metaquantome_viz: metaquantome

annotate metaquantome_viz.xml @ 1:8c30496a665a draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"

author	galaxyp
date	Wed, 23 Sep 2020 17:01:47 +0000
parents	6cfd42b015b4
children	02da24eac445

rev	line source
0 6cfd42b015b4 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@">
6cfd42b015b4 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>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	3 <macros>
6cfd42b015b4 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>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	5 <xml name="barcol">
6cfd42b015b4 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">
6cfd42b015b4 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>
6cfd42b015b4 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>
6cfd42b015b4 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>
6cfd42b015b4 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>
6cfd42b015b4 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>
6cfd42b015b4 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>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	13 <help>
6cfd42b015b4 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,
6cfd42b015b4 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
6cfd42b015b4 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.
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	17 </help>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	18 </param>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	19 </xml>
6cfd42b015b4 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">
6cfd42b015b4 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"
6cfd42b015b4 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">
6cfd42b015b4 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"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	24 </param>
6cfd42b015b4 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"
6cfd42b015b4 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"
6cfd42b015b4 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"
6cfd42b015b4 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"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	29 </xml>
6cfd42b015b4 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">
6cfd42b015b4 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">
6cfd42b015b4 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"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	33 </param>
1 8c30496a665a "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">
8c30496a665a "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"/>
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	36 </param>
0 6cfd42b015b4 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"
6cfd42b015b4 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."/>
6cfd42b015b4 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"
6cfd42b015b4 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)"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	41 </xml>
6cfd42b015b4 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">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	43 <conditional name="heatmap">
6cfd42b015b4 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"
6cfd42b015b4 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`"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	46 <when value="true">
6cfd42b015b4 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"
6cfd42b015b4 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"
6cfd42b015b4 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 8c30496a665a "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">
8c30496a665a "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"/>
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	52 </param>
0 6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	53 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	54 <when value="false">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	55 <!-- do nothing -->
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	56 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	57 </conditional>
1 8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	58 <param argument="--feature_cluster_size" type="integer" label="For tabular output. Number of clusters 'k' to cut the feature dendrogram tree. Default = 2"/>
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	59 <param argument="--sample_cluster_size" type="integer" label="For tabular output. Number of clusters 'k' to cut the sample dendrogram tree. Default = 2"/>
0 6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	60 </xml>
6cfd42b015b4 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">
6cfd42b015b4 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"
6cfd42b015b4 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?"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	64 </xml>
6cfd42b015b4 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">
6cfd42b015b4 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"
6cfd42b015b4 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">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	68 <help>
6cfd42b015b4 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
6cfd42b015b4 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.
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	71 </help>
6cfd42b015b4 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>
6cfd42b015b4 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>
6cfd42b015b4 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>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	75 </param>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	76 </xml>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	77 </macros>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	78 <expand macro="requirements" />
6cfd42b015b4 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[
1 8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	80 cp '$infile' '$infile.name'
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	81 &&
0 6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	82 metaquantome viz
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	83 --samps '$samps'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	84 --mode '$mode_args.mode'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	85 #if str($mode_args.mode) == 'f'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	86 --ontology='$mode_args.ontology'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	87 #end if
1 8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	88 --infile='$infile.name'
0 6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	89 --plottype='$mode_args.plot.plottype'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	90 #if $mode_args.plot.plottype == 'bar':
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	91 #if str($mode_args.mode) == 't':
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	92 --target_rank='$mode_args.plot.target_rank'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	93 #end if
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	94 --meancol='$mode_args.plot.meancol'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	95 #if str($mode_args.plot.nterms) == '':
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	96 --nterms='all'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	97 #else
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	98 --nterms=$mode_args.plot.nterms
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	99 #end if
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	100 #if str($mode_args.mode) == 'f':
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	101 --target_onto='$mode_args.plot.target_onto'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	102 #end if
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	103 --barcol=$mode_args.plot.barcol
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	104 #elif $mode_args.plot.plottype == 'volcano':
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	105 --fc_name='$mode_args.plot.fc_name'
1 8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	106 --fc_corr_p='$mode_args.plot.fc_corr_p'
0 6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	107 #if $mode_args.plot.textannot:
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	108 --textannot='$mode_args.plot.textannot'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	109 #end if
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	110 $mode_args.plot.flip_fc
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	111 #if $mode_args.mode == 'f':
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	112 $mode_args.plot.gosplit
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	113 #end if
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	114 #elif $mode_args.plot.plottype == 'heatmap':
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	115 #if $mode_args.plot.heatmap.filter_to_sig:
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	116 --filter_to_sig
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	117 --alpha=$mode_args.plot.heatmap.alpha
1 8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	118 --fc_corr_p='mode_args.plot.fc_corr_p'
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	119 #end if
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	120 #if feature_cluster_size:
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	121 --feature_cluster_size='$mode_args.plot.feature_cluster_size'
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	122 #end if
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	123 #if sample_cluster_size:
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	124 --sample_cluster_size='$mode_args.plot.sample_cluster_size'
0 6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	125 #end if
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	126 #elif $mode_args.plot.plottype == 'pca':
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	127 $mode_args.plot.calculate_sep
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	128 #elif $mode_args.plot.plottype == 'ft_dist':
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	129 --barcol='$mode_args.plot.barcol'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	130 --whichway='$mode_args.plot.margin.whichway'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	131 --meancol='$mode_args.plot.meancol'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	132 #if $mode_args.plot.margin.term.id_or_name == 'id':
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	133 --id='$mode_args.plot.margin.term.id'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	134 #else:
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	135 --name='$mode_args.plot.margin.term.name'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	136 #end if
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	137 #if $mode_args.plot.margin.whichway == 't_dist':
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	138 --target_rank='$mode_args.plot.margin.target_rank'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	139 #end if
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	140 #if $mode_args.plot.margin.whichway == 'f_dist':
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	141 --target_onto=$mode_args.plot.margin.target_onto
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	142 #end if
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	143 #end if
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	144 #if $width:
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	145 --width=$width
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	146 #end if
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	147 #if $height:
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	148 --height=$height
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	149 #end if
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	150 --img='outfile.png'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	151 --tabfile='plotdata.tab' &&
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	152 mkdir '${ wrapped_outfile.files_path }' &&
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	153 cp outfile.png '${ wrapped_outfile.files_path }' &&
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	154 echo "<!DOCTYPE html>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	155 <html>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	156 <body>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	157 <img src=\"outfile.png\" width=600>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	158 <br>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	159 <p>To download the image, right-click and choose \"Save image as...\"</p>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	160 <br>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	161 <p>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	162 If text is cut off or the plot is not displaying properly,
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	163 the easiest fix is to increase the plot dimensions
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	164 </p>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	165 </body>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	166 </html>" > wrapped_outfile.html
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	167 ]]></command>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	168 <inputs>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	169 <param argument="--infile" type="data"
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	170 format="tabular" label="Tabular file from metaQuantome stats or metaQuantome filter" help=""/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	171 <expand macro="SAMPS"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	172 <conditional name="mode_args">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	173 <param argument="--mode" type="select" label="Mode">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	174 <option value="f">Functional analysis</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	175 <option value="t">Taxonomic analysis</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	176 <option value="ft">Functional-taxonomic interaction analysis</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	177 </param>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	178 <when value="f">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	179 <param name="ontology" type="select" label="Ontology">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	180 <option value="go">Gene Ontology (GO terms)</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	181 <option value="ec">Enzyme Commission (EC) numbers</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	182 <option value="cog">Clusters of Orthologous Groups (COG categories)</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	183 </param>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	184 <conditional name="plot">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	185 <param argument="--plottype" type="select" label="Plot type">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	186 <option value="bar">Bar Chart (bar)</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	187 <option value="volcano">Volcano Plot (volcano)</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	188 <option value="heatmap">Heatmap (heatmap)</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	189 <option value="pca">Principal Components Analysis (pca)</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	190 </param>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	191 <when value="bar">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	192 <expand macro="common_bar_params"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	193 <expand macro="target_onto"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	194 <expand macro="barcol"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	195 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	196 <when value="volcano">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	197 <expand macro="common_volc_params"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	198 <param argument="--gosplit" type="boolean" truevalue="--gosplit" falsevalue="" checked="false"
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	199 label="Make one plot for each of BiologicalProcess, CellularComponent, and MolecularFunction GO term categories."/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	200 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	201 <when value="heatmap">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	202 <expand macro="common_heatmap_params"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	203 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	204 <when value="pca">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	205 <expand macro="pca_calcsep"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	206 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	207 </conditional>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	208 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	209 <when value="t">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	210 <conditional name="plot">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	211 <param argument="--plottype" type="select" label="Plot type">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	212 <option value="bar">Bar Chart (bar)</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	213 <option value="volcano">Volcano Plot (volcano)</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	214 <option value="heatmap">Heatmap (heatmap)</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	215 <option value="pca">Principal Components Analysis (pca)</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	216 </param>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	217 <when value="bar">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	218 <param argument="--target_rank" type="select"
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	219 label="Taxonomic rank to restrict to in the plot"
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	220 help="possibilities are taken from the input dataset.">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	221 <options from_dataset="infile">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	222 <column name="value" index="2"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	223 <filter type="unique_value" name="unique_taxon" column="2"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	224 <!-- <filter type="remove_value" value="rank" column="2"/> -->
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	225 </options>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	226 </param>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	227 <expand macro="common_bar_params"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	228 <expand macro="barcol"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	229 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	230 <when value="volcano">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	231 <expand macro="common_volc_params"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	232 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	233 <when value="heatmap">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	234 <expand macro="common_heatmap_params"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	235 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	236 <when value="pca">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	237 <expand macro="pca_calcsep"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	238 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	239 </conditional>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	240 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	241 <when value="ft">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	242 <conditional name="plot">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	243 <param argument="--plottype" type="select" label="Plot type">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	244 <option value="ft_dist" selected="true">Functional Taxonomic Distribution (ft_dist)</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	245 </param>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	246 <when value="ft_dist">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	247 <param argument="--meancol" type="text" label="Mean intensity column name"
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	248 help="Mean intensity column name for desired experimental condition">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	249 <validator type="empty_field"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	250 </param>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	251 <conditional name="margin">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	252 <param argument="--whichway" type="select" label="which distribution">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	253 <option value="f_dist">functional distribution for a taxon (f_dist)</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	254 <option value="t_dist">taxonomic distribution for a function (t_dist)</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	255 </param>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	256 <when value="f_dist">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	257 <conditional name="term">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	258 <param name="id_or_name" type="select" label="">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	259 <option value="id" selected="true">Taxon ID</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	260 <option value="name">Taxon name</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	261 </param>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	262 <when value="id">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	263 <param argument="--id" type="select" label="Taxon id">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	264 <options from_dataset="infile">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	265 <column name="value" index="3"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	266 <filter type="unique_value" column="3"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	267 <!-- <filter type="remove_value" value="tax_id"/> -->
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	268 </options>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	269 </param>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	270 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	271 <when value="name">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	272 <param argument="--name" type="select" label="Taxon name">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	273 <options from_dataset="infile">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	274 <column name="value" index="4"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	275 <filter type="unique_value" column="4"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	276 <!-- <filter type="remove_value" value="taxon_name"/> -->
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	277 </options>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	278 </param>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	279 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	280 </conditional>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	281 <expand macro="target_onto"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	282 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	283 <when value="t_dist">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	284 <conditional name="term">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	285 <param name="id_or_name" type="select" label="">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	286 <option value="id" selected="true">Functional term ID</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	287 <option value="name">Functional term name</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	288 </param>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	289 <when value="id">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	290 <param argument="--id" type="select" label="Functional term id">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	291 <options from_dataset="infile">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	292 <column name="value" index="0"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	293 <filter type="unique_value" column="0"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	294 <!-- <filter type="remove_value" value="go_id"/> -->
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	295 </options>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	296 </param>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	297 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	298 <when value="name">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	299 <param argument="--name" type="select" label="Functional term name">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	300 <options from_dataset="infile">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	301 <column name="value" index="1"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	302 <filter type="unique_value" column="1"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	303 <!-- <filter type="remove_value" value="name"/> -->
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	304 </options>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	305 </param>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	306 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	307 </conditional>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	308 <param argument="--target_rank" type="select"
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	309 label="Taxonomic rank to restrict to in the plot"
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	310 help="possibilities are taken from the input dataset.">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	311 <options from_dataset="infile">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	312 <column name="value" index="5"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	313 <filter type="unique_value" name="unique_taxon" column="5"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	314 <!-- <filter type="remove_value" value="rank" column="5"/> -->
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	315 </options>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	316 </param>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	317 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	318 </conditional>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	319 <expand macro="barcol"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	320 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	321 </conditional>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	322 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	323 </conditional>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	324 <param argument="--width" type="float" value="" optional="true" label="Image width in inches"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	325 <param argument="--height" type="float" value="" optional="true" label="Image height in inches"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	326 </inputs>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	327 <outputs>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	328 <data format="html" name="wrapped_outfile"
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	329 label="${tool.name} on ${on_string} ${mode_args.plot.plottype}.html"
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	330 from_work_dir="wrapped_outfile.html"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	331 <data format="tabular" name="plotdata"
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	332 label="${tool.name} ${on_string} ${mode_args.plot.plottype}: plot data"
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	333 from_work_dir="plotdata.tab">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	334 <filter>mode_args['plot']['plottype'] in ["bar", "volcano"]</filter>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	335 </data>
1 8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	336
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	337 <data format="tabular" name="heatmap_feature_cluster"
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	338 label="${mode_args.plot.plottype}: feature cluster data"
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	339 from_work_dir="feature_cluster_${infile.name.rsplit('.',1)[0]}.txt">
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	340 <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	341 </data>
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	342 <data format="tabular" name="heatmap_sample_cluster"
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	343 label="${mode_args.plot.plottype}: sample cluster data"
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	344 from_work_dir="sample_cluster_${infile.name.rsplit('.',1)[0]}.txt">
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	345 <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	346 </data>
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	347
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	348 <data format="tabular" name="heatmap_sample_cluster"
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	349 label="${mode_args.plot.plottype}: sample cluster data"
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	350 from_work_dir="PC_Data_${infile.name.rsplit('.',1)[0]}.txt">
8c30496a665a "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 ["pca"]</filter>
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	352 </data>
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	353
0 6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	354 </outputs>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	355 <tests>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	356 <test>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	357 <param name="infile" value="tax_filt_out.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	358 <param name="mode" value="t" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	359 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	360 <param name="plottype" value="bar" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	361 <param name="target_rank" value="genus" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	362 <param name="meancol" value="NS_mean" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	363 <output name="wrapped_outfile">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	364 <assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	365 <has_text text="To download the image" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	366 </assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	367 </output>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	368 </test>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	369 <test>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	370 <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	371 <param name="mode" value="t" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	372 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	373 <param name="plottype" value="volcano" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	374 <param name="target_rank" value="genus" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	375 <param name="fc_name" value="log2fc_NS_over_WS" />
1 8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	376 <param name="fc_corr_p" value="corrected_p_NS_over_WS"/>
0 6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	377 <param name="textannot" value="taxon_name" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	378 <output name="wrapped_outfile">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	379 <assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	380 <has_text text="To download the image" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	381 </assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	382 </output>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	383 </test>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	384 <test>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	385 <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	386 <param name="mode" value="t" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	387 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	388 <param name="plottype" value="heatmap" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	389 <output name="wrapped_outfile">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	390 <assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	391 <has_text text="To download the image" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	392 </assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	393 </output>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	394 </test>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	395 <test>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	396 <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	397 <param name="mode" value="t" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	398 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	399 <param name="plottype" value="pca" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	400 <output name="wrapped_outfile">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	401 <assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	402 <has_text text="To download the image" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	403 </assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	404 </output>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	405 </test>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	406 <test>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	407 <param name="infile" value="func_full_test_out.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	408 <param name="mode" value="f" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	409 <param name="ontology" value="go" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	410 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	411 <param name="plottype" value="bar" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	412 <param name="meancol" value="NS_mean" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	413 <param name="target_onto" value="bp"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	414 <output name="wrapped_outfile">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	415 <assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	416 <has_text text="To download the image" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	417 </assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	418 </output>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	419 </test>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	420 <test>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	421 <param name="infile" value="func_full_test_out.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	422 <param name="mode" value="f" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	423 <param name="ontology" value="go"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	424 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	425 <param name="plottype" value="volcano" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	426 <param name="fc_name" value="log2fc_NS_over_WS" />
1 8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3" galaxyp parents: 0 diff changeset	427 <param name="fc_corr_p" value="corrected_p_NS_over_WS"/>
0 6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	428 <output name="wrapped_outfile">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	429 <assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	430 <has_text text="To download the image" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	431 </assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	432 </output>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	433 </test>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	434 <test>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	435 <param name="infile" value="tf_filt_out.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	436 <param name="mode" value="ft" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	437 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	438 <param name="plottype" value="ft_dist" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	439 <param name="meancol" value="NS_mean" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	440 <param name="whichway" value="f_dist" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	441 <param name="id_or_name" value="id" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	442 <param name="id" value="1301" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	443 <param name="target_onto" value="bp" />
6cfd42b015b4 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">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	445 <assert_contents>
6cfd42b015b4 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" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	447 </assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	448 </output>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	449 </test>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	450 </tests>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	451 <help><![CDATA[
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	452 metaQuantome viz
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	453 ===================
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	454
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	455 The viz module is the final step in the metaQuantome analysis workflow.
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	456 The available visualizations are:
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	457
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	458 - bar plot
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	459 - volcano plot
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	460 - heatmap
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	461 - PCA plot
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	462
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	463 Please consult the manuscript for full details on each of these plots.
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	464
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	465 Questions, Comments, Problems, Kudos
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	466 --------------------------------------
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	467
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	468 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	469 ]]></help>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	470 <expand macro="citations" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a galaxyp parents: diff changeset	471 </tool>

Mercurial > repos > galaxyp > metaquantome_viz

annotate metaquantome_viz.xml @ 1:8c30496a665a draft