w4mclassfilter: w4mclassfilter.xml annotate

annotate w4mclassfilter.xml @ 2:23c6d271def9 draft

planemo upload

author	eschen42
date	Wed, 10 May 2017 02:51:58 -0400
parents	bab3a658f74e
children	191a720488ce

rev	line source
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	1 <tool id="W4MClassFilter" name="W4MClassFilter" version="0.98.1">
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	2 <description>Filter W4M data by sample class</description>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	3
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	4 <requirements>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	5 <requirement type="package" version="3.3.1">r-base</requirement>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	6 <requirement type="package" version="1.1_4">r-batch</requirement>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	7 <requirement type="package" version="0.98.1">w4mclassfilter</requirement>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	8 </requirements>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	9
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	10 <stdio>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	11 <exit_code range="1:" level="fatal" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	12 </stdio>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	13
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	14
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	15 <command detect_errors="aggressive"><![CDATA[
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	16 Rscript $__tool_directory__/w4mclassfilter_wrapper.R
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	17 dataMatrix_in "$dataMatrix_in"
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	18 sampleMetadata_in "$sampleMetadata_in"
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	19 variableMetadata_in "$variableMetadata_in"
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	20 sampleclassNames "$sampleclassNames"
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	21 inclusive "$inclusive"
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	22 classnameColumn "$classnameColumn"
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	23 samplenameColumn "$samplenameColumn"
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	24 dataMatrix_out "$dataMatrix_out"
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	25 sampleMetadata_out "$sampleMetadata_out"
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	26 variableMetadata_out "$variableMetadata_out"
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	27 ]]></command>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	28
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	29 <inputs>
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	30 <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	31 <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	32 <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata columns, separator: tab" />
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	33 <param name="sampleclassNames" label="Names of sample classes" type="text" value = "" help="comma-separated names of sample classes to filter in or out; defaults to no names" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	34 <param name="inclusive" label="Include named classes" type="select" help="filter-in - include only the named sample classes; filter-out (the default) - exclude only the named sample classes">
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	35 <option value="TRUE">filter-in</option>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	36 <option value="FALSE" selected="true">filter-out</option>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	37 </param>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	38 <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 'classes' input parameter - defaults to 'class'" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	39 <param name="samplenameColumn" label="Column that names the sample" type="text" value = "sampleMetadata" help="name of the column in sample metadata that has the name of the sample - defaults to 'sampleMetadata'" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	40 </inputs>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	41 <outputs>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	42 <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	43 <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	44 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	45 </outputs>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	46
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	47 <tests>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	48 <test>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	49 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	50 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	51 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	52 <param name="classnameColumn" value="gender"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	53 <param name="sampleclassNames" value="M"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	54 <param name="samplenameColumn" value="sampleMetadata"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	55 <param name="inclusive" value="filter-in"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	56 <output name="dataMatrix_out">
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	57 <assert_contents>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	58 <not_has_text text="HU_028" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	59 <not_has_text text="HU_051" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	60 <not_has_text text="HU_060" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	61 <not_has_text text="HU_110" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	62 <not_has_text text="HU_149" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	63 <not_has_text text="HU_152" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	64 <not_has_text text="HU_175" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	65 <not_has_text text="HU_178" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	66 <not_has_text text="HU_185" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	67 <not_has_text text="HU_204" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	68 <not_has_text text="HU_208" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	69 <has_text text="HU_017" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	70 <has_text text="HU_034" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	71 <has_text text="HU_078" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	72 <has_text text="HU_091" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	73 <has_text text="HU_093" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	74 <has_text text="HU_099" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	75 <has_text text="HU_130" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	76 <has_text text="HU_134" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	77 <has_text text="HU_138" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	78 <has_text text="HMDB03193" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	79 <not_has_text text="HMDB00822" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	80 <has_text text="HMDB01101" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	81 <has_text text="HMDB01101.1" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	82 <has_text text="HMDB10348" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	83 <has_text text="HMDB59717" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	84 <has_text text="HMDB13189" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	85 <has_text text="HMDB00299" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	86 <has_text text="HMDB00191" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	87 <has_text text="HMDB00518" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	88 <has_text text="HMDB00715" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	89 <has_text text="HMDB01032" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	90 <has_text text="HMDB00208" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	91 <has_text text="HMDB04824" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	92 <has_text text="HMDB00512" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	93 <has_text text="HMDB00251" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	94 </assert_contents>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	95 </output>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	96 </test>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	97 <test>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	98 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	99 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	100 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	101 <param name="classnameColumn" value="gender"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	102 <param name="sampleclassNames" value="M"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	103 <param name="samplenameColumn" value="sampleMetadata"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	104 <param name="inclusive" value="filter-in"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	105 <output name="sampleMetadata_out">
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	106 <assert_contents>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	107 <not_has_text text="HU_028" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	108 <not_has_text text="HU_051" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	109 <not_has_text text="HU_060" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	110 <not_has_text text="HU_110" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	111 <not_has_text text="HU_149" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	112 <not_has_text text="HU_152" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	113 <not_has_text text="HU_175" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	114 <not_has_text text="HU_178" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	115 <not_has_text text="HU_185" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	116 <not_has_text text="HU_204" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	117 <not_has_text text="HU_208" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	118 <has_text text="HU_017" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	119 <has_text text="HU_034" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	120 <has_text text="HU_078" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	121 <has_text text="HU_091" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	122 <has_text text="HU_093" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	123 <has_text text="HU_099" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	124 <has_text text="HU_130" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	125 <has_text text="HU_134" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	126 <has_text text="HU_138" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	127 </assert_contents>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	128 </output>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	129 </test>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	130 <test>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	131 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	132 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	133 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	134 <param name="classnameColumn" value="gender"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	135 <param name="sampleclassNames" value="M"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	136 <param name="samplenameColumn" value="sampleMetadata"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	137 <param name="inclusive" value="filter-in"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	138 <output name="variableMetadata_out">
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	139 <assert_contents>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	140 <has_text text="HMDB03193" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	141 <not_has_text text="HMDB00822" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	142 <has_text text="HMDB01101" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	143 <has_text text="HMDB01101.1" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	144 <has_text text="HMDB10348" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	145 <has_text text="HMDB59717" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	146 <has_text text="HMDB13189" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	147 <has_text text="HMDB00299" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	148 <has_text text="HMDB00191" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	149 <has_text text="HMDB00518" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	150 <has_text text="HMDB00715" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	151 <has_text text="HMDB01032" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	152 <has_text text="HMDB00208" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	153 <has_text text="HMDB04824" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	154 <has_text text="HMDB00512" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	155 <has_text text="HMDB00251" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	156 </assert_contents>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	157 </output>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	158 </test>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	159 </tests>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	160
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	161
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	162
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	163 <help>
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	164 <![CDATA[
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	165
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	166 .. class:: infomark
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	167
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	168 Author Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	169
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	170 --------------------------------------------------------------------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	171
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	172 .. class:: infomark
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	173
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	174 R package
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	175
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	176 The w4mclassfilter package is available from the Hegeman lab github repository (https://github.com/HegemanLab/w4mclassfilter/releases).
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	177
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	178 -----------------------------------------------------------------------------------------------------------------------------------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	179
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	180 .. class:: infomark
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	181
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	182 Tool updates
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	183
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	184 See the NEWS section at the bottom of this page
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	185
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	186 ---------------------------------------------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	187
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	188 ==============================================
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	189 Filter Workflow4Metabolomics data matrix files
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	190 ==============================================
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	191
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	192 -----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	193 Description
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	194 -----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	195
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	196 Filter set of retention-corrected W4M files (dataMatrix, sampleMetadata, variableMetadata) by sample class
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	197
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	198 --------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	199 Comments
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	200 --------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	201
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	202 The inclusive parameter indicates:
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	203 - when 'filter-in', that only the sample-classes named should be included
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	204 - when 'filter-out', that all sample-classes should be included excepting the sample-classes named
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	205
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	206 -----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	207 Input files
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	208 -----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	209
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	210 +---------------------------+------------+
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	211 \| File \| Format \|
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	212 +===========================+============+
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	213 \| Data matrix \| tabular \|
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	214 +---------------------------+------------+
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	215 \| Sample metadata \| tabular \|
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	216 +---------------------------+------------+
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	217 \| Variable metadata \| tabular \|
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	218 +---------------------------+------------+
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	219
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	220
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	221 ----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	222 Parameters
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	223 ----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	224
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	225 Data matrix file
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	226 \| 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 to the rownames of the sample and variable metadata, respectively (see below)
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	227 \|
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	228
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	229 Sample metadata file
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	230 \| 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	231 \|
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	232
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	233 Variable metadata file
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	234 \| 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	235 \|
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	236
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	237 Names of sample classes (default = no names)
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	238 \| comma-separated names of sample classes to include or exclude
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	239 \|
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	240
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	241 Include named classes (default = filter-out)
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	242 \| filter-in - include only the named sample classes
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	243 \| filter-out - exclude only the named sample classes
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	244 \|
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	245
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	246
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	247 Column that names the sample-class (default = 'class')
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	248 \| name of the column in sample metadata that has the values to be tested against the 'classes' input parameter
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	249 \|
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	250
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	251 Column that names the sample (default = 'sampleMetadata')
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	252 \| name of the column in sample metadata that has the name of the sample
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	253 \|
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	254
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	255
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	256 ------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	257 Output files
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	258 ------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	259
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	260
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	261 sampleMetadata
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	262 \| (tabular separated values) file identical to the sampleMetadata file given as an input argument, excepting lacking rows for samples (xC-MS features) that have been filtered out (by the sample-class filter or because of zero variance)
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	263 \|
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	264
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	265 variableMetadata
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	266 \| (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 (because of zero variance)
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	267 \|
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	268
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	269 dataMatrix
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	270 \| (tabular separated values) file identical to the dataMatrix file given as an input argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (because of zero variance) and columns that have been filtered out (by the sample-class filter or because of zero variance)
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	271 \|
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	272
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	273
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	274 ---------------
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	275 Working example
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	276 ---------------
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	277
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	278 .. class:: infomark
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	279
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	280 Input files
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	281
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	282 +-------------------+--------------------------------------------------------------------------------------------------------------+
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	283 \| Input File \| Download from URL \|
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	284 +===================+==============================================================================================================+
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	285 \| Data matrix \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/input_dataMatrix.tsv \|
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	286 +-------------------+--------------------------------------------------------------------------------------------------------------+
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	287 \| Sample metadata \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/input_sampleMetadata.tsv \|
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	288 +-------------------+--------------------------------------------------------------------------------------------------------------+
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	289 \| Variable metadata \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/input_variableMetadata.tsv \|
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	290 +-------------------+--------------------------------------------------------------------------------------------------------------+
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	291
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	292 .. class:: infomark
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	293
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	294 Other input parameters
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	295
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	296 +------------------------------------+-----------------+
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	297 \| Input Parameter \| Value \|
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	298 +====================================+=================+
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	299 \| Names of sample classes \| M \|
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	300 +------------------------------------+-----------------+
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	301 \| Include named classes \| filter-in \|
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	302 +------------------------------------+-----------------+
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	303 \| Column that names the sample-class \| gender \|
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	304 +------------------------------------+-----------------+
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	305 \| Column that names the sample \| sampleMetadata \|
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	306 +------------------------------------+-----------------+
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	307
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	308 .. class:: infomark
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	309
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	310 Expected outputs
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	311
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	312 +-------------------+-----------------------------------------------------------------------------------------------------------------+
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	313 \| Expected Output \| Download from URL \|
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	314 +===================+=================================================================================================================+
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	315 \| Data matrix \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/expected_dataMatrix.tsv \|
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	316 +-------------------+-----------------------------------------------------------------------------------------------------------------+
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	317 \| Sample metadata \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/expected_sampleMetadata.tsv \|
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	318 +-------------------+-----------------------------------------------------------------------------------------------------------------+
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	319 \| Variable metadata \| https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/expected_variableMetadata.tsv \|
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	320 +-------------------+-----------------------------------------------------------------------------------------------------------------+
23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	321
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	322
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	323 -----------------------------------------------------------------------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	324
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	325 ----
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	326 NEWS
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	327 ----
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	328
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	329 CHANGES IN VERSION 0.98.1
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	330 =========================
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	331
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	332 NEW FEATURES
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	333
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	334 First release - R package that implements filtering of W4M data matrix, variable metadata, and sample metadata by class of sample.
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	335
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	336 dataMatrix is modified by the tool, so it does appear as an output file
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	337
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	338 INTERNAL MODIFICATIONS
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	339
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	340 none
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	341 ]]>
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	342 </help>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	343 <citations>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	344 </citations>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	345 </tool>
2 23c6d271def9 planemo upload eschen42 parents: 0 diff changeset	346 <!-- vim: noet sw=4 ts=4 :
0 bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79 eschen42 parents: diff changeset	347 -->

Mercurial > repos > eschen42 > w4mclassfilter

annotate w4mclassfilter.xml @ 2:23c6d271def9 draft