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comparison w4mclassfilter.xml @ 15:f9cb2244fd01 draft

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"planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit aaac8e2f8de03c01e5064abf8a2e30020fabe7ca"
author eschen42
date Thu, 11 Mar 2021 21:07:10 +0000
parents 87ec0d3c2266
children
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14:87ec0d3c2266 15:f9cb2244fd01
1 <tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.18"> 1 <tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.19">
2 <description>Filter W4M data by values or metadata</description> 2 <description>Filter W4M data by values or metadata</description>
3 <!-- Here is the hyphenation standard that I *try* to apply consistently in my documentation:
4 https://web.archive.org/web/20161014025757/http://www.sandranoonan.com/dont-let-hyphenation-drive-crazy/
5 -->
6 <requirements> 3 <requirements>
7 <requirement type="package" version="3.6.2">r-base</requirement> 4 <requirement type="package" version="4.0.3">r-base</requirement>
8 <requirement type="package" version="1.1_5">r-batch</requirement> 5 <requirement type="package" version="1.1_5">r-batch</requirement>
9 <requirement type="package" version="0.98.18">w4mclassfilter</requirement> 6 <requirement type="package" version="0.98.19">w4mclassfilter</requirement>
10 </requirements> 7 </requirements>
11 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
12 unset R_HOME; 9 unset R_HOME;
13 if [ '$centering' == 'medoid' -a '$imputation' == 'none' ]; then 10 if [ '$centering' == 'medoid' -a '$imputation' == 'none' ]; then
14 (echo 'medoid' centering may not be chosen with imputation 'none' 1>&2); 11 (echo 'medoid' centering may not be chosen with imputation 'none' 1>&2);
600 <has_text text="HU_110" /> 597 <has_text text="HU_110" />
601 <has_text text="HU_078" /> 598 <has_text text="HU_078" />
602 </assert_contents> 599 </assert_contents>
603 </output> 600 </output>
604 </test> 601 </test>
602 <!-- test 13 -->
603 <test>
604 <param name="dataMatrix_in" value="input_med1_dm.tsv"/>
605 <param name="sampleMetadata_in" value="input_med1_sm.tsv"/>
606 <param name="variableMetadata_in" value="input_med1_vm.tsv"/>
607 <param name="classnameColumn" value="pcgroup"/>
608 <param name="sampleclassNames" value=""/>
609 <param name="wildcards" value="TRUE"/>
610 <param name="inclusive" value="FALSE"/>
611 <param name="imputation" value="zero"/>
612 <param name="order_vrbl" value="sample"/>
613 <param name="order_smpl" value="pcgroup"/>
614 <param name="centering" value="medoid"/>
615 <output name="sampleMetadata_out">
616 <assert_contents>
617 <has_text text="X10" />
618 <has_text text="M70T1043" />
619 <has_text text="70.01229" />
620 <has_text text="1042.837" />
621 <has_text text="X345" />
622 <has_text text="M74T33" />
623 <not_has_text text="M70T1042_1" />
624 <not_has_text text="M74T34" />
625 </assert_contents>
626 </output>
627 <output name="dataMatrix_out">
628 <assert_contents>
629 <has_text text="X10" />
630 <has_text text="X345" />
631 </assert_contents>
632 </output>
633 </test>
605 </tests> 634 </tests>
635 <!-- Here is the hyphenation standard that I *try* to apply consistently in my documentation:
636 https://web.archive.org/web/20161014025757/http://www.sandranoonan.com/dont-let-hyphenation-drive-crazy/
637 -->
606 <help><![CDATA[ 638 <help><![CDATA[
607 639
608 640
609 **Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu) 641 **Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
610 642
623 See https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper#news 655 See https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper#news
624 656
625 --------------------------------------------------- 657 ---------------------------------------------------
626 658
627 ====================================================== 659 ======================================================
628 "W4M Data Subset" - Filter Workflow4Metabolomics data 660 "W4M Data Subset" - Filter Workflow4Metabolomics data
629 ====================================================== 661 ======================================================
630 662
631 ---------- 663 ----------
632 Motivation 664 Motivation
633 ---------- 665 ----------