build" />
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85 <repeat name="samps">
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86 <param name="group_name" value="s1"/>
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87 <param name="col_names" value="int1,int2,int3"/>
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88 </repeat>
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89 <repeat name="samps">
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90 <param name="group_name" value="s2"/>
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91 <param name="col_names" value="int4,int5,int6"/>
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92 </repeat>
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93 <param name="min_peptides" value="1" />
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94 <param name="min_pep_nsamp" value="1" />
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95 <param name="min_children_non_leaf" value="2" />
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96 <param name="min_child_nsamp" value="1" />
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97 <param name="qthreshold" value="2" />
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98 <output name="outfile" file="go_filtered.tab" ftype="tabular"/>
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99 </test>
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100 </tests>
0
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101 <help><![CDATA[
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102 metaQuantome filter
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103 ===================
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104
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105 The *filter* module is the second step in the metaQuantome analysis workflow. The
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106 purpose of the filter module is to filter expanded terms to those that are
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107 representative and well-supported by the data.
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108
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109
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110 The image below illustrates the filtering process.
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111
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112 .. image:: filtering.png
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113 :width: 100 %
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114
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115 **Filtering methods**. The circles indicate terms, the grey arrows indicate ‘is a’ relationships, and the blue arrows indicate metaQuantome filtering procedures. (A) Filtering results by number of unique peptides. The numbers inside each term indicate the hypothetical number of peptides giving evidence to each term. (B) Filtering by the number of sample children. The number inside each term indicates the number of children (direct descendants) that term has within the sample. metaQuantome filters out terms that are neither leaves nor meet the user-specified criterion for minimum sample children (here, 2, which is the default). (C) Filtering by the number of samples in which the term was quantified.
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116
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117
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118 Questions, Comments, Problems, Kudos
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119 --------------------------------------
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120
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121 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
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122 ]]></help>
0
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
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123 <expand macro="citations" />
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
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124 </tool>