w4mclassfilter: w4mclassfilter.xml annotate

annotate w4mclassfilter.xml @ 9:1ced8b5dfa3e draft

planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit ac7c79636d17f7d33f1e8e644db0ddd33d2057e8

author	eschen42
date	Wed, 28 Mar 2018 12:04:22 -0400
parents	d5cf23369d12
children	649cb1bafd3e

rev	line source
9 1ced8b5dfa3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit ac7c79636d17f7d33f1e8e644db0ddd33d2057e8 eschen42 parents: 8 diff changeset	1 <tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.9">
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	2 <description>Filter W4m data by values or metadata</description>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	3
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	4 <!-- Here is the hyphenation standard that I try to apply consistently in my documentation: http://www.sandranoonan.com/dont-let-hyphenation-drive-crazy/ -->
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	5
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	6 <requirements>
7 582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704 eschen42 parents: 6 diff changeset	7 <!-- <requirement type="package" version="6.2">readline</requirement> -->
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	8 <requirement type="package" version="3.4.1">r-base</requirement>
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	9 <requirement type="package" version="1.1_4">r-batch</requirement>
7 582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704 eschen42 parents: 6 diff changeset	10 <requirement type="package" version="0.98.7">w4mclassfilter</requirement>
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	11 </requirements>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	12
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	13 <stdio>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	14 <exit_code range="1:" level="fatal" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	15 </stdio>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	16
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	17
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	18 <command detect_errors="aggressive"><![CDATA[
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	19 Rscript $__tool_directory__/w4mclassfilter_wrapper.R
4 499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	20 dataMatrix_in '$dataMatrix_in'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	21 sampleMetadata_in '$sampleMetadata_in'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	22 variableMetadata_in '$variableMetadata_in'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	23 sampleclassNames '$sampleclassNames'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	24 inclusive '$inclusive'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	25 wildcards '$wildcards'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	26 classnameColumn '$classnameColumn'
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	27 samplenameColumn 'sampleMetadata'
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	28 variable_range_filter '$variableRangeFilter'
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	29 transformation '$transformation'
4 499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	30 dataMatrix_out '$dataMatrix_out'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	31 sampleMetadata_out '$sampleMetadata_out'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	32 variableMetadata_out '$variableMetadata_out'
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	33 ]]></command>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	34
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	35 <inputs>
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	36 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, separator: tab" />
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	37 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata columns, separator: tab" />
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	38 <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata columns, separator: tab" />
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	39 <param name="classnameColumn" label="Column that names the sample-class" type="text" value = "class" 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'">
5 2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	40 <sanitizer>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	41 <valid initial="string.letters">
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	42 <add preset="string.digits"/>
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	43 <add value="-" /> <!-- dash, hyphen -->
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	44 <add value="." /> <!-- dot, period -->
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	45 <add value="_" /> <!-- underscore -->
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	46 </valid>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	47 </sanitizer>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	48 </param>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	49 <param name="sampleclassNames" label="Names of sample-classes" type="text" value = "" help="comma-separated names (or regular expressions to match names) of sample-classes to filter in or out; defaults to no names">
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	50 <sanitizer>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	51 <valid initial="string.letters">
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	52 <add preset="string.digits"/>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	53 <add value="{" /> <!-- l-cube, left-curly-bracket -->
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	54 <add value="\|" /> <!-- pipe -->
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	55 <add value="}" /> <!-- r-cube, right-curly-bracket -->
5 2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	56 <add value="$" /> <!-- dollar, dollar-sign -->
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	57 <add value="(" /> <!-- left-paren -->
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	58 <add value=")" /> <!-- right-paren -->
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	59 <add value="*" /> <!-- splat, asterisk -->
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	60 <add value="+" /> <!-- plus -->
9 1ced8b5dfa3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit ac7c79636d17f7d33f1e8e644db0ddd33d2057e8 eschen42 parents: 8 diff changeset	61 <add value="-" /> <!-- dash, hyphen -->
5 2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	62 <add value="," /> <!-- comma -->
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	63 <add value="." /> <!-- dot, period -->
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	64 <add value=":" /> <!-- colon -->
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	65 <add value=";" /> <!-- semi, semicolon -->
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	66 <add value="?" /> <!-- what, question mark -->
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	67 <add value="[" /> <!-- l-squib, left-squre-bracket -->
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	68 <add value="\" /> <!-- whack, backslash -->
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	69 <add value="]" /> <!-- r-squib, right-squre-bracket -->
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	70 <add value="^" /> <!-- hat, caret -->
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	71 <add value="_" /> <!-- underscore -->
5 2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	72 </valid>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	73 </sanitizer>
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	74 </param>
5 2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	75
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	76 <param name="wildcards" label="Use 'wild cards' or 'regular expressions'" type="select" help="'wild-cards' (the default) - use '*' and '?' to match class names; 'regular-expressions' - use regular expressions to match class names">
4 499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	77 <option value="TRUE" selected="true">wild-cards</option>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	78 <option value="FALSE">regular-expressions</option>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	79 </param>
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	80 <param name="inclusive" label="Exclude/include named classes" type="select" help="'filter-out' (the default) - exclude only the named sample-classes; 'filter-in' - include only the named sample-classes">
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	81 <option value="TRUE">filter-in</option>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	82 <option value="FALSE" selected="true">filter-out</option>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	83 </param>
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	84
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	85 <param name="variableRangeFilter" label="Variable-range filters" type="text" value = "" help="comma-separated filters, each specified as 'variableMetadataColumnName:min:max'; default is no filters. (See help below.)">
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	86 <sanitizer>
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	87 <valid initial="string.letters">
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	88 <add preset="string.digits"/>
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	89 <add value="," /> <!-- comma -->
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	90 <add value="-" /> <!-- dash, hyphen -->
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	91 <add value="." /> <!-- dot, period -->
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	92 <add value=":" /> <!-- colon -->
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	93 <add value="_" /> <!-- underscore -->
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	94 </valid>
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	95 </sanitizer>
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	96 </param>
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	97 <param name="transformation" label="Data-transformation" type="select" help="'none' (the default) - do not transform data; 'log2' - log base 2 of data; 'log10' - log base 10 of data; in all cases, negative and missing values are imputed to zero">
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	98 <option value="none" selected="true">none</option>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	99 <option value="log2">log2</option>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	100 <option value="log10">log10</option>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	101 </param>
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	102
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	103 </inputs>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	104 <outputs>
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	105 <data name="dataMatrix_out" label="${dataMatrix_in.name}.subset" format="tabular" ></data>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	106 <data name="sampleMetadata_out" label="${sampleMetadata_in.name}.subset" format="tabular" ></data>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	107 <data name="variableMetadata_out" label="${variableMetadata_in.name}.subset" format="tabular" ></data>
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	108 </outputs>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	109
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	110 <tests>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	111 <test>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	112 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	113 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	114 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	115 <param name="classnameColumn" value="gender"/>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	116 <param name="sampleclassNames" value="M"/>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	117 <param name="wildcards" value="FALSE"/>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	118 <param name="inclusive" value="filter-in"/>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	119 <param name="variableRangeFilter" value="FEATMAX:6.30103:,mz:200:,rt::800"/>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	120 <param name="transformation" value="log10"/>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	121 <output name="dataMatrix_out">
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	122 <assert_contents>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	123 <has_text text="5.87336711011293" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	124 </assert_contents>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	125 </output>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	126 <output name="sampleMetadata_out">
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	127 <assert_contents>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	128 <not_has_text text="HU_028" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	129 <not_has_text text="HU_051" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	130 <not_has_text text="HU_060" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	131 <not_has_text text="HU_110" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	132 <not_has_text text="HU_149" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	133 <not_has_text text="HU_152" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	134 <not_has_text text="HU_175" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	135 <not_has_text text="HU_178" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	136 <not_has_text text="HU_185" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	137 <not_has_text text="HU_204" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	138 <not_has_text text="HU_208" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	139 <has_text text="HU_017" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	140 <has_text text="HU_034" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	141 <has_text text="HU_078" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	142 <has_text text="HU_091" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	143 <has_text text="HU_093" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	144 <has_text text="HU_099" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	145 <has_text text="HU_130" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	146 <has_text text="HU_134" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	147 <has_text text="HU_138" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	148 </assert_contents>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	149 </output>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	150 <output name="variableMetadata_out">
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	151 <assert_contents>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	152 <not_has_text text="HMDB00191" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	153 <has_text text="HMDB00208" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	154 <not_has_text text="HMDB00251" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	155 <not_has_text text="HMDB00299" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	156 <not_has_text text="HMDB00512" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	157 <not_has_text text="HMDB00518" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	158 <not_has_text text="HMDB00715" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	159 <not_has_text text="HMDB00822" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	160 <has_text text="HMDB01032" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	161 <has_text text="HMDB01101.1" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	162 <not_has_text text="HMDB03193" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	163 <not_has_text text="HMDB04824" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	164 <not_has_text text="HMDB10348" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	165 <has_text text="HMDB13189" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	166 <not_has_text text="HMDB59717" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	167 </assert_contents>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	168 </output>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	169 </test>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	170 <test>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	171 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	172 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	173 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
9 1ced8b5dfa3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit ac7c79636d17f7d33f1e8e644db0ddd33d2057e8 eschen42 parents: 8 diff changeset	174 <param name="classnameColumn" value="sampleMetadata"/>
1ced8b5dfa3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit ac7c79636d17f7d33f1e8e644db0ddd33d2057e8 eschen42 parents: 8 diff changeset	175 <!-- test that hyphens in regular expressions work -->
1ced8b5dfa3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit ac7c79636d17f7d33f1e8e644db0ddd33d2057e8 eschen42 parents: 8 diff changeset	176 <param name="sampleclassNames" value="HU_[0-9][0-9][0-9]"/>
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	177 <param name="wildcards" value="FALSE"/>
9 1ced8b5dfa3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit ac7c79636d17f7d33f1e8e644db0ddd33d2057e8 eschen42 parents: 8 diff changeset	178 <param name="inclusive" value="filter-in"/>
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	179 <param name="variableRangeFilter" value="FEATMAX:20.93157:,mz:200:,rt::800"/>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	180 <param name="transformation" value="log2"/>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	181 <output name="dataMatrix_out">
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	182 <assert_contents>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	183 <has_text text="19.5109032146715" />
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	184 </assert_contents>
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	185 </output>
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	186 <output name="sampleMetadata_out">
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	187 <assert_contents>
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	188 <has_text text="HU_028" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	189 <has_text text="HU_051" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	190 <has_text text="HU_060" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	191 <has_text text="HU_110" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	192 <has_text text="HU_149" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	193 <has_text text="HU_152" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	194 <has_text text="HU_175" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	195 <has_text text="HU_178" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	196 <has_text text="HU_185" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	197 <not_has_text text="HU_204" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	198 <has_text text="HU_208" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	199 <has_text text="HU_017" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	200 <has_text text="HU_034" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	201 <has_text text="HU_078" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	202 <has_text text="HU_091" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	203 <has_text text="HU_093" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	204 <has_text text="HU_099" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	205 <has_text text="HU_130" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	206 <has_text text="HU_134" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	207 <has_text text="HU_138" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	208 </assert_contents>
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	209 </output>
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	210 <output name="variableMetadata_out">
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	211 <assert_contents>
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	212 <has_text text="HMDB00191" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	213 <has_text text="HMDB00208" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	214 <not_has_text text="HMDB00251" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	215 <not_has_text text="HMDB00299" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	216 <not_has_text text="HMDB00512" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	217 <not_has_text text="HMDB00518" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	218 <not_has_text text="HMDB00715" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	219 <not_has_text text="HMDB00822" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	220 <has_text text="HMDB01032" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	221 <has_text text="HMDB01101.1" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	222 <not_has_text text="HMDB03193" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	223 <not_has_text text="HMDB04824" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	224 <not_has_text text="HMDB10348" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	225 <has_text text="HMDB13189" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	226 <not_has_text text="HMDB59717" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	227 </assert_contents>
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	228 </output>
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	229 </test>
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	230 <test>
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	231 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	232 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	233 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	234 <param name="classnameColumn" value="gender"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	235 <param name="sampleclassNames" value="M"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	236 <param name="inclusive" value="filter-in"/>
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	237 <param name="transformation" value="none"/>
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	238 <output name="dataMatrix_out">
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	239 <assert_contents>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	240 <not_has_text text="HU_028" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	241 <not_has_text text="HU_051" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	242 <not_has_text text="HU_060" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	243 <not_has_text text="HU_110" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	244 <not_has_text text="HU_149" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	245 <not_has_text text="HU_152" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	246 <not_has_text text="HU_175" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	247 <not_has_text text="HU_178" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	248 <not_has_text text="HU_185" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	249 <not_has_text text="HU_204" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	250 <not_has_text text="HU_208" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	251 <has_text text="HU_017" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	252 <has_text text="HU_034" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	253 <has_text text="HU_078" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	254 <has_text text="HU_091" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	255 <has_text text="HU_093" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	256 <has_text text="HU_099" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	257 <has_text text="HU_130" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	258 <has_text text="HU_134" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	259 <has_text text="HU_138" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	260 <has_text text="HMDB03193" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	261 <not_has_text text="HMDB00822" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	262 <has_text text="HMDB01101" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	263 <has_text text="HMDB01101.1" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	264 <has_text text="HMDB10348" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	265 <has_text text="HMDB59717" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	266 <has_text text="HMDB13189" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	267 <has_text text="HMDB00299" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	268 <has_text text="HMDB00191" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	269 <has_text text="HMDB00518" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	270 <has_text text="HMDB00715" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	271 <has_text text="HMDB01032" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	272 <has_text text="HMDB00208" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	273 <has_text text="HMDB04824" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	274 <has_text text="HMDB00512" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	275 <has_text text="HMDB00251" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	276 </assert_contents>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	277 </output>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	278 </test>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	279 <test>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	280 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	281 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	282 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	283 <param name="classnameColumn" value="gender"/>
5 2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	284 <param name="sampleclassNames" value="*"/>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	285 <param name="wildcards" value="TRUE"/>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	286 <param name="inclusive" value="filter-in"/>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	287 <output name="sampleMetadata_out">
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	288 <assert_contents>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	289 <not_has_text text="HU_204" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	290 <has_text text="HU_028" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	291 <has_text text="HU_051" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	292 <has_text text="HU_060" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	293 <has_text text="HU_110" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	294 <has_text text="HU_149" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	295 <has_text text="HU_152" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	296 <has_text text="HU_175" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	297 <has_text text="HU_178" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	298 <has_text text="HU_185" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	299 <has_text text="HU_208" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	300 <has_text text="HU_017" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	301 <has_text text="HU_034" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	302 <has_text text="HU_078" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	303 <has_text text="HU_091" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	304 <has_text text="HU_093" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	305 <has_text text="HU_099" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	306 <has_text text="HU_130" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	307 <has_text text="HU_134" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	308 <has_text text="HU_138" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	309 </assert_contents>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	310 </output>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	311 </test>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	312 <test>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	313 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	314 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	315 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	316 <param name="classnameColumn" value="gender"/>
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	317 <param name="sampleclassNames" value="M"/>
5 2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	318 <param name="wildcards" value="FALSE"/>
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	319 <param name="inclusive" value="filter-in"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	320 <output name="sampleMetadata_out">
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	321 <assert_contents>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	322 <not_has_text text="HU_028" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	323 <not_has_text text="HU_051" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	324 <not_has_text text="HU_060" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	325 <not_has_text text="HU_110" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	326 <not_has_text text="HU_149" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	327 <not_has_text text="HU_152" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	328 <not_has_text text="HU_175" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	329 <not_has_text text="HU_178" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	330 <not_has_text text="HU_185" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	331 <not_has_text text="HU_204" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	332 <not_has_text text="HU_208" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	333 <has_text text="HU_017" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	334 <has_text text="HU_034" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	335 <has_text text="HU_078" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	336 <has_text text="HU_091" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	337 <has_text text="HU_093" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	338 <has_text text="HU_099" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	339 <has_text text="HU_130" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	340 <has_text text="HU_134" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	341 <has_text text="HU_138" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	342 </assert_contents>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	343 </output>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	344 </test>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	345 <test>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	346 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	347 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	348 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	349 <param name="classnameColumn" value="gender"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	350 <param name="sampleclassNames" value="M"/>
5 2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	351 <param name="wildcards" value="FALSE"/>
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	352 <param name="inclusive" value="filter-in"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	353 <output name="variableMetadata_out">
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	354 <assert_contents>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	355 <has_text text="HMDB03193" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	356 <not_has_text text="HMDB00822" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	357 <has_text text="HMDB01101" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	358 <has_text text="HMDB01101.1" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	359 <has_text text="HMDB10348" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	360 <has_text text="HMDB59717" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	361 <has_text text="HMDB13189" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	362 <has_text text="HMDB00299" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	363 <has_text text="HMDB00191" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	364 <has_text text="HMDB00518" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	365 <has_text text="HMDB00715" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	366 <has_text text="HMDB01032" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	367 <has_text text="HMDB00208" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	368 <has_text text="HMDB04824" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	369 <has_text text="HMDB00512" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	370 <has_text text="HMDB00251" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	371 </assert_contents>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	372 </output>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	373 </test>
4 499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	374 <test>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	375 <param name="dataMatrix_in" value="input_nofilter_dataMatrix.tsv"/>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	376 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	377 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	378 <param name="classnameColumn" value="gender"/>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	379 <param name="sampleclassNames" value="M"/>
5 2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	380 <param name="wildcards" value="FALSE"/>
4 499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	381 <param name="inclusive" value="filter-in"/>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	382 <output name="variableMetadata_out">
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	383 <assert_contents>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	384 <has_text text="HMDB03193" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	385 <not_has_text text="HMDB00822" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	386 <has_text text="HMDB01101" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	387 <has_text text="HMDB01101.1" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	388 <has_text text="HMDB10348" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	389 <has_text text="HMDB59717" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	390 <not_has_text text="HMDB13189" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	391 <has_text text="HMDB00299" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	392 <has_text text="HMDB00191" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	393 <has_text text="HMDB00518" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	394 <has_text text="HMDB00715" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	395 <has_text text="HMDB01032" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	396 <has_text text="HMDB00208" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	397 <has_text text="HMDB04824" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	398 <has_text text="HMDB00512" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	399 <has_text text="HMDB00251" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	400 </assert_contents>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	401 </output>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	402 </test>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	403 <test>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	404 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	405 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	406 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	407 <param name="classnameColumn" value="gender"/>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	408 <param name="sampleclassNames" value="[Mm],[fF]"/>
5 2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	409 <param name="wildcards" value="FALSE"/>
4 499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	410 <param name="inclusive" value="filter-in"/>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	411 <output name="sampleMetadata_out">
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	412 <assert_contents>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	413 <has_text text="HU_028" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	414 <has_text text="HU_051" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	415 <has_text text="HU_060" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	416 <has_text text="HU_110" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	417 <has_text text="HU_149" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	418 <has_text text="HU_152" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	419 <has_text text="HU_175" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	420 <has_text text="HU_178" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	421 <has_text text="HU_185" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	422 <not_has_text text="HU_204" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	423 <has_text text="HU_208" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	424 <has_text text="HU_017" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	425 <has_text text="HU_034" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	426 <has_text text="HU_078" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	427 <has_text text="HU_091" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	428 <has_text text="HU_093" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	429 <has_text text="HU_099" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	430 <has_text text="HU_130" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	431 <has_text text="HU_134" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	432 <has_text text="HU_138" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	433 </assert_contents>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	434 </output>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	435 </test>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	436 <test>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	437 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	438 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	439 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	440 <param name="classnameColumn" value=""/>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	441 <param name="sampleclassNames" value="M"/>
5 2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	442 <param name="wildcards" value="FALSE"/>
4 499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	443 <param name="inclusive" value="filter-in"/>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	444 <output name="sampleMetadata_out">
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	445 <assert_contents>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	446 <has_text text="HU_028" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	447 <has_text text="HU_051" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	448 <has_text text="HU_060" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	449 <has_text text="HU_110" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	450 <has_text text="HU_149" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	451 <has_text text="HU_152" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	452 <has_text text="HU_175" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	453 <has_text text="HU_178" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	454 <has_text text="HU_185" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	455 <not_has_text text="HU_204" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	456 <has_text text="HU_208" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	457 <has_text text="HU_017" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	458 <has_text text="HU_034" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	459 <has_text text="HU_078" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	460 <has_text text="HU_091" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	461 <has_text text="HU_093" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	462 <has_text text="HU_099" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	463 <has_text text="HU_130" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	464 <has_text text="HU_134" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	465 <has_text text="HU_138" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	466 </assert_contents>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	467 </output>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	468 </test>
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	469 </tests>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	470
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	471
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	472
5 2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	473 <help><![CDATA[
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	474
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	475
5 2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	476 Author Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	477
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	478 --------------------------------------------------------------------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	479
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	480
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	481 R package
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	482
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	483 The w4mclassfilter package (which is used by the W4m Data Subset tool) is available from the Hegeman lab github repository (https://github.com/HegemanLab/w4mclassfilter/releases).
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	484
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	485 -----------------------------------------------------------------------------------------------------------------------------------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	486
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	487
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	488 Tool updates
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	489
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	490 See the NEWS section at the bottom of this page
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	491
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	492 ---------------------------------------------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	493
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	494 ===========================================================
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	495 "W4m Data Subset" - Filter Workflow4Metabolomics data files
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	496 ===========================================================
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	497
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	498 ----------
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	499 Motivation
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	500 ----------
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	501
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	502 GC-MS and LC-MS experiments seek to resolve as features chemicals that have distinct chromatographic retention-time ("rt") and (after ionization) mass-to-charge ratio ("m/z" or "mz").
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	503 (If the MS protocol includes fragmentation, several features may result for each chemical.)
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	504 Data for a sample are collected as MS intensities, each of which is associated with a position on a 2D plane with dimensions of rt and m/z.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	505 Ideally, features would be sufficiently reproducible among sample-runs to distinguish features that are commmon among samples from those that differ.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	506
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	507 The chromatographic retention-time for a chemical can vary from one chromatography run to the next.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	508 Workflow4Metabolomics (W4m, [Giacomoni et al., 2014, Guitton et al. 2017]) is a "flavor" of Galaxy that uses the XCMS preprocessing tools for "retention-time correction" to align features among samples.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	509 Features may be better aligned if pooled samples and blanks are included.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	510
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	511 Multivariate statistical techniques may be used to discover clusters of similar samples (Th]]>é<![CDATA[venot et al., 2015).
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	512 However, once retention-time alignment of features has been achieved among samples in GC-MS and LC-MS datasets:
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	513
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	514 - The presence of pools and blanks may confound identification and separation of clusters.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	515 - Multivariate statistical algorithms may be impacted by missing values or dimensions that have zero variance.
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	516
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	517 -----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	518 Description
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	519 -----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	520
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	521 The W4m Data Subset tool selects subsets of samples, features, or data values for further analysis.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	522
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	523 - The tool takes as input the data matrix, sample metadata, and variable metadata datasets produced by W4m's XCMS [Smith et al., 2006] and CAMERA [Kuhl et al., 2012] tools.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	524 - The tool produces the same trio of output datasets, modified as follows.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	525
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	526 This tool can perform several operations to reduce the number samples or features to be analyzed (although this should be done only in a statistically sound manner consistent with the nature of the experiment):
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	527
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	528 - Samples may be eliminated by filtering on a designated “sample class” column in sampleMetadata.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	529 - Features may be eliminated by specifying minimum or maximum value (or both) allowable in columns of variableMetadata.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	530 - Features may be eliminated by “range of row-maximum for each feature”, i.e., by specifying minimum or maximum intensity (or both) allowable in each row of the dataMatrix (i.e., for the feature across all samples).
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	531
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	532 This tool also performs several operations to address several data issues that may impede downstream statistical analysis:
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	533
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	534 - Missing values in dataMatrix are imputed to zero.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	535 - The values in the dataMatrix may be log-transformed if desired.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	536 - Samples that are missing from either sampleMetadata or dataMatrix are eliminated.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	537 - Features that are missing from either variableMetadata or dataMatrix are eliminated.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	538 - Features and samples that have zero variance are eliminated.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	539 - Samples and features are sorted alphabetically in rows and columns of dataMatrix and in rows of variableMetadata and sampleMetadata.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	540 - The names of the first columns of variableMetadata and sampleMetadata are set respectively to "variableMetadata" and "sampleMetadata".
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	541
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	542 This tool may be applied several times sequentially, which may be useful for:
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	543
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	544 - analyzing subsets of samples for progressively smaller sets of treatment-levels, or
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	545 - choosing subsets of samples based on criteria in several columns of the sampleMetadata table.
3 191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0 eschen42 parents: 2 diff changeset	546
191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0 eschen42 parents: 2 diff changeset	547 -----------------
191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0 eschen42 parents: 2 diff changeset	548 Workflow Position
191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0 eschen42 parents: 2 diff changeset	549 -----------------
191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0 eschen42 parents: 2 diff changeset	550
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	551 This tool can be used at any point downstream of Preprocessing.
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	552
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	553 - Possible upstream tool categories: Preprocessing, Quality Control, Statistical Analysis, Filter and Sort
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	554 - Possible downstream tool categories: Normalisation, Statistical Analysis, Quality Control, Filter and Sort
3 191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0 eschen42 parents: 2 diff changeset	555
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	556 -----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	557 Input files
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	558 -----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	559
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	560 +---------------------------+------------+
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	561 \| File \| Format \|
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	562 +===========================+============+
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	563 \| Data matrix \| tabular \|
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	564 +---------------------------+------------+
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	565 \| Sample metadata \| tabular \|
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	566 +---------------------------+------------+
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	567 \| Variable metadata \| tabular \|
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	568 +---------------------------+------------+
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	569
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	570
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	571 ----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	572 Parameters
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	573 ----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	574
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	575 Data matrix file
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	576 \| variable x sample dataMatrix (tabular separated values) file of the numeric data matrix, with . as decimal, and NA for missing values; the table must not contain metadata apart from row and column names; the row and column names must be identical, respectively, to the rownames of the sample metadata file and variable metadata file
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	577 \|
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	578
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	579 Sample metadata file
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	580 \| sample x metadata sampleMetadata (tabular separated values) file of the numeric and/or character sample metadata, with . as decimal and NA for missing values
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	581 \|
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	582
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	583 Variable metadata file
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	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
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	585 \|
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	586
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	587 Column that names the sample-class (default = '``class``')
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	588 \| name of the column in sampleMetadata that has the values to be tested against the '``Names of sample-classes``' input parameter
4 499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	589 \|
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	590
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	591 Names of sample-classes (default = no names)
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	592 \| comma-separated names (or regular expressions to match names) of sample-classes to include or exclude
4 499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	593 \|
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	594
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	595 'Wild cards' or 'regular expressions' (default = '``wild-cards``')
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	596 \| '``wild-cards``' - use wild cards to match names of sample-classes (see the 'Wild card patterns to match class-names' section below)
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	597 \| '``regular-expressions``' - use regular expressions to match the named sample-classes (see the 'Regular expression patterns to match class-names' section below)
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	598 \|
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	599
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	600 Exclude/include named classes (default = '``filter-out``')
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	601 \| '``filter-in``' - include only the named sample-classes
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	602 \| '``filter-out``' - exclude only the named sample-classes
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	603 \|
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	604
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	605 Variable-range filters (default = no filters)
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	606 \| comma-separated names of variable-range filters (see the 'Variable-range filters' section below)
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	607 \|
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	608
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	609 Data-transformation (default = '``none``')
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	610 \| '``none``' - do not transform data matrix values
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	611 \| '``log2``' - take the log base 2 of the values in the data matrix
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	612 \| '``log10``' - take the log base 10 of the values in the data matrix
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	613 \| In both cases, negative and missing values are imputed to zero.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	614 \|
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	615
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	616
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	617 ------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	618 Output files
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	619 ------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	620
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	621 sampleMetadata
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	622 \| (tabular separated values) file identical to the sampleMetadata file given as an input argument, excepting lacking rows for samples that have been filtered out (by the sample-class filter, or because of zero variance, or because they were missing in the input data matrix)
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	623 \|
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	624
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	625 variableMetadata
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	626 \| (tabular separated values) file identical to the variableMetadata file given as an input argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (by the variable-range filter, or because of zero variance, or because they were missing in the input data matrix)
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	627 \|
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	628
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	629 dataMatrix
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	630 \| (tabular separated values) file identical to the dataMatrix file given as an input argument, excepting lacking rows and columns for variables and samples that have been filtered out, respectively
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	631 \|
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	632
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	633
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	634 -----------------------------------------
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	635 'Wild card' patterns to match class-names
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	636 -----------------------------------------
4 499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	637
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	638 W4m Data Subset supports use of R "wild card" patterns to select class-names.
4 499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	639
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	640 - use '``?``' to match a single character
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	641 - use '``*``' to match zero or more characters
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	642 - the entire pattern must match the sample name
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	643
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	644 For example
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	645
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	646 - '``??.samp*``' matches '``my.sample``' but not '``my.own.sample``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	647 - '``*.sample``' matches '``my.sample``' and '``my.own.sample``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	648 - '``*.sampl``' matches neither '``my.sample``' nor '``my.own.sample``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	649
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	650 --------------------------------------------------
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	651 'Regular expression' patterns to match class-names
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	652 --------------------------------------------------
4 499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	653
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	654 W4m Data Subset supports use of R "regular expression" patterns to select class-names.
4 499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	655
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	656 R uses POSIX 1003.2 standard regular expressions, which allow precise pattern-matching and are exhaustively defined at:
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	657 http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap09.html
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	658
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	659 However, only a few basic building blocks of regular expressions need to be mastered for most cases:
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	660
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	661 - '``^``' matches the beginning of a class-name
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	662 - '``$``' matches the end of a class-name
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	663 - '``.``' outside of square brackets matches a single character
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	664 - '``*``' matches character specified immediately before zero or more times
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	665 - square brackets specify a set of characters to be matched.
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	666
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	667 Within square brackets
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	668
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	669 - '``^``' as the first character specifies that the list of characters are those that should not be matched.
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	670 - '``-``' is used to specify ranges of characters
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	671
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	672 Caveat: The tool wrapper uses the comma ('``,``') to split a list of sample-class names, so commas may not be used within regular expressions for this tool
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	673
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	674 First Example: Consider a field of class-names consisting of '``marq3,marq6,marq9,marq12,front3,front6,front9,front12``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	675
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	676 - The regular expression '``^front[0-9][0-9]*$``' will match the same sample-classes as '``front3,front6,front9,front12``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	677 - The regular expression '``^[a-z][a-z]3$``' will match the same sample-classes as '``front3,marq3``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	678 - The regular expression '``^[a-z][a-z]12$``' will match the same sample-classes as '``front12,marq12``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	679 - The regular expression '``^[a-z][a-z][0-9]$``' will match the same sample-classes as '``front3,front6,front9,marq3,marq6,marq9``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	680
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	681 Second Example: Consider these regular expression patterns as possible matches to a sample-class name '``AB0123``':
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	682
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	683 - '``^[A-Z][A-Z][0-9][0-9]$``' - MATCHES '``^AB0123$*``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	684 - '``^[A-Z][A-Z][0-9][0-9]$``' - MATCHES '``^AB0123$``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	685 - '``^[A-Z][0-9]``' - MATCHES '``^A* B0123$``' - first character is a letter, '``*``' can specify zero characters, and end of line did not need to be matched.
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	686 - '``^[A-Z][A-Z][0-9]``' - MATCHES '``^AB0 123$``' - first two characters are letters aind the third is a digit.
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	687 - '``^[A-Z][A-Z]*[0-9][0-9]$``' - NO MATCH - the name does not end with the pattern '``[A-Z][0-9][0-9]$``', i.e., it ends with four digits, not two.
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	688 - '``^[A-Z][0-9]*$``' - NO MATCH - the pattern specifies that second character and all those that follow, if present, must be digits.
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	689
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	690 ----------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	691 Variable-range filters
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	692 ----------------------
4 499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	693
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	694 An array of range-specification strings may be supplied in the `variableRangeFilter`
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	695 argument. If supplied, only features having numerical values in the specified column
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	696 of `variableMetadata` that fall within the specified ranges will be retained
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	697 in the output. Each range is a string of three colon-separated values (e.g., "mz:200:800") in the
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	698 following order:
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	699
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	700 - the name of a column of `variableMetadata` which must have numerical data (e.g., "mz");
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	701 - the minimum allowed value in that column for the feature to be retained (e.g., 200);
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	702 - the maximum allowed value (e.g., 800).
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	703
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	704 Note for the range specification strings:
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	705
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	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)
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	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.
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	708
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	709 - Note, however, that when the "maximum" is greater than the "minimum" for the FEATMAX range specification, then the specification is ignored.
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	710
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	711 -----------------------------------------------------------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	712
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	713 ----------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	714 WORKING EXAMPLES
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	715 ----------------
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	716
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	717 .. class:: infomark
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	718
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	719 -----------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	720 Input Files
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	721 -----------
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	722
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	723 +------------------------------------------------------------------------------------------------------------------------+
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	724 \| Input File URL \|
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	725 +========================================================================================================================+
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	726 \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/input_dataMatrix.tsv \|
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	727 +------------------------------------------------------------------------------------------------------------------------+
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	728 \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/input_sampleMetadata.tsv \|
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	729 +------------------------------------------------------------------------------------------------------------------------+
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	730 \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/input_variableMetadata.tsv \|
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	731 +------------------------------------------------------------------------------------------------------------------------+
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	732
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	733 .. class:: infomark
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	734
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	735 -------------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	736 Running Without Range-Filtering
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	737 -------------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	738
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	739 This example retains only samples whose 'gender' attribute is 'M'.
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	740
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	741 Input parameters
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	742
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	743 +------------------------------------+-------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	744 \| Input Parameter \| Value \|
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	745 +====================================+===============================+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	746 \| Names of sample-classes \| M \|
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	747 +------------------------------------+-------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	748 \| Include named classes \| filter-in \|
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	749 +------------------------------------+-------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	750 \| Column that names the sample-class \| gender \|
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	751 +------------------------------------+-------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	752 \| Variable range-filters \| (Leave this field empty.) \|
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	753 +------------------------------------+-------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	754 \| Data transforamtion \| none \|
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	755 +------------------------------------+-------------------------------+
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	756
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	757 Expected outputs
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	758
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	759 +-------------------+---------------------------------------------------------------------------------------------------------------------------+
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	760 \| Expected Output \| Download from URL \|
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	761 +===================+===========================================================================================================================+
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	762 \| Data matrix \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/expected_dataMatrix.tsv \|
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	763 +-------------------+---------------------------------------------------------------------------------------------------------------------------+
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	764 \| Sample metadata \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/expected_sampleMetadata.tsv \|
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	765 +-------------------+---------------------------------------------------------------------------------------------------------------------------+
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	766 \| Variable metadata \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/expected_variableMetadata.tsv \|
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	767 +-------------------+---------------------------------------------------------------------------------------------------------------------------+
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	768
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	769 .. class:: infomark
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	770
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	771 ----------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	772 Running With Range-Filtering
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	773 ----------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	774
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	775 This example retains only features whose mz is greater than 200, whose rt is less than 800, and whose maximum intensity across all samples is 2,000,000.
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	776 This example retains all samples (except those having zero variance for all feature), although it would be possible to filter on samples as well.
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	777
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	778 Input parameters
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	779
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	780 +------------------------------------+------------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	781 \| Input Parameter \| Value \|
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	782 +====================================+====================================+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	783 \| Names of sample-classes \| (Leave this field empty.) \|
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	784 +------------------------------------+------------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	785 \| Include named classes \| filter-out \|
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	786 +------------------------------------+------------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	787 \| Column that names the sample-class \| gender \|
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	788 +------------------------------------+------------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	789 \| Variable range-filters \| FEATMAX:20.93157:,mz:200:,rt::800 \|
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	790 +------------------------------------+------------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	791 \| Data transforamtion \| log2 \|
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	792 +------------------------------------+------------------------------------+
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	793
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	794 Expected outputs
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	795
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	796 +-------------------+------------------------------------------------------------------------------------------------------------------------------+
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	797 \| Expected Output \| Download from URL \|
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	798 +===================+==============================================================================================================================+
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	799 \| Data matrix \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/rangefilter_dataMatrix.tsv \|
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	800 +-------------------+------------------------------------------------------------------------------------------------------------------------------+
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	801 \| Sample metadata \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/rangefilter_sampleMetadata.tsv \|
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	802 +-------------------+------------------------------------------------------------------------------------------------------------------------------+
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	803 \| Variable metadata \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/rangefilter_variableMetadata.tsv \|
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	804 +-------------------+------------------------------------------------------------------------------------------------------------------------------+
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	805
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	806 -----------------------------------------------------------------------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	807
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	808 ----
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	809 NEWS
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	810 ----
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	811
9 1ced8b5dfa3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit ac7c79636d17f7d33f1e8e644db0ddd33d2057e8 eschen42 parents: 8 diff changeset	812 Changes in version 0.98.9
1ced8b5dfa3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit ac7c79636d17f7d33f1e8e644db0ddd33d2057e8 eschen42 parents: 8 diff changeset	813 =========================
1ced8b5dfa3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit ac7c79636d17f7d33f1e8e644db0ddd33d2057e8 eschen42 parents: 8 diff changeset	814
1ced8b5dfa3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit ac7c79636d17f7d33f1e8e644db0ddd33d2057e8 eschen42 parents: 8 diff changeset	815 New features
1ced8b5dfa3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit ac7c79636d17f7d33f1e8e644db0ddd33d2057e8 eschen42 parents: 8 diff changeset	816
1ced8b5dfa3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit ac7c79636d17f7d33f1e8e644db0ddd33d2057e8 eschen42 parents: 8 diff changeset	817 - Fixed bug.
1ced8b5dfa3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit ac7c79636d17f7d33f1e8e644db0ddd33d2057e8 eschen42 parents: 8 diff changeset	818
1ced8b5dfa3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit ac7c79636d17f7d33f1e8e644db0ddd33d2057e8 eschen42 parents: 8 diff changeset	819 Internal modifications
1ced8b5dfa3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit ac7c79636d17f7d33f1e8e644db0ddd33d2057e8 eschen42 parents: 8 diff changeset	820
1ced8b5dfa3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit ac7c79636d17f7d33f1e8e644db0ddd33d2057e8 eschen42 parents: 8 diff changeset	821 - Added the hyphen to the characters permitted within regular expressions.
1ced8b5dfa3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit ac7c79636d17f7d33f1e8e644db0ddd33d2057e8 eschen42 parents: 8 diff changeset	822
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	823 Changes in version 0.98.8
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	824 =========================
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	825
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	826 New features
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	827
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	828 - The tool now appears in Galaxy with a new, more representative name: "W4m Data Subset". (Earlier versions of this tool appeared in Galaxy with the name "Sample Subset".)
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	829 - Option was added to log-transform data matrix values.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	830 - Output datasets are named in conformance with the W4m convention of appending the name of each preprocessing tool to the input dataset name.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	831 - Superflous "Column that names the sample" input parameter was eliminated.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	832 - Some documentation was updated or clarified.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	833
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	834 Internal modifications
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	835
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	836 - None
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	837
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	838 Changes in version 0.98.7
7 582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704 eschen42 parents: 6 diff changeset	839 =========================
582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704 eschen42 parents: 6 diff changeset	840
582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704 eschen42 parents: 6 diff changeset	841 New features
582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704 eschen42 parents: 6 diff changeset	842
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	843 - First column of output variableMetadata (that has feature names) now is always named "variableMetadata".
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	844 - First column of output sampleMetadata now (that has sample names) now is always named "sampleMetadata".
7 582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704 eschen42 parents: 6 diff changeset	845
582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704 eschen42 parents: 6 diff changeset	846 Internal modifications
582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704 eschen42 parents: 6 diff changeset	847
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	848 - Now uses w4mclassfilter R package v0.98.7.
7 582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704 eschen42 parents: 6 diff changeset	849
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	850 Changes in version 0.98.6
5 2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	851 =========================
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	852
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	853 New features
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	854
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	855 - Added support for filtering out features whose attributes fall outside specified ranges.
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	856 For more detail, see "Variable-range filters" above.
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	857
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	858 Internal modifications
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	859
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	860 - Now uses w4mclassfilter R package v0.98.6.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	861 - Now sorts sample names and feature names in output files because some statistical tools expect the same order in `dataMatrix` row and column names as in the corresponding metadata files.
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	862
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	863 Changes in version 0.98.3
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	864 =========================
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	865
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	866 Internal modifications
5 2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	867
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	868 - Improved input handling.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	869 - Now uses w4mclassfilter R package v0.98.3, although that version has no functional implications for this tool.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	870 - Improved reference-list.
5 2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	871
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	872 Changes in version 0.98.2
4 499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	873 =========================
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	874
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	875 New features
4 499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	876
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	877 - Added support for R-flavored regular expression pattern-matching when selecting names of sample-classes.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	878 - Empty classes argument or zero-length class_column result in no samples filtered out.
4 499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	879
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	880 Internal modifications
4 499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	881
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	882 - Support and tests for new features.
4 499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba eschen42 parents: 3 diff changeset	883
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	884 Changes in version 0.98.1
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	885 =========================
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	886
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	887 First release - Wrap the w4mclassfilter R package that implements filtering of W4m data matrix, variable metadata, and sample metadata by class of sample.
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	888
6 38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f eschen42 parents: 5 diff changeset	889 New features
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	890
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	891 - Output dataMatrix is input dataMatrix as modified by the tool
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	892 - Output sampleMetadata is input sampleMetadata as modified by the tool
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	893 - Output variableMetadata is input variableMetadata as modified by the tool
3 191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0 eschen42 parents: 2 diff changeset	894
5 2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	895 ]]></help>
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	896 <citations>
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	897 <!-- Giacomoni_2014 W4m 2.5 -->
5 2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	898 <citation type="doi">10.1093/bioinformatics/btu813</citation>
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	899 <!-- Guitton_2017 W4m 3.0 -->
5 2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	900 <citation type="doi">10.1016/j.biocel.2017.07.002</citation>
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	901 <!-- Kuhl_2012 CAMERA -->
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	902 <citation type="doi">10.1021/ac202450g</citation>
5 2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	903 <!-- Smith_2006 XCMS -->
3 191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0 eschen42 parents: 2 diff changeset	904 <citation type="doi">10.1021/ac051437y</citation>
8 d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1 eschen42 parents: 7 diff changeset	905 <!-- Thevenot_2015 Urinary metabolome statistics -->
5 2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64 eschen42 parents: 4 diff changeset	906 <citation type="doi">10.1021/acs.jproteome.5b00354</citation>
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	907 </citations>
3 191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0 eschen42 parents: 2 diff changeset	908 <!--
7 582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704 eschen42 parents: 6 diff changeset	909 vim:noet:sw=2:ts=2
3 191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0 eschen42 parents: 2 diff changeset	910 --> </tool>

Mercurial > repos > eschen42 > w4mclassfilter

annotate w4mclassfilter.xml @ 9:1ced8b5dfa3e draft