metaquantome_viz: metaquantome

annotate metaquantome_viz.xml @ 3:5bbedd902998 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2"

author	galaxyp
date	Sat, 30 Jan 2021 17:53:48 +0000
parents	51bc1ccad6aa
children	f1f24035f571

rev	line source
0 f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	1 <tool id="metaquantome_viz" name="metaQuantome: visualize" version="@GVERSION@">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	2 <description>taxonomic analysis, functional analysis, and function-taxonomy analysis results</description>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	3 <macros>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	4 <import>macros.xml</import>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	5 <xml name="barcol">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	6 <param argument="--barcol" type="select" label="Color for the bar fill">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	7 <option value="1">Blue</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	8 <option value="2">Orange</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	9 <option value="3">Yellow</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	10 <option value="4">Red</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	11 <option value="5">Violet</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	12 <option value="6">Black</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	13 <help>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	14 These same colors are also used in the heatmap and PCA plot,
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	15 so the colors can be tweaked to match. Note that these colors
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	16 are coded as 1 through 6 in the command line tool.
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	17 </help>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	18 </param>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	19 </xml>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	20 <xml name="common_bar_params">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	21 <param argument="--meancol" type="text" label="Mean intensity column name"
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	22 help="Mean intensity column name for desired experimental condition">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	23 <validator type="empty_field"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	24 </param>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	25 <param argument="--nterms" type="integer"
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	26 value="5" min="1" optional="true"
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	27 label="Number of terms to display"
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	28 help="leave blank for all terms"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	29 </xml>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	30 <xml name="common_volc_params">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	31 <param argument="--fc_name" type="text" label="Name of the fold change column in the stat dataframe">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	32 <validator type="empty_field"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	33 </param>
1 1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	34 <param argument="--fc_corr_p" type="text" label="Name of the Corrected p-value column in the stat dataframe">
1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	35 <validator type="empty_field"/>
1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	36 </param>
0 f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	37 <param argument="--textannot" type="text" optional="true" label="Name of the annotation column"
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	38 help="Provides text annotatation for the plot. Optional. If missing, no text will be plotted."/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	39 <param argument="--flip_fc" type="boolean" truevalue="--flip_fc" falsevalue="" checked="false"
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	40 label="Flip the fold change (i.e., multiply log fold change by -1)"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	41 </xml>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	42 <xml name="common_heatmap_params">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	43 <conditional name="heatmap">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	44 <param argument="--filter_to_sig" type="boolean" checked="false"
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	45 label="Only plot significant term" help="Necessitates use of results from `test`"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	46 <when value="true">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	47 <param argument="--alpha" type="float"
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	48 value="0.05" min="0.0" max="1.0"
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	49 label="The q-value significance level"/>
1 1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	50 <param argument="--fc_corr_p" type="text" label="Name of the Corrected p-value column in the stat dataframe">
1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	51 <validator type="empty_field"/>
1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	52 </param>
0 f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	53 </when>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	54 <when value="false">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	55 <!-- do nothing -->
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	56 </when>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	57 </conditional>
2 51bc1ccad6aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4" galaxyp parents: 1 diff changeset	58 <param argument="--feature_cluster_size" value="2" type="integer" label="For tabular output. Number of clusters 'k' to cut the feature dendrogram tree."/>
51bc1ccad6aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4" galaxyp parents: 1 diff changeset	59 <param argument="--sample_cluster_size" value="2" type="integer" label="For tabular output. Number of clusters 'k' to cut the sample dendrogram tree."/>
0 f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	60 </xml>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	61 <xml name="pca_calcsep">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	62 <param argument="--calculate_sep" type="boolean" truevalue="--calculate_sep" falsevalue="" checked="false"
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	63 label="Calculate separation between groups and include in title?"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	64 </xml>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	65 <xml name="target_onto">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	66 <param argument="--target_onto" type="select" optional="false"
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	67 label="GO category to restrict to">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	68 <help>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	69 Only the values from this category
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	70 of GO terms will be displayed.
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	71 </help>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	72 <option value="bp">Biological Process</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	73 <option value="mf">Molecular Function</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	74 <option value="cc">Cellular Component</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	75 </param>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	76 </xml>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	77 </macros>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	78 <expand macro="requirements" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	79 <command detect_errors="exit_code"><![CDATA[
2 51bc1ccad6aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4" galaxyp parents: 1 diff changeset	80 #import re
51bc1ccad6aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4" galaxyp parents: 1 diff changeset	81 #set $safename = re.sub('[^\w\-_\.]', '_', $infile.element_identifier)
51bc1ccad6aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4" galaxyp parents: 1 diff changeset	82 ln -s '$infile' '$safename'
1 1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	83 &&
0 f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	84 metaquantome viz
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	85 --samps '$samps'
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	86 --mode '$mode_args.mode'
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	87 #if str($mode_args.mode) == 'f'
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	88 --ontology='$mode_args.ontology'
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	89 #end if
2 51bc1ccad6aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4" galaxyp parents: 1 diff changeset	90 --infile='$safename'
0 f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	91 --plottype='$mode_args.plot.plottype'
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	92 #if $mode_args.plot.plottype == 'bar':
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	93 #if str($mode_args.mode) == 't':
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	94 --target_rank='$mode_args.plot.target_rank'
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	95 #end if
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	96 --meancol='$mode_args.plot.meancol'
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	97 #if str($mode_args.plot.nterms) == '':
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	98 --nterms='all'
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	99 #else
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	100 --nterms=$mode_args.plot.nterms
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	101 #end if
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	102 #if str($mode_args.mode) == 'f':
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	103 --target_onto='$mode_args.plot.target_onto'
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	104 #end if
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	105 --barcol=$mode_args.plot.barcol
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	106 #elif $mode_args.plot.plottype == 'volcano':
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	107 --fc_name='$mode_args.plot.fc_name'
1 1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	108 --fc_corr_p='$mode_args.plot.fc_corr_p'
0 f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	109 #if $mode_args.plot.textannot:
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	110 --textannot='$mode_args.plot.textannot'
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	111 #end if
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	112 $mode_args.plot.flip_fc
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	113 #if $mode_args.mode == 'f':
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	114 $mode_args.plot.gosplit
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	115 #end if
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	116 #elif $mode_args.plot.plottype == 'heatmap':
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	117 #if $mode_args.plot.heatmap.filter_to_sig:
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	118 --filter_to_sig
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	119 --alpha=$mode_args.plot.heatmap.alpha
3 5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	120 --fc_corr_p='$mode_args.plot.heatmap.fc_corr_p'
1 1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	121 #end if
2 51bc1ccad6aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4" galaxyp parents: 1 diff changeset	122 #if $mode_args.plot.feature_cluster_size:
1 1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	123 --feature_cluster_size='$mode_args.plot.feature_cluster_size'
1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	124 #end if
2 51bc1ccad6aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4" galaxyp parents: 1 diff changeset	125 #if $mode_args.plot.sample_cluster_size:
1 1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	126 --sample_cluster_size='$mode_args.plot.sample_cluster_size'
0 f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	127 #end if
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	128 #elif $mode_args.plot.plottype == 'pca':
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	129 $mode_args.plot.calculate_sep
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	130 #elif $mode_args.plot.plottype == 'ft_dist':
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	131 --barcol='$mode_args.plot.barcol'
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	132 --whichway='$mode_args.plot.margin.whichway'
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	133 --meancol='$mode_args.plot.meancol'
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	134 #if $mode_args.plot.margin.term.id_or_name == 'id':
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	135 --id='$mode_args.plot.margin.term.id'
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	136 #else:
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	137 --name='$mode_args.plot.margin.term.name'
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	138 #end if
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	139 #if $mode_args.plot.margin.whichway == 't_dist':
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	140 --target_rank='$mode_args.plot.margin.target_rank'
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	141 #end if
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	142 #if $mode_args.plot.margin.whichway == 'f_dist':
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	143 --target_onto=$mode_args.plot.margin.target_onto
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	144 #end if
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	145 #end if
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	146 #if $width:
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	147 --width=$width
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	148 #end if
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	149 #if $height:
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	150 --height=$height
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	151 #end if
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	152 --img='outfile.png'
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	153 --tabfile='plotdata.tab' &&
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	154 mkdir '${ wrapped_outfile.files_path }' &&
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	155 cp outfile.png '${ wrapped_outfile.files_path }' &&
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	156 echo "<!DOCTYPE html>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	157 <html>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	158 <body>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	159 <img src=\"outfile.png\" width=600>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	160 <br>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	161 <p>To download the image, right-click and choose \"Save image as...\"</p>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	162 <br>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	163 <p>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	164 If text is cut off or the plot is not displaying properly,
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	165 the easiest fix is to increase the plot dimensions
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	166 </p>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	167 </body>
3 5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	168 </html>" > wrapped_outfile.html &&
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	169 if test -f 'feature_cluster_${infile.name}.txt'; then mv 'feature_cluster_${infile.name}.txt' feature_cluster_data.txt; fi &&
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	170 if test -f 'sample_cluster_${infile.name}.txt'; then mv 'sample_cluster_${infile.name}.txt' sample_cluster_data.txt; fi &&
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	171 if test -f 'PC_Data_${infile.name}.txt'; then mv 'PC_Data_${infile.name}.txt' PC_Data.txt; fi
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	172
0 f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	173 ]]></command>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	174 <inputs>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	175 <param argument="--infile" type="data"
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	176 format="tabular" label="Tabular file from metaQuantome stats or metaQuantome filter" help=""/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	177 <expand macro="SAMPS"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	178 <conditional name="mode_args">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	179 <param argument="--mode" type="select" label="Mode">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	180 <option value="f">Functional analysis</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	181 <option value="t">Taxonomic analysis</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	182 <option value="ft">Functional-taxonomic interaction analysis</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	183 </param>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	184 <when value="f">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	185 <param name="ontology" type="select" label="Ontology">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	186 <option value="go">Gene Ontology (GO terms)</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	187 <option value="ec">Enzyme Commission (EC) numbers</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	188 <option value="cog">Clusters of Orthologous Groups (COG categories)</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	189 </param>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	190 <conditional name="plot">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	191 <param argument="--plottype" type="select" label="Plot type">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	192 <option value="bar">Bar Chart (bar)</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	193 <option value="volcano">Volcano Plot (volcano)</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	194 <option value="heatmap">Heatmap (heatmap)</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	195 <option value="pca">Principal Components Analysis (pca)</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	196 </param>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	197 <when value="bar">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	198 <expand macro="common_bar_params"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	199 <expand macro="target_onto"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	200 <expand macro="barcol"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	201 </when>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	202 <when value="volcano">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	203 <expand macro="common_volc_params"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	204 <param argument="--gosplit" type="boolean" truevalue="--gosplit" falsevalue="" checked="false"
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	205 label="Make one plot for each of BiologicalProcess, CellularComponent, and MolecularFunction GO term categories."/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	206 </when>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	207 <when value="heatmap">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	208 <expand macro="common_heatmap_params"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	209 </when>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	210 <when value="pca">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	211 <expand macro="pca_calcsep"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	212 </when>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	213 </conditional>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	214 </when>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	215 <when value="t">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	216 <conditional name="plot">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	217 <param argument="--plottype" type="select" label="Plot type">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	218 <option value="bar">Bar Chart (bar)</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	219 <option value="volcano">Volcano Plot (volcano)</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	220 <option value="heatmap">Heatmap (heatmap)</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	221 <option value="pca">Principal Components Analysis (pca)</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	222 </param>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	223 <when value="bar">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	224 <param argument="--target_rank" type="select"
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	225 label="Taxonomic rank to restrict to in the plot"
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	226 help="possibilities are taken from the input dataset.">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	227 <options from_dataset="infile">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	228 <column name="value" index="2"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	229 <filter type="unique_value" name="unique_taxon" column="2"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	230 <!-- <filter type="remove_value" value="rank" column="2"/> -->
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	231 </options>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	232 </param>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	233 <expand macro="common_bar_params"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	234 <expand macro="barcol"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	235 </when>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	236 <when value="volcano">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	237 <expand macro="common_volc_params"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	238 </when>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	239 <when value="heatmap">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	240 <expand macro="common_heatmap_params"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	241 </when>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	242 <when value="pca">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	243 <expand macro="pca_calcsep"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	244 </when>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	245 </conditional>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	246 </when>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	247 <when value="ft">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	248 <conditional name="plot">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	249 <param argument="--plottype" type="select" label="Plot type">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	250 <option value="ft_dist" selected="true">Functional Taxonomic Distribution (ft_dist)</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	251 </param>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	252 <when value="ft_dist">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	253 <param argument="--meancol" type="text" label="Mean intensity column name"
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	254 help="Mean intensity column name for desired experimental condition">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	255 <validator type="empty_field"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	256 </param>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	257 <conditional name="margin">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	258 <param argument="--whichway" type="select" label="which distribution">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	259 <option value="f_dist">functional distribution for a taxon (f_dist)</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	260 <option value="t_dist">taxonomic distribution for a function (t_dist)</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	261 </param>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	262 <when value="f_dist">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	263 <conditional name="term">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	264 <param name="id_or_name" type="select" label="">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	265 <option value="id" selected="true">Taxon ID</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	266 <option value="name">Taxon name</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	267 </param>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	268 <when value="id">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	269 <param argument="--id" type="select" label="Taxon id">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	270 <options from_dataset="infile">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	271 <column name="value" index="3"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	272 <filter type="unique_value" column="3"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	273 <!-- <filter type="remove_value" value="tax_id"/> -->
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	274 </options>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	275 </param>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	276 </when>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	277 <when value="name">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	278 <param argument="--name" type="select" label="Taxon name">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	279 <options from_dataset="infile">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	280 <column name="value" index="4"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	281 <filter type="unique_value" column="4"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	282 <!-- <filter type="remove_value" value="taxon_name"/> -->
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	283 </options>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	284 </param>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	285 </when>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	286 </conditional>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	287 <expand macro="target_onto"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	288 </when>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	289 <when value="t_dist">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	290 <conditional name="term">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	291 <param name="id_or_name" type="select" label="">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	292 <option value="id" selected="true">Functional term ID</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	293 <option value="name">Functional term name</option>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	294 </param>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	295 <when value="id">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	296 <param argument="--id" type="select" label="Functional term id">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	297 <options from_dataset="infile">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	298 <column name="value" index="0"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	299 <filter type="unique_value" column="0"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	300 <!-- <filter type="remove_value" value="go_id"/> -->
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	301 </options>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	302 </param>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	303 </when>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	304 <when value="name">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	305 <param argument="--name" type="select" label="Functional term name">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	306 <options from_dataset="infile">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	307 <column name="value" index="1"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	308 <filter type="unique_value" column="1"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	309 <!-- <filter type="remove_value" value="name"/> -->
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	310 </options>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	311 </param>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	312 </when>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	313 </conditional>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	314 <param argument="--target_rank" type="select"
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	315 label="Taxonomic rank to restrict to in the plot"
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	316 help="possibilities are taken from the input dataset.">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	317 <options from_dataset="infile">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	318 <column name="value" index="5"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	319 <filter type="unique_value" name="unique_taxon" column="5"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	320 <!-- <filter type="remove_value" value="rank" column="5"/> -->
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	321 </options>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	322 </param>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	323 </when>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	324 </conditional>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	325 <expand macro="barcol"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	326 </when>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	327 </conditional>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	328 </when>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	329 </conditional>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	330 <param argument="--width" type="float" value="" optional="true" label="Image width in inches"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	331 <param argument="--height" type="float" value="" optional="true" label="Image height in inches"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	332 </inputs>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	333 <outputs>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	334 <data format="html" name="wrapped_outfile"
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	335 label="${tool.name} on ${on_string} ${mode_args.plot.plottype}.html"
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	336 from_work_dir="wrapped_outfile.html"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	337 <data format="tabular" name="plotdata"
2 51bc1ccad6aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4" galaxyp parents: 1 diff changeset	338 label="${tool.name} on ${on_string} ${mode_args.plot.plottype}: plot data"
0 f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	339 from_work_dir="plotdata.tab">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	340 <filter>mode_args['plot']['plottype'] in ["bar", "volcano"]</filter>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	341 </data>
1 1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	342
1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	343 <data format="tabular" name="heatmap_feature_cluster"
3 5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	344 label="${mode_args.plot.plottype}: feature cluster data"
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	345 from_work_dir="feature_cluster_data.txt">
1 1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	346 <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	347 </data>
1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	348 <data format="tabular" name="heatmap_sample_cluster"
3 5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	349 label="${mode_args.plot.plottype}: sample cluster data"
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	350 from_work_dir="sample_cluster_data.txt">
1 1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	351 <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	352 </data>
1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	353
2 51bc1ccad6aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4" galaxyp parents: 1 diff changeset	354 <data format="tabular" name="pca_sample_cluster"
3 5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	355 label="${mode_args.plot.plottype}: sample cluster data"
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	356 from_work_dir="PC_Data.txt">
1 1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	357 <filter>mode_args['plot']['plottype'] in ["pca"]</filter>
1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	358 </data>
1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	359
0 f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	360 </outputs>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	361 <tests>
2 51bc1ccad6aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4" galaxyp parents: 1 diff changeset	362 <test expect_num_outputs="2">
0 f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	363 <param name="infile" value="tax_filt_out.tab" ftype="tabular"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	364 <param name="mode" value="t" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	365 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	366 <param name="plottype" value="bar" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	367 <param name="target_rank" value="genus" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	368 <param name="meancol" value="NS_mean" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	369 <output name="wrapped_outfile">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	370 <assert_contents>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	371 <has_text text="To download the image" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	372 </assert_contents>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	373 </output>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	374 </test>
2 51bc1ccad6aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4" galaxyp parents: 1 diff changeset	375 <test expect_num_outputs="2">
0 f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	376 <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	377 <param name="mode" value="t" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	378 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	379 <param name="plottype" value="volcano" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	380 <param name="target_rank" value="genus" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	381 <param name="fc_name" value="log2fc_NS_over_WS" />
1 1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	382 <param name="fc_corr_p" value="corrected_p_NS_over_WS"/>
0 f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	383 <param name="textannot" value="taxon_name" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	384 <output name="wrapped_outfile">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	385 <assert_contents>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	386 <has_text text="To download the image" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	387 </assert_contents>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	388 </output>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	389 </test>
2 51bc1ccad6aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4" galaxyp parents: 1 diff changeset	390 <test expect_num_outputs="3">
3 5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	391 <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	392 <param name="mode" value="t" />
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	393 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	394 <param name="plottype" value="heatmap" />
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	395 <param name="filter_to_sig" />
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	396 <param name="alpha" value="0.05" />
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	397 <param name="fc_corr_p" value="corrected_p_NS_over_WS" />
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	398 <param name="feature_cluster_size" value="2" />
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	399 <param name="sample_cluster_size" value="2" />
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	400 <output name="wrapped_outfile">
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	401 <assert_contents>
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	402 <has_text text="To download the image" />
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	403 </assert_contents>
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	404 </output>
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	405 <output name="heatmap_feature_cluster">
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	406 <assert_contents>
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	407 <has_text text="481" />
5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	408 </assert_contents>
0 f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	409 </output>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	410 </test>
2 51bc1ccad6aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4" galaxyp parents: 1 diff changeset	411 <test expect_num_outputs="2">
0 f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	412 <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	413 <param name="mode" value="t" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	414 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	415 <param name="plottype" value="pca" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	416 <output name="wrapped_outfile">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	417 <assert_contents>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	418 <has_text text="To download the image" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	419 </assert_contents>
3 5bbedd902998 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2" galaxyp parents: 2 diff changeset	420 </output>
0 f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	421 </test>
2 51bc1ccad6aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4" galaxyp parents: 1 diff changeset	422 <test expect_num_outputs="2">
0 f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	423 <param name="infile" value="func_full_test_out.tab" ftype="tabular"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	424 <param name="mode" value="f" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	425 <param name="ontology" value="go" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	426 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	427 <param name="plottype" value="bar" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	428 <param name="meancol" value="NS_mean" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	429 <param name="target_onto" value="bp"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	430 <output name="wrapped_outfile">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	431 <assert_contents>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	432 <has_text text="To download the image" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	433 </assert_contents>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	434 </output>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	435 </test>
2 51bc1ccad6aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4" galaxyp parents: 1 diff changeset	436 <test expect_num_outputs="2">
0 f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	437 <param name="infile" value="func_full_test_out.tab" ftype="tabular"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	438 <param name="mode" value="f" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	439 <param name="ontology" value="go"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	440 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	441 <param name="plottype" value="volcano" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	442 <param name="fc_name" value="log2fc_NS_over_WS" />
1 1a402023bdec "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	443 <param name="fc_corr_p" value="corrected_p_NS_over_WS"/>
0 f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	444 <output name="wrapped_outfile">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	445 <assert_contents>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	446 <has_text text="To download the image" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	447 </assert_contents>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	448 </output>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	449 </test>
2 51bc1ccad6aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4" galaxyp parents: 1 diff changeset	450 <test expect_num_outputs="1">
0 f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	451 <param name="infile" value="tf_filt_out.tab" ftype="tabular"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	452 <param name="mode" value="ft" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	453 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	454 <param name="plottype" value="ft_dist" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	455 <param name="meancol" value="NS_mean" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	456 <param name="whichway" value="f_dist" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	457 <param name="id_or_name" value="id" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	458 <param name="id" value="1301" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	459 <param name="target_onto" value="bp" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	460 <output name="wrapped_outfile">
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	461 <assert_contents>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	462 <has_text text="To download the image" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	463 </assert_contents>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	464 </output>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	465 </test>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	466 </tests>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	467 <help><![CDATA[
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	468 metaQuantome viz
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	469 ===================
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	470
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	471 The viz module is the final step in the metaQuantome analysis workflow.
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	472 The available visualizations are:
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	473
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	474 - bar plot
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	475 - volcano plot
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	476 - heatmap
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	477 - PCA plot
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	478
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	479 Please consult the manuscript for full details on each of these plots.
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	480
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	481 Questions, Comments, Problems, Kudos
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	482 --------------------------------------
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	483
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	484 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	485 ]]></help>
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	486 <expand macro="citations" />
f36abbd809dc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	487 </tool>

Mercurial > repos > galaxyp > metaquantome_viz

annotate metaquantome_viz.xml @ 3:5bbedd902998 draft