Mercurial > repos > galaxyp > metaquantome_filter

annotate metaquantome_filter.xml @ 6:35cc7ca0bdc7 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
author galaxyp
date Mon, 18 Mar 2024 12:35:03 +0000
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deaf035bbe9f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 9204193c3442e427c149b90f15fe3a56fc9802e9"
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1 <tool id="metaquantome_filter" name="metaQuantome: filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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>
6
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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6 <expand macro="xrefs"/>
0
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 metaquantome filter
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10 --samps '$samps'
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11 --mode '$mode_args.mode'
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12 #if $mode_args.mode == 'f' or $mode_args.mode == 'ft'
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13 --ontology='$mode_args.ontology_args.ontology'
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14 #end if
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15 --expand_file '$expand_file'
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16 --min_peptides $min_peptides
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17 #if $min_pep_nsamp != "":
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18 --min_pep_nsamp $min_pep_nsamp
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19 #else
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20 --min_pep_nsamp all
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21 #end if
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22 --min_children_non_leaf $min_children_non_leaf
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23 #if $min_child_nsamp != "":
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24 --min_child_nsamp $min_child_nsamp
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25 #else
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26 --min_child_nsamp all
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27 #end if
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28 --qthreshold $qthreshold
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29 --outfile='$outfile'
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30 ]]></command>
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31 <inputs>
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32 <conditional name="mode_args">
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33 <param argument="--mode" type="select" label="Mode">
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34 <option value="f">Functional analysis</option>
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35 <option value="t">Taxonomic analysis</option>
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36 <option value="ft">Functional-taxonomic interaction analysis</option>
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37 </param>
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38 <when value="f">
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39 <expand macro="ONTOLOGY_ARGS"/>
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40 </when>
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41 <when value="t">
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42 </when>
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43 <when value="ft">
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44 <expand macro="ONTOLOGY_ARGS"/>
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45 </when>
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46 </conditional>
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47 <expand macro="SAMPS"/>
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48 <param argument="--expand_file" type="data" format="tabular" label="metaquantome expand file"
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49 help=""/>
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50 <param argument="--min_peptides" type="integer" value="0" min="0" label="min_peptides">
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51 <help>
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52 Used for filtering to well-supported annotations. The
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53 number of peptides providing evidence for a term is
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54 the number of peptides directly annotated with that
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55 term plus the number of peptides annotated with any of
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56 its descendants. Terms with a number of peptides
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57 greater than or equal to min_peptides are retained.
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58 The default is 0.
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59 </help>
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60 </param>
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61 <param argument="--min_pep_nsamp" type="integer" value="" min="0" optional="true" label="min_pep_nsamp">
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62 <help>
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63 Number of samples per group that must meet or exceed
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64 min_peptides. Default is 'all'.
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65 </help>
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66 </param>
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67 <param argument="--min_children_non_leaf" type="integer" value="0" min="0" label="min_children_non_leaf">
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68 <help>
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69 Used for filtering to informative annotations. A term
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70 is retained if it has a number of children greater
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71 than or equal to min_children_non_leaf. The default is 0.
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72 </help>
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73 </param>
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74 <param argument="--min_child_nsamp" type="integer" value="" min="0" optional="true" label="min_child_nsamp">
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75 <help>
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76 Number of samples per group that must meet or exceed
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77 min_children_nsamp. The default is all samples.
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78 </help>
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79 </param>
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80 <param argument="--qthreshold" type="integer" value="3" min="0" label="qthreshold">
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81 <help>
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82 Minimum number of intensities in each sample group.
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83 Any functional/taxonomic term with lower number of
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84 per-group intensities will be filtered out. The
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85 default is 3, because this is the minimum number for
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86 t-tests.
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87 </help>
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88 </param>
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89 </inputs>
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90 <outputs>
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91 <data format="tabular" name="outfile" label="${tool.name} on ${on_string} filtered"/>
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92 </outputs>
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93 <tests>
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94 <test>
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95 <param name="expand_file" value="go_expanded.tab" ftype="tabular"/>
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96 <param name="mode" value="f" />
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97 <param name="ontology" value="go" />
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98 <param name="samps" value="samples_basic.tab" ftype="tabular"/>
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99 <param name="min_peptides" value="2" />
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100 <param name="min_pep_nsamp" value="" />
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101 <param name="min_children_non_leaf" value="2" />
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102 <param name="min_child_nsamp" value="" />
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103 <param name="qthreshold" value="0" />
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104 <output name="outfile" file="go_filtered.tab" ftype="tabular"/>
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105 </test>
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106 </tests>
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107 <help><![CDATA[
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108 metaQuantome filter
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109 ===================
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110
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111 The *filter* module is the second step in the metaQuantome analysis workflow. The
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112 purpose of the filter module is to filter expanded terms to those that are
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113 representative and well-supported by the data. Please see the manuscript for further
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114 details about filtering.
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115
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116
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117 Questions, Comments, Problems, Kudos
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118 --------------------------------------
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119
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120 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
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121 ]]></help>
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122 <expand macro="citations" />
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123 </tool>