aldex2: aldex2.xml annotate

annotate aldex2.xml @ 1:75214276e2b7 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit f9acc7c5710d6eb99a883cb83b7967e6af972f1b

author	iuc
date	Fri, 14 Jun 2024 21:21:29 +0000
parents	f4d0bd4b4d6d
children

rev	line source
0 f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	1 <tool id="aldex2" name="ALDEx2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	2 <description>differential abundance analysis</description>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	3 <macros>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	4 <import>macros.xml</import>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	5 </macros>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	6 <expand macro="biotools"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	7 <expand macro="requirements"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	8 <command detect_errors="exit_code"><![CDATA[
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	9 ## Enable building the conditions_vector.
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	10 #set group_names = []
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	11 #set num_cols = []
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	12 #for $condition_items in $conditions:
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	13 $group_names.append(str($condition_items.group_name))
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	14 $num_cols.append(str($condition_items.num_cols))
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	15 #end for
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	16 #set group_names = ','.join($group_names)
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	17 #set num_cols = ','.join($num_cols)
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	18
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	19 #if str($analysis_type_cond.analysis_type) == 'aldex_corr':
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	20 ## Enable building the cond_var (a continuous numeric vector).
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	21 #set group_nums = []
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	22 #set num_cols_in_groups = []
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	23 #for $cont_var_items in $analysis_type_cond.cont_var:
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	24 $group_nums.append(str($cont_var_items.group_num))
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	25 $num_cols_in_groups.append(str($cont_var_items.num_cols_in_group))
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	26 #end for
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	27 #set group_nums = ','.join($group_nums)
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	28 #set num_cols_in_groups = ','.join($num_cols_in_groups)
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	29 #end if
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	30
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	31 Rscript '${__tool_directory__}/aldex2.R'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	32 --reads '$reads'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	33 --group_names '$group_names'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	34 --num_cols '$num_cols'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	35 --num_mc_samples $num_mc_samples
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	36 --denom '$denom'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	37 --analysis_type '$analysis_type_cond.analysis_type'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	38 #if str($analysis_type_cond.analysis_type) == 'aldex':
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	39 --aldex_test '$analysis_type_cond.aldex_test'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	40 --effect '$analysis_type_cond.effect'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	41 --include_sample_summary '$analysis_type_cond.include_sample_summary'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	42 --iterate '$analysis_type_cond.iterate'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	43 #else if str($analysis_type_cond.analysis_type) == 'aldex_corr':
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	44 --group_nums '$group_nums'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	45 --num_cols_in_groups '$num_cols_in_groups'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	46 #else if str($analysis_type_cond.analysis_type) == 'aldex_effect':
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	47 --include_sample_summary '$analysis_type_cond.include_sample_summary'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	48 #else if str($analysis_type_cond.analysis_type) == 'aldex_plot':
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	49 --aldex_test '$analysis_type_cond.aldex_test'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	50 --effect '$analysis_type_cond.effect'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	51 --include_sample_summary '$analysis_type_cond.include_sample_summary'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	52 --iterate '$analysis_type_cond.iterate'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	53 --plot_type '$analysis_type_cond.plot_type'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	54 --plot_test '$analysis_type_cond.plot_test'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	55 --cutoff_pval $analysis_type_cond.cutoff_pval
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	56 --cutoff_effect $analysis_type_cond.cutoff_effect
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	57 #if str($analysis_type_cond.xlab) != '':
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	58 --xlab '$analysis_type_cond.xlab'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	59 #end if
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	60 #if str($analysis_type_cond.ylab) != '':
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	61 --ylab '$analysis_type_cond.ylab'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	62 #end if
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	63 #else if str($analysis_type_cond.analysis_type) == 'aldex_plot_feature':
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	64 --feature_name '$analysis_type_cond.feature_name'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	65 #else if str($analysis_type_cond.analysis_type) == 'aldex_ttest':
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	66 --paired_test '$analysis_type_cond.paired_test'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	67 --hist_plot '$analysis_type_cond.hist_plot'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	68 #end if
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	69 #if str($analysis_type_cond.analysis_type) == 'aldex':
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	70 --output '$output_aldex'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	71 #else if str($analysis_type_cond.analysis_type) == 'aldex_corr':
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	72 --output '$output_aldex_corr'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	73 #else if str($analysis_type_cond.analysis_type) == 'aldex_effect':
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	74 --output '$output_aldex_effect'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	75 #else if str($analysis_type_cond.analysis_type) == 'aldex_expected_distance':
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	76 --output '$output_aldex_expected_distance'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	77 #else if str($analysis_type_cond.analysis_type) == 'aldex_kw':
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	78 --output '$output_aldex_kw'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	79 #else if str($analysis_type_cond.analysis_type) == 'aldex_plot':
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	80 --output '$output_aldex_plot'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	81 #else if str($analysis_type_cond.analysis_type) == 'aldex_plot_feature':
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	82 --output '$output_aldex_plot_feature'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	83 #else if str($analysis_type_cond.analysis_type) == 'aldex_ttest':
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	84 --output '$output_aldex_ttest'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	85 #if str($analysis_type_cond.hist_plot) == 'true':
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	86 && mv 'Rplots.pdf' '$output_aldex_ttest_plot'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	87 #end if
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	88 #end if
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	89 ]]></command>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	90 <inputs>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	91 <param argument="--reads" type="data" format="tabular" label="Reads table file" help="Rows contain genes and columns contain sequencing read counts"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	92 <repeat name="conditions" title="Comparison group" min="1">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	93 <param name="group_name" type="text" value="Grp1" label="Group name" help="Specify a group label and the number of sequencing read count columns associated with it">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	94 <validator type="empty_field"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	95 <expand macro="sanitize_query" validinitial="string.ascii_letters,string.punctuation"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	96 </param>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	97 <param name="num_cols" type="integer" min="1" value="1" label="Number of columns in group"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	98 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	99 <param argument="--num_mc_samples" type="integer" min="1" value="128" label="Number of Monte Carlo samples to use when estimating the underlying distributions"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	100 <param argument="--denom" type="select" label="Select features to retain as the denominator for the Geometric Mean calculation">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	101 <option value="all" selected="true">All features</option>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	102 <option value="median">Median abundance of all features</option>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	103 <option value="iqlr">Features that are between the first and third quartile of the variance of the clr values across all samples</option>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	104 <option value="zero">Non-zero features in each group as the denominator</option>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	105 <option value="lvha">features that have low variance and high relative abundance</option>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	106 </param>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	107 <conditional name="analysis_type_cond">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	108 <param name="analysis_type" type="select" label="Select the analysis to be performed">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	109 <option value="aldex" selected="true">Compute an ALDEx2 object (aldex)</option>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	110 <option value="aldex_corr">Calculate correlation with a continuous variable (aldex.corr)</option>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	111 <option value="aldex_effect">Calculate effect sizes and differences between conditions (aldex.effect)</option>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	112 <option value="aldex_expected_distance">Calculate the expected values of distances between samples (aldex.expectedDistance)</option>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	113 <option value="aldex_kw">Calculate the Kruskal-Wallis test and glm ANOVA statistics (aldex.kw)</option>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	114 <option value="aldex_plot">Plot an ALDEx2 object (aldex.plot)</option>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	115 <option value="aldex_plot_feature">Show dispersion of the expected values returned by aldex.effect (aldex.plotFeature)</option>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	116 <option value="aldex_ttest">Calculate Welch’s t-test and Wilcoxon test statistics (aldex.ttest)</option>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	117 </param>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	118 <when value="aldex">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	119 <expand macro="aldex_test_param"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	120 <expand macro="effect_param"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	121 <expand macro="include_sample_summary_param"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	122 <expand macro="iterate_param"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	123 </when>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	124 <when value="aldex_corr">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	125 <repeat name="cont_var" title="Group number" min="1">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	126 <param name="group_num" type="integer" min="1" value="1" label="Group number" help="Specify a group number and the number of columns from the Reads table file associated with the group"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	127 <param name="num_cols_in_group" type="integer" min="1" value="1" label="Number of columns in group"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	128 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	129 </when>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	130 <when value="aldex_effect">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	131 <expand macro="include_sample_summary_param"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	132 </when>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	133 <when value="aldex_expected_distance"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	134 <when value="aldex_kw"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	135 <when value="aldex_plot">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	136 <expand macro="aldex_test_param"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	137 <expand macro="effect_param"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	138 <expand macro="include_sample_summary_param"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	139 <expand macro="iterate_param"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	140 <param name="plot_type" type="select" label="Select the plot type">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	141 <option value="MA" selected="true">A Bland-Altman style plot</option>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	142 <option value="MW">A difference between to a variance within plot</option>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	143 </param>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	144 <param name="plot_test" type="select" label="Select the method of calculating significance">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	145 <option value="welch" selected="true">Welch’s t test</option>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	146 <option value="wilcox">Wilcox rank test</option>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	147 <option value="kruskal">Kruskal-Wallace test</option>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	148 </param>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	149 <param name="cutoff_pval" type="float" value="0.1" min="0" label="Benjamini-Hochberg fdr cutoff"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	150 <param name="cutoff_effect" type="integer" value="1" min="0" label="Effect size cutoff for plotting"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	151 <param name="xlab" type="text" value="" optional="true" label="x-label for the plot">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	152 <expand macro="sanitize_query" validinitial="string.ascii_letters,string.punctuation"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	153 </param>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	154 <param name="ylab" type="text" value="" optional="true" label="y-label for the plot">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	155 <expand macro="sanitize_query" validinitial="string.ascii_letters,string.punctuation"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	156 </param>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	157 </when>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	158 <when value="aldex_plot_feature">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	159 <param name="feature_name" type="text" value="" label="Name of the feature from the input data to be plotted">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	160 <expand macro="sanitize_query" validinitial="string.ascii_letters,string.punctuation"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	161 </param>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	162 </when>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	163 <when value="aldex_ttest">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	164 <param argument="--paired_test" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculate effect size for paired samples?"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	165 <param argument="--hist_plot" type="select" label="Plot a histogram of p-values for the first Dirichlet Monte Carlo instance?">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	166 <option value="false" selected="true">No</option>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	167 <option value="true">Yes</option>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	168 </param>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	169 </when>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	170 </conditional>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	171 </inputs>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	172 <outputs>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	173 <data name="output_aldex" format="tabular" label="${tool.name} on ${on_string}: (aldex)">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	174 <filter>analysis_type_cond['analysis_type'] == 'aldex'</filter>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	175 </data>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	176 <data name="output_aldex_corr" format="tabular" label="${tool.name} on ${on_string}: (aldex.corr)">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	177 <filter>analysis_type_cond['analysis_type'] == 'aldex_corr'</filter>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	178 </data>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	179 <data name="output_aldex_effect" format="tabular" label="${tool.name} on ${on_string}: (aldex.effect)">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	180 <filter>analysis_type_cond['analysis_type'] == 'aldex_effect'</filter>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	181 </data>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	182 <data name="output_aldex_expected_distance" format="png" label="${tool.name} on ${on_string}: (aldex.expectedDistance)">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	183 <filter>analysis_type_cond['analysis_type'] == 'aldex_expected_distance'</filter>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	184 </data>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	185 <data name="output_aldex_kw" format="tabular" label="${tool.name} on ${on_string}: (aldex.kw)">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	186 <filter>analysis_type_cond['analysis_type'] == 'aldex_kw'</filter>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	187 </data>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	188 <data name="output_aldex_plot" format="png" label="${tool.name} on ${on_string}: (aldex.plot)">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	189 <filter>analysis_type_cond['analysis_type'] == 'aldex_plot'</filter>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	190 </data>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	191 <data name="output_aldex_plot_feature" format="png" label="${tool.name} on ${on_string}: (aldex.plotFeature)">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	192 <filter>analysis_type_cond['analysis_type'] == 'aldex_plot_feature'</filter>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	193 </data>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	194 <data name="output_aldex_ttest" format="tabular" label="${tool.name} on ${on_string}: (aldex.ttest)">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	195 <filter>analysis_type_cond['analysis_type'] == 'aldex_ttest'</filter>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	196 </data>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	197 <data name="output_aldex_ttest_plot" format="pdf" label="${tool.name} on ${on_string}: (aldex.ttest hist plot)">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	198 <filter>analysis_type_cond['analysis_type'] == 'aldex_ttest' and analysis_type_cond['hist_plot'] == 'true'</filter>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	199 </data>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	200 </outputs>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	201 <tests>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	202 <test expect_num_outputs="1">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	203 <param name="reads" value="reads.tabular" ftype="tabular"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	204 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	205 <param name="group_name" value="NS"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	206 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	207 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	208 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	209 <param name="group_name" value="S"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	210 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	211 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	212 <output name="output_aldex" ftype="tabular">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	213 <assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	214 <has_text text="rab.all"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	215 <has_size value="39906" delta="100"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	216 </assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	217 </output>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	218 </test>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	219 <test expect_num_outputs="1">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	220 <param name="reads" value="reads.tabular" ftype="tabular"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	221 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	222 <param name="group_name" value="NS"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	223 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	224 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	225 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	226 <param name="group_name" value="S"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	227 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	228 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	229 <param name="denom" value="zero"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	230 <output name="output_aldex" ftype="tabular">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	231 <assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	232 <has_text text="rab.all"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	233 <has_size value="39908" delta="100"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	234 </assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	235 </output>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	236 </test>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	237 <test expect_num_outputs="1">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	238 <param name="reads" value="reads.tabular" ftype="tabular"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	239 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	240 <param name="group_name" value="NS"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	241 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	242 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	243 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	244 <param name="group_name" value="S"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	245 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	246 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	247 <param name="effect" value="false"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	248 <param name="include_sample_summary" value="true"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	249 <param name="iterate" value="true"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	250 <output name="output_aldex" ftype="tabular">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	251 <assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	252 <has_text text="we.ep"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	253 <has_size value="14595" delta="100"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	254 </assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	255 </output>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	256 </test>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	257 <test expect_num_outputs="1">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	258 <param name="reads" value="reads.tabular" ftype="tabular"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	259 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	260 <param name="group_name" value="NS"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	261 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	262 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	263 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	264 <param name="group_name" value="S"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	265 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	266 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	267 <param name="aldex_test" value="kw"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	268 <output name="output_aldex" ftype="tabular">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	269 <assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	270 <has_text text="kw.ep"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	271 <has_size value="14615" delta="100"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	272 </assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	273 </output>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	274 </test>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	275 <test expect_num_outputs="1">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	276 <param name="reads" value="reads.tabular" ftype="tabular"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	277 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	278 <param name="group_name" value="NS"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	279 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	280 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	281 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	282 <param name="group_name" value="S"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	283 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	284 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	285 <param name="analysis_type" value="aldex_corr"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	286 <repeat name="cont_var">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	287 <param name="group_num" value="1"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	288 <param name="num_cols_in_group" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	289 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	290 <repeat name="cont_var">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	291 <param name="group_num" value="2"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	292 <param name="num_cols_in_group" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	293 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	294 <output name="output_aldex_corr" ftype="tabular">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	295 <assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	296 <has_text text="pearson.ecor"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	297 <has_size value="33232" delta="100"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	298 </assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	299 </output>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	300 </test>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	301 <test expect_num_outputs="1">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	302 <param name="reads" value="reads.tabular" ftype="tabular"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	303 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	304 <param name="group_name" value="NS"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	305 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	306 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	307 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	308 <param name="group_name" value="S"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	309 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	310 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	311 <param name="analysis_type" value="aldex_effect"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	312 <output name="output_aldex_effect" ftype="tabular">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	313 <assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	314 <has_text text="rab.all"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	315 <has_size value="25268" delta="100"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	316 </assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	317 </output>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	318 </test>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	319 <test expect_num_outputs="1">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	320 <param name="reads" value="reads.tabular" ftype="tabular"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	321 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	322 <param name="group_name" value="NS"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	323 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	324 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	325 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	326 <param name="group_name" value="S"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	327 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	328 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	329 <param name="analysis_type" value="aldex_expected_distance"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	330 <output name="output_aldex_expected_distance" ftype="png">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	331 <assert_contents>
1 75214276e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit f9acc7c5710d6eb99a883cb83b7967e6af972f1b iuc parents: 0 diff changeset	332 <has_size value="70183" delta="4000"/>
0 f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	333 </assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	334 </output>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	335 </test>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	336 <test expect_num_outputs="1">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	337 <param name="reads" value="reads.tabular" ftype="tabular"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	338 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	339 <param name="group_name" value="NS"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	340 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	341 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	342 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	343 <param name="group_name" value="S"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	344 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	345 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	346 <param name="analysis_type" value="aldex_kw"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	347 <output name="output_aldex_kw" ftype="tabular">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	348 <assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	349 <has_text text="kw.ep"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	350 <has_size value="14623" delta="100"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	351 </assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	352 </output>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	353 </test>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	354 <test expect_num_outputs="1">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	355 <param name="reads" value="reads.tabular" ftype="tabular"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	356 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	357 <param name="group_name" value="NS"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	358 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	359 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	360 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	361 <param name="group_name" value="S"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	362 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	363 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	364 <param name="analysis_type" value="aldex_plot"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	365 <output name="output_aldex_plot" ftype="png">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	366 <assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	367 <has_size value="19064" delta="500"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	368 </assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	369 </output>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	370 </test>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	371 <test expect_num_outputs="1">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	372 <param name="reads" value="reads.tabular" ftype="tabular"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	373 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	374 <param name="group_name" value="NS"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	375 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	376 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	377 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	378 <param name="group_name" value="S"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	379 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	380 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	381 <param name="analysis_type" value="aldex_plot_feature"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	382 <param name="feature_name" value="A:D:A:E"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	383 <output name="output_aldex_plot_feature" ftype="png">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	384 <assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	385 <has_size value="30772" delta="2000"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	386 </assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	387 </output>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	388 </test>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	389 <test expect_num_outputs="1">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	390 <param name="reads" value="reads.tabular" ftype="tabular"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	391 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	392 <param name="group_name" value="NS"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	393 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	394 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	395 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	396 <param name="group_name" value="S"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	397 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	398 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	399 <param name="analysis_type" value="aldex_ttest"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	400 <output name="output_aldex_ttest" ftype="tabular">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	401 <assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	402 <has_text text="we.ep"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	403 <has_size value="14596" delta="100"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	404 </assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	405 </output>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	406 </test>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	407 <test expect_num_outputs="2">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	408 <param name="reads" value="reads.tabular" ftype="tabular"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	409 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	410 <param name="group_name" value="NS"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	411 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	412 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	413 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	414 <param name="group_name" value="S"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	415 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	416 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	417 <param name="analysis_type" value="aldex_ttest"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	418 <param name="paired_test" value="true"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	419 <param name="hist_plot" value="true"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	420 <output name="output_aldex_ttest" ftype="tabular">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	421 <assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	422 <has_text text="we.ep"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	423 <has_size value="13822" delta="100"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	424 </assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	425 </output>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	426 <output name="output_aldex_ttest_plot" ftype="pdf">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	427 <assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	428 <has_text text="%PDF"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	429 <has_size value="7331" delta="100"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	430 </assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	431 </output>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	432 </test>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	433 </tests>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	434 <help>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	435 What it does
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	436
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	437 Performs a differential abundance analysis for the comparison of two or more conditions (e.g., single-organism
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	438 and meta-RNA-seq high-throughput sequencing assays, or of selected and unselected values from in-vitro sequence
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	439 selections). This tool generates Monte Carlo samples of the Dirichlet distribution for each sample, converts
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	440 each instance using a log-ratio transform, then returns test results for two sample (Welch’s t, Wilcoxon) or
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	441 multi-sample (glm, Kruskal-Wallace) tests. The tool also estimates effect size for two sample analyses.
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	442
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	443 Options
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	444
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	445 * Reads table file - a tabular file with unique names for all rows and columns. Rows should contain genes and columns should contain sequencing read counts (i.e., sample vectors). Rows with 0 reads in each sample are deleted prior to analysis.
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	446 * Define the comparison groups describing the reads data structure - Specify a group label and the number of sequencing read count columns associated with it. The total number of columns must be equal to the number of numeric columns in the selected Reads table file.
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	447 * Number of Monte Carlo samples to use - the number of Monte Carlo samples to use when estimating the underlying distributions. Since we are estimating central tendencies, 128 is usually sufficient.
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	448 * Select features to retain as the denominator for the Geometric Mean calculation - indicates which features to retain as the denominator for the Geometric Mean calculation.
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	449 * Select the analysis to be performed
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	450
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	451 * Compute an ALDEx2 object (aldex) - performs log-ratio transformation and statistical testing. Specifically, this function: (a) generates Monte Carlo samples of the Dirichlet distribution for each sample, (b) converts each instance using a log-ratio transform, then (c) retcalculates the expected values for the correlation between each feature and a contin- uous variable, using data returned returned by aldex.clr and a vector of the continuous variable. Returns results of Pearson, Spearman and Kendall tests.urns test results for two sample (Welch’s t, Wilcoxon) or multi-sample (glm, Kruskal-Wallace) tests. This function also estimates effect size for two sample analyses.
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	452
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	453 * Select the tests to be performed - select the tests to be performed when crearing the ALDEx2 object.
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	454 * Calculate abundances and effect sizes - applies only if the selected test is Welch’s t and Wilcox tests, or if tests are performed iteratively.
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	455 * Include median clr values for each sample - specify whether to include median clr values for each sample (applies only if abundances and effect sizes are calculated).
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	456 * Perform tests iteratively - Specify whether to iteratively perform a test. For example, this will use the results from an initial Welch’s t and Wilcox test routine to seed the reference (i.e., denominator of Geometric Mean calculation) for a second Welch’s t and Wilcox test routine.
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	457
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	458 * Calculate correlation with a continuous variable (aldex.corr) - calculates the expected values for the correlation between each feature and a continuous variable using data returned by aldex.clr and a vector of the continuous variable. Returns results of Pearson, Spearman and Kendall tests.
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	459 * Calculate effect sizes and differences between conditions (aldex.effect) - calculates (1) the median clr abundances per sample, per condition, (2) the median differences in abundance between 2 conditions and (3) the median effect size and proportion of effect that overlaps 0.
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	460 * Calculate the expected values of distances between samples (aldex.expectedDistance) - calculates the expected value of distances between samples using the median value of distances derived from N Monte-Carlo replicates.
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	461 * Calculate the Kruskal-Wallis test and glm ANOVA statistics (aldex.kw) - calculates the expected values of the Kruskal-Wallis test and a glm ANOVA.
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	462 * Plot an ALDEx2 object (aldex.plot) - generate an MW-plot or an MA-plot of the given ALDEx2 object.
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	463 * Show dispersion of the expected values returned by aldex.effect (aldex.plotFeature) - generates density plots showing the dispersion of the expected values given in the output from aldex.effect. The expected values are shown in the plots. This is a diagnostic visualization to help determine if the expected values are trustworthy.
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	464 * Calculate Welch’s t-test and Wilcoxon test statistics (aldex.ttest) - calculate the expected values of the Wilcoxon Rank Sum test and Welch's t-test on the data returned by aldex.clr
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	465
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	466 * Calculate paired tests - specify whether to calculate effect size for paired samples (applies only if abundances and effect sizes are calculated and the selected test is Welch’s t and Wilcox tests).
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	467 * Plot a histogram of p-values for the first Dirichlet Monte Carlo instance - specify whether to plot a histogram of p-values for the first Dirichlet Monte Carlo instance.
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	468 </help>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	469 <expand macro="citations"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	470 </tool>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60 iuc parents: diff changeset	471

Mercurial > repos > iuc > aldex2

annotate aldex2.xml @ 1:75214276e2b7 draft default tip