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comparison metaquantome_filter.xml @ 4:80ce9ca55697 draft

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planemo upload commit d27827cf38d30b9c98923f73bc9cae4ffe41361b
author galaxyp
date Fri, 07 Dec 2018 13:43:06 -0500
parents 28180bbb8fe4
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3:28180bbb8fe4 4:80ce9ca55697
1 <tool id="metaquantome_filter" name="MetaQuantome Filter" version="@VERSION@.0"> 1 <tool id="metaquantome_filter" name="metaQuantome: filter" version="@VERSION@.0">
2 <description>for quality, redundancy, and sample coverage</description> 2 <description>for quality, redundancy, and sample coverage</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 @MAKE_SAMPS_TSV@ 8 @MAKE_SAMPS_TSV@
9 metaquantome filter 9 metaquantome filter
10 @COMMON_PARAMS@ 10 @COMMON_PARAMS@
11 --expand_file '$expand_file' 11 --expand_file '$expand_file'
12 --min_peptides $min_peptides 12 --min_peptides $min_peptides
13 #if $min_pep_nsamp: 13 #if $min_pep_nsamp:
14 #set $nsamp = max(int($min_peptides),int($min_pep_nsamp)) 14 #set $nsamp = max(int($min_peptides),int($min_pep_nsamp))
15 --min_pep_nsamp $nsamp 15 --min_pep_nsamp $nsamp
16 #else 16 #else
17 --min_pep_nsamp all 17 --min_pep_nsamp all
97 <param name="qthreshold" value="2" /> 97 <param name="qthreshold" value="2" />
98 <output name="outfile" file="go_filtered.tab" ftype="tabular"/> 98 <output name="outfile" file="go_filtered.tab" ftype="tabular"/>
99 </test> 99 </test>
100 </tests> 100 </tests>
101 <help><![CDATA[ 101 <help><![CDATA[
102 TODO: Fill in help. 102 metaQuantome filter
103 ]]></help> 103 ===================
104
105 The *filter* module is the second step in the metaQuantome analysis workflow. The
106 purpose of the filter module is to filter expanded terms to those that are
107 representative and well-supported by the data.
108
109
110 The image below illustrates the filtering process.
111
112 .. image:: filtering.png
113 :width: 100 %
114
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.
116
117
118 Questions, Comments, Problems, Kudos
119 --------------------------------------
120
121 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
122 ]]></help>
104 <expand macro="citations" /> 123 <expand macro="citations" />
105 </tool> 124 </tool>