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comparison w4mclassfilter.xml @ 11:9f5c0e23c205 draft

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planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 32cf96ed6c39a93eb9c6cf00494b128bd3c3febe
author eschen42
date Mon, 03 Sep 2018 22:34:35 -0400
parents 649cb1bafd3e
children 38f509903a0b
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10:649cb1bafd3e 11:9f5c0e23c205
1 <tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.10"> 1 <tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.11">
2 <description>Filter W4m data by values or metadata</description> 2 <description>Filter W4m data by values or metadata</description>
3 <!-- Here is the hyphenation standard that I *try* to apply consistently in my documentation: http://www.sandranoonan.com/dont-let-hyphenation-drive-crazy/ --> 3 <!-- Here is the hyphenation standard that I *try* to apply consistently in my documentation: http://www.sandranoonan.com/dont-let-hyphenation-drive-crazy/ -->
4 <requirements> 4 <requirements>
5 <!-- <requirement type="package" version="6.2">readline</requirement> --> 5 <!-- <requirement type="package" version="6.2">readline</requirement> -->
6 <requirement type="package" version="3.4.1">r-base</requirement> 6 <requirement type="package" version="3.4.1">r-base</requirement>
7 <requirement type="package" version="1.1_4">r-batch</requirement> 7 <requirement type="package" version="1.1_4">r-batch</requirement>
8 <requirement type="package" version="0.98.7">w4mclassfilter</requirement> 8 <requirement type="package" version="0.98.8">w4mclassfilter</requirement>
9 </requirements> 9 </requirements>
10 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
11 Rscript $__tool_directory__/w4mclassfilter_wrapper.R 11 Rscript $__tool_directory__/w4mclassfilter_wrapper.R
12 dataMatrix_in '$dataMatrix_in' 12 dataMatrix_in '$dataMatrix_in'
13 sampleMetadata_in '$sampleMetadata_in' 13 sampleMetadata_in '$sampleMetadata_in'
33 <param name="classnameColumn" label="Column that names the sample-class" type="text" value = "class" 33 <param name="classnameColumn" label="Column that names the sample-class" type="text" value = "class"
34 help="name of the column in sample metadata that has the values to be tested against the 'Names of sample-classes' input parameter - defaults to 'class'"> 34 help="name of the column in sample metadata that has the values to be tested against the 'Names of sample-classes' input parameter - defaults to 'class'">
35 <sanitizer> 35 <sanitizer>
36 <valid initial="string.letters"> 36 <valid initial="string.letters">
37 <add preset="string.digits"/> 37 <add preset="string.digits"/>
38 <add value="&#45;" /> <!-- dash, hyphen -->
39 <add value="&#46;" /> <!-- dot, period --> 38 <add value="&#46;" /> <!-- dot, period -->
40 <add value="&#95;" /> <!-- underscore --> 39 <add value="&#95;" /> <!-- underscore -->
41 </valid> 40 </valid>
42 </sanitizer> 41 </sanitizer>
43 </param> 42 </param>
82 help="comma-separated filters, each specified as 'variableMetadataColumnName:min:max'; default is no filters. (See help below.)"> 81 help="comma-separated filters, each specified as 'variableMetadataColumnName:min:max'; default is no filters. (See help below.)">
83 <sanitizer> 82 <sanitizer>
84 <valid initial="string.letters"> 83 <valid initial="string.letters">
85 <add preset="string.digits"/> 84 <add preset="string.digits"/>
86 <add value="&#44;" /> <!-- comma --> 85 <add value="&#44;" /> <!-- comma -->
87 <add value="&#45;" /> <!-- dash, hyphen -->
88 <add value="&#46;" /> <!-- dot, period --> 86 <add value="&#46;" /> <!-- dot, period -->
89 <add value="&#58;" /> <!-- colon --> 87 <add value="&#58;" /> <!-- colon -->
90 <add value="&#95;" /> <!-- underscore --> 88 <add value="&#95;" /> <!-- underscore -->
91 </valid> 89 </valid>
92 </sanitizer> 90 </sanitizer>
585 Variable metadata file 583 Variable metadata file
586 | variable x metadata **variableMetadata** (tabular separated values) file of the numeric and/or character variable metadata, with . as decimal and NA for missing values 584 | variable x metadata **variableMetadata** (tabular separated values) file of the numeric and/or character variable metadata, with . as decimal and NA for missing values
587 | 585 |
588 586
589 Column that names the sample-class (default = '``class``') 587 Column that names the sample-class (default = '``class``')
590 | name of the column in **sampleMetadata** that has the values to be tested against the '``Names of sample-classes``' input parameter 588 | name of the column in **sampleMetadata** that has the values to be tested against the '``Names of sample-classes``' input parameter; only letters, digits, periods, and underscores are permitted.
591 | 589 |
592 590
593 Names of sample-classes (default = no names) 591 Names of sample-classes (default = no names)
594 | comma-separated names (or regular expressions to match names) of sample-classes to include or exclude 592 | comma-separated names (or regular expressions to match names) of sample-classes to include or exclude
595 | 593 |
697 argument. If supplied, only features having numerical values in the specified column 695 argument. If supplied, only features having numerical values in the specified column
698 of `variableMetadata` that fall within the specified ranges will be retained 696 of `variableMetadata` that fall within the specified ranges will be retained
699 in the output. Each range is a string of three colon-separated values (e.g., "mz:200:800") in the 697 in the output. Each range is a string of three colon-separated values (e.g., "mz:200:800") in the
700 following order: 698 following order:
701 699
702 - the **name of a column of `variableMetadata`** which must have numerical data (e.g., "mz"); 700 - the **name of a column of `variableMetadata`** which must have numerical data (only letters, digits, periods, and underscores are permitted in the name itself), e.g., 'mz';
703 - the **minimum allowed value** in that column for the feature to be retained (e.g., 200); 701 - the **minimum allowed value** in that column for the feature to be retained, e.g., '200';
704 - the **maximum allowed value** (e.g., 800). 702 - the **maximum allowed value**, e.g., '800'.
705 703
706 Note for the range specification strings: 704 Note for the range specification strings:
707 705
708 - **If the "maximum" is less than the "minimum", then the range is exclusive** (e.g., "mz:800:200" means retain only features whose mz is NOT in the range 200-800) 706 - **If the "maximum" is less than the "minimum", then the range is exclusive** (e.g., "mz:800:200" means retain only features whose mz is NOT in the range 200-800)
709 - **If the name supplied in the first field is 'FEATMAX',** then the string is defining the minimum (and possibly, though less useful, maximum) intensity for each feature in the dataMatrix. For example, "FEATMAX:1e6:" would specify that any feature would be excluded if no sample had an intensity for that feature greater than 1000000. 707 - **If the name supplied in the first field is 'FEATMAX',** then the string is defining the minimum (and possibly, though less useful, maximum) intensity for each feature in the dataMatrix. For example, "FEATMAX:1e6:" would specify that any feature would be excluded if no sample had an intensity for that feature greater than 1000000.