b2btools_single_sequence: b2btools_single

author	iuc
date	Tue, 09 Aug 2022 12:30:52 +0000
parents
children

rev	line source
0 b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	1 <tool
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	2 id="b2btools_single_sequence"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	3 name="b2bTools: Biophysical predictors for single sequences"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	4 version="3.0.5+galaxy0"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	5 license="GPL-3.0"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	6 python_template_version="3.5"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	7 profile="21.05">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	8 <description>from their amino-acid sequences</description>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	9 <xrefs>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	10 <xref type="bio.tools">b2btools</xref>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	11 </xrefs>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	12 <requirements>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	13 <requirement type="package" version="3.0.5">b2btools</requirement>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	14 </requirements>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	15 <command detect_errors="exit_code"><![CDATA[
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	16 mkdir -p ./tabular ./plots &&
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	17 python '$__tool_directory__/script.py' --file '$input' --output ./tabular --json '$predictions_output'
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	18 $section_predictors.dynamine
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	19 $section_predictors.disomine
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	20 $section_predictors.efoldmine
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	21 $section_predictors.agmata
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	22 #if $section_plot.plot == '--plot' or $section_plot.plot_all == '--plot_all':
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	23 --plot-output ./plots
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	24 #end if
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	25 $section_plot.plot
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	26 $section_plot.plot_all
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	27 $section_plot.highlight
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	28 ]]></command>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	29 <inputs>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	30 <param type="data" name="input" format="fasta" label="Protein sequences in FASTA format" help="FASTA file of protein sequences"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	31 <section name="section_predictors" title="Biophyisical predictors" help="Configure this section to select the predictions to be executed">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	32 <param
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	33 argument="--dynamine"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	34 type="boolean"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	35 checked="true"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	36 truevalue="--dynamine"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	37 falsevalue=""
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	38 label="DynaMine: Prediction of protein backbone dynamics from sequence only"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	39 help="Fast predictor of protein backbone dynamics using only sequence information as input. The version here also predicts side-chain dynamics and secondary structure predictors using the same principle." />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	40 <param
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	41 argument="--disomine"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	42 type="boolean"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	43 checked="true"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	44 truevalue="--disomine"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	45 falsevalue=""
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	46 label="DisoMine: Prediction of protein disorder from sequence only"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	47 help="Predicts protein disorder with recurrent neural networks not directly from the amino acid sequence, but instead from more generic predictions of key biophysical properties, here protein dynamics, secondary structure and early folding."/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	48 <param
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	49 argument="--efoldmine"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	50 type="boolean"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	51 checked="true"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	52 truevalue="--efoldmine"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	53 falsevalue=""
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	54 label="EFoldMine: Prediction of protein early folding regions from sequence only"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	55 help="Predicts from the primary amino acid sequence of a protein, which amino acids are likely involved in early folding events."/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	56 <param
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	57 argument="--agmata"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	58 type="boolean"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	59 checked="true"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	60 truevalue="--agmata"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	61 falsevalue=""
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	62 label="Agmata: Prediction of protein regions that are likely to cause beta-aggregation"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	63 help="Agmata is a single-sequence based predictor of protein regions that are likely to cause beta-aggregation. It is based on a model that uses the biophysical predictions of protein behaviour, not on amino acid codes directly."/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	64 </section>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	65 <section name="section_plot" title="Plot options" help="Configure plot output">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	66 <param
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	67 name="plot"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	68 argument="--plot"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	69 type="boolean"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	70 label="Plot predicted values by sequence"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	71 truevalue="--plot"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	72 falsevalue=""
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	73 help="This option plots predicted values in different files"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	74 <param
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	75 name="plot_all"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	76 argument="--plot_all"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	77 type="boolean"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	78 label="Plot all sequences together"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	79 truevalue="--plot_all"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	80 falsevalue=""
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	81 help="This option plots all sequences together in order to compare predicted values of different sequences"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	82 <param
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	83 name="highlight"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	84 argument="--highlight"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	85 type="boolean"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	86 label="Highlight regions of interest"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	87 truevalue="--highlight"
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	88 falsevalue=""
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	89 help="Highlight biophysical regions on the background of the plots"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	90 </section>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	91 </inputs>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	92 <outputs>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	93 <data name="predictions_output" label="Predictions in JSON format" format="json" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	94 <collection name="split_output" type="list" label="Tabular predictions by sequence">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	95 <discover_datasets pattern="__name_and_ext__" format="tabular" directory="tabular" visible="true" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	96 </collection>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	97 <collection name="split_output_plots" type="list" label="Plots">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	98 <discover_datasets pattern="__name_and_ext__" format="png" directory="plots" visible="true" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	99 </collection>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	100 </outputs>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	101 <tests>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	102 <!-- Test 1: All the predictors were selected, plotting both individual and aggregated charts -->
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	103 <test expect_exit_code="0" expect_num_outputs="3">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	104 <param name="input" value="input.fasta" ftype="fasta"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	105 <section name="section_predictors">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	106 <param name="dynamine" value="true"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	107 <param name="disomine" value="true"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	108 <param name="efoldmine" value="true"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	109 <param name="agmata" value="true"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	110 </section>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	111 <section name="section_plot">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	112 <param name="plot" value="true"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	113 <param name="plot_all" value="true"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	114 <param name="highlight" value="true"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	115 </section>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	116 <assert_command>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	117 <has_text text="--dynamine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	118 <has_text text="--disomine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	119 <has_text text="--agmata" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	120 <has_text text="--efoldmine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	121 <has_text text="--json" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	122 <has_text text="--plot_all" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	123 <has_text text="--highlight" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	124 <has_text text="--highlight" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	125 <has_text text="--output" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	126 <has_text text="--plot-output" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	127 </assert_command>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	128 <output name="predictions_output" value="test_output.json" ftype="json"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	129 <!-- 11 sequences = 11 TSV files -->
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	130 <output_collection name="split_output" type="list" count="11">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	131 <element name="random_sequence_01_consisting_of_40_residues" file="random_sequence_01_consisting_of_40_residues.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	132 <element name="random_sequence_02_consisting_of_40_residues" file="random_sequence_02_consisting_of_40_residues.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	133 <element name="random_sequence_03_consisting_of_30_residues" file="random_sequence_03_consisting_of_30_residues.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	134 <element name="random_sequence_04_consisting_of_40_residues" file="random_sequence_04_consisting_of_40_residues.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	135 <element name="random_sequence_05_consisting_of_30_residues" file="random_sequence_05_consisting_of_30_residues.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	136 <element name="random_sequence_06_consisting_of_45_residues" file="random_sequence_06_consisting_of_45_residues.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	137 <element name="random_sequence_07_consisting_of_30_residues" file="random_sequence_07_consisting_of_30_residues.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	138 <element name="random_sequence_08_consisting_of_40_residues" file="random_sequence_08_consisting_of_40_residues.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	139 <element name="random_sequence_09_consisting_of_30_residues" file="random_sequence_09_consisting_of_30_residues.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	140 <element name="random_sequence_10_consisting_of_65_residues" file="random_sequence_10_consisting_of_65_residues.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	141 <element name="random_sequence_11_consisting_of_30_residues" file="random_sequence_11_consisting_of_30_residues.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	142 </output_collection>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	143 <!-- 9 predicted values x 11 sequences + 9 predicted values aggregated = (99 + 9) charts = 108 charts -->
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	144 <output_collection name="split_output_plots" type="list" count="108" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	145 </test>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	146 <!-- Test 2: Only one predictor was selected, plotting both individual and aggregated charts -->
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	147 <test expect_exit_code="0" expect_num_outputs="3">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	148 <param name="input" value="input.fasta" ftype="fasta"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	149 <section name="section_predictors">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	150 <param name="dynamine" value="true"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	151 <param name="disomine" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	152 <param name="efoldmine" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	153 <param name="agmata" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	154 </section>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	155 <section name="section_plot">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	156 <param name="plot" value="true"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	157 <param name="plot_all" value="true"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	158 <param name="highlight" value="true"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	159 </section>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	160 <assert_command>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	161 <has_text text="--dynamine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	162 <not_has_text text="--disomine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	163 <not_has_text text="--agmata" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	164 <not_has_text text="--efoldmine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	165 <has_text text="--json" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	166 <has_text text="--plot " />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	167 <has_text text="--plot_all" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	168 <has_text text="--highlight" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	169 <has_text text="--output" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	170 <has_text text="--plot-output" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	171 </assert_command>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	172 <output name="predictions_output" value="test_output_dynamine.json" ftype="json"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	173 <!-- 11 sequences = 11 TSV files -->
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	174 <output_collection name="split_output" type="list" count="11">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	175 <element name="random_sequence_01_consisting_of_40_residues" file="random_sequence_01_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	176 <element name="random_sequence_02_consisting_of_40_residues" file="random_sequence_02_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	177 <element name="random_sequence_03_consisting_of_30_residues" file="random_sequence_03_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	178 <element name="random_sequence_04_consisting_of_40_residues" file="random_sequence_04_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	179 <element name="random_sequence_05_consisting_of_30_residues" file="random_sequence_05_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	180 <element name="random_sequence_06_consisting_of_45_residues" file="random_sequence_06_consisting_of_45_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	181 <element name="random_sequence_07_consisting_of_30_residues" file="random_sequence_07_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	182 <element name="random_sequence_08_consisting_of_40_residues" file="random_sequence_08_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	183 <element name="random_sequence_09_consisting_of_30_residues" file="random_sequence_09_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	184 <element name="random_sequence_10_consisting_of_65_residues" file="random_sequence_10_consisting_of_65_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	185 <element name="random_sequence_11_consisting_of_30_residues" file="random_sequence_11_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	186 </output_collection>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	187 <!-- 6 predicted values x 11 sequences + 6 predicted values aggregated = (66 + 6) charts = 72 charts -->
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	188 <output_collection name="split_output_plots" type="list" count="72" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	189 </test>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	190 <!-- Test 3: Only one predictor was selected, plotting individual charts -->
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	191 <test expect_exit_code="0" expect_num_outputs="3">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	192 <param name="input" value="input.fasta" ftype="fasta"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	193 <section name="section_predictors">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	194 <param name="dynamine" value="true"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	195 <param name="disomine" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	196 <param name="efoldmine" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	197 <param name="agmata" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	198 </section>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	199 <section name="section_plot">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	200 <param name="plot" value="true"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	201 <param name="plot_all" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	202 <param name="highlight" value="true"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	203 </section>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	204 <assert_command>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	205 <has_text text="--dynamine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	206 <not_has_text text="--disomine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	207 <not_has_text text="--agmata" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	208 <not_has_text text="--efoldmine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	209 <has_text text="--json" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	210 <has_text text="--plot " />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	211 <not_has_text text="--plot_all" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	212 <has_text text="--highlight" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	213 <has_text text="--output" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	214 <has_text text="--plot-output" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	215 </assert_command>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	216 <output name="predictions_output" value="test_output_dynamine.json" ftype="json"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	217 <!-- 11 sequences = 11 TSV files -->
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	218 <output_collection name="split_output" type="list" count="11">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	219 <element name="random_sequence_01_consisting_of_40_residues" file="random_sequence_01_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	220 <element name="random_sequence_02_consisting_of_40_residues" file="random_sequence_02_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	221 <element name="random_sequence_03_consisting_of_30_residues" file="random_sequence_03_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	222 <element name="random_sequence_04_consisting_of_40_residues" file="random_sequence_04_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	223 <element name="random_sequence_05_consisting_of_30_residues" file="random_sequence_05_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	224 <element name="random_sequence_06_consisting_of_45_residues" file="random_sequence_06_consisting_of_45_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	225 <element name="random_sequence_07_consisting_of_30_residues" file="random_sequence_07_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	226 <element name="random_sequence_08_consisting_of_40_residues" file="random_sequence_08_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	227 <element name="random_sequence_09_consisting_of_30_residues" file="random_sequence_09_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	228 <element name="random_sequence_10_consisting_of_65_residues" file="random_sequence_10_consisting_of_65_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	229 <element name="random_sequence_11_consisting_of_30_residues" file="random_sequence_11_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	230 </output_collection>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	231 <!-- 6 predicted values x 11 sequences = 66 charts -->
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	232 <output_collection name="split_output_plots" type="list" count="66" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	233 </test>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	234 <!-- Test 4: Only one predictor was selected, plotting aggregated charts -->
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	235 <test expect_exit_code="0" expect_num_outputs="3">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	236 <param name="input" value="input.fasta" ftype="fasta"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	237 <section name="section_predictors">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	238 <param name="dynamine" value="true"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	239 <param name="disomine" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	240 <param name="efoldmine" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	241 <param name="agmata" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	242 </section>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	243 <section name="section_plot">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	244 <param name="plot" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	245 <param name="plot_all" value="true"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	246 <param name="highlight" value="true"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	247 </section>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	248 <assert_command>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	249 <has_text text="--dynamine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	250 <not_has_text text="--disomine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	251 <not_has_text text="--agmata" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	252 <not_has_text text="--efoldmine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	253 <has_text text="--json" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	254 <has_text text="--plot_all" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	255 <has_text text="--highlight" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	256 <not_has_text text="--plot " />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	257 <has_text text="--output" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	258 <has_text text="--plot-output" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	259 </assert_command>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	260 <output name="predictions_output" value="test_output_dynamine.json" ftype="json"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	261 <!-- 11 sequences = 11 TSV files -->
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	262 <output_collection name="split_output" type="list" count="11">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	263 <element name="random_sequence_01_consisting_of_40_residues" file="random_sequence_01_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	264 <element name="random_sequence_02_consisting_of_40_residues" file="random_sequence_02_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	265 <element name="random_sequence_03_consisting_of_30_residues" file="random_sequence_03_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	266 <element name="random_sequence_04_consisting_of_40_residues" file="random_sequence_04_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	267 <element name="random_sequence_05_consisting_of_30_residues" file="random_sequence_05_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	268 <element name="random_sequence_06_consisting_of_45_residues" file="random_sequence_06_consisting_of_45_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	269 <element name="random_sequence_07_consisting_of_30_residues" file="random_sequence_07_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	270 <element name="random_sequence_08_consisting_of_40_residues" file="random_sequence_08_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	271 <element name="random_sequence_09_consisting_of_30_residues" file="random_sequence_09_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	272 <element name="random_sequence_10_consisting_of_65_residues" file="random_sequence_10_consisting_of_65_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	273 <element name="random_sequence_11_consisting_of_30_residues" file="random_sequence_11_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	274 </output_collection>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	275 <!-- 6 predicted values aggregated = 6 charts -->
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	276 <output_collection name="split_output_plots" type="list" count="6" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	277 </test>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	278 <!-- Test 5: Only one predictor was selected, plotting aggregated charts with no highlighting -->
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	279 <test expect_exit_code="0" expect_num_outputs="3">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	280 <param name="input" value="input.fasta" ftype="fasta"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	281 <section name="section_predictors">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	282 <param name="dynamine" value="true"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	283 <param name="disomine" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	284 <param name="efoldmine" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	285 <param name="agmata" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	286 </section>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	287 <section name="section_plot">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	288 <param name="plot" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	289 <param name="plot_all" value="true"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	290 </section>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	291 <assert_command>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	292 <has_text text="--dynamine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	293 <has_text text="--json" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	294 <has_text text="--plot_all" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	295 <has_text text="--output" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	296 <has_text text="--plot-output" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	297 <not_has_text text="--disomine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	298 <not_has_text text="--agmata" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	299 <not_has_text text="--efoldmine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	300 <not_has_text text="--highlight" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	301 <not_has_text text="--plot " />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	302 </assert_command>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	303 <output name="predictions_output" value="test_output_dynamine.json" ftype="json"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	304 <!-- 11 sequences = 11 TSV files -->
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	305 <output_collection name="split_output" type="list" count="11">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	306 <element name="random_sequence_01_consisting_of_40_residues" file="random_sequence_01_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	307 <element name="random_sequence_02_consisting_of_40_residues" file="random_sequence_02_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	308 <element name="random_sequence_03_consisting_of_30_residues" file="random_sequence_03_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	309 <element name="random_sequence_04_consisting_of_40_residues" file="random_sequence_04_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	310 <element name="random_sequence_05_consisting_of_30_residues" file="random_sequence_05_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	311 <element name="random_sequence_06_consisting_of_45_residues" file="random_sequence_06_consisting_of_45_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	312 <element name="random_sequence_07_consisting_of_30_residues" file="random_sequence_07_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	313 <element name="random_sequence_08_consisting_of_40_residues" file="random_sequence_08_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	314 <element name="random_sequence_09_consisting_of_30_residues" file="random_sequence_09_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	315 <element name="random_sequence_10_consisting_of_65_residues" file="random_sequence_10_consisting_of_65_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	316 <element name="random_sequence_11_consisting_of_30_residues" file="random_sequence_11_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	317 </output_collection>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	318 <!-- 6 predicted values aggregated = 6 charts -->
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	319 <output_collection name="split_output_plots" type="list" count="6" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	320 </test>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	321 <!-- Test 6: Only one predictor was selected, plotting was disabled -->
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	322 <test expect_exit_code="0" expect_num_outputs="3">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	323 <param name="input" value="input.fasta" ftype="fasta"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	324 <section name="section_predictors">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	325 <param name="dynamine" value="true"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	326 <param name="disomine" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	327 <param name="efoldmine" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	328 <param name="agmata" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	329 </section>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	330 <section name="section_plot">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	331 <param name="plot" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	332 <param name="plot_all" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	333 <param name="highlight" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	334 </section>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	335 <assert_command>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	336 <has_text text="--dynamine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	337 <has_text text="--json" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	338 <has_text text="--output" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	339 <not_has_text text="--disomine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	340 <not_has_text text="--agmata" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	341 <not_has_text text="--efoldmine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	342 <not_has_text text="--plot " />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	343 <not_has_text text="--plot_all" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	344 <not_has_text text="--highlight" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	345 <not_has_text text="--plot-output" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	346 </assert_command>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	347 <output name="predictions_output" value="test_output_dynamine.json" ftype="json"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	348 <!-- 11 sequences = 11 TSV files -->
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	349 <output_collection name="split_output" type="list" count="11">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	350 <element name="random_sequence_01_consisting_of_40_residues" file="random_sequence_01_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	351 <element name="random_sequence_02_consisting_of_40_residues" file="random_sequence_02_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	352 <element name="random_sequence_03_consisting_of_30_residues" file="random_sequence_03_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	353 <element name="random_sequence_04_consisting_of_40_residues" file="random_sequence_04_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	354 <element name="random_sequence_05_consisting_of_30_residues" file="random_sequence_05_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	355 <element name="random_sequence_06_consisting_of_45_residues" file="random_sequence_06_consisting_of_45_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	356 <element name="random_sequence_07_consisting_of_30_residues" file="random_sequence_07_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	357 <element name="random_sequence_08_consisting_of_40_residues" file="random_sequence_08_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	358 <element name="random_sequence_09_consisting_of_30_residues" file="random_sequence_09_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	359 <element name="random_sequence_10_consisting_of_65_residues" file="random_sequence_10_consisting_of_65_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	360 <element name="random_sequence_11_consisting_of_30_residues" file="random_sequence_11_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	361 </output_collection>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	362 <output_collection name="split_output_plots" type="list" count="0" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	363 </test>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	364 <!-- Test 7: No predictor selected, it must fail -->
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	365 <test expect_failure="true" expect_exit_code="2">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	366 <param name="input" value="input.fasta" ftype="fasta"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	367 <section name="section_predictors">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	368 <param name="dynamine" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	369 <param name="disomine" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	370 <param name="efoldmine" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	371 <param name="agmata" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	372 </section>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	373 <section name="section_plot">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	374 <param name="plot" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	375 <param name="plot_all" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	376 <param name="highlight" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	377 </section>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	378 <assert_command>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	379 <not_has_text text="--dynamine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	380 <not_has_text text="--disomine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	381 <not_has_text text="--agmata" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	382 <not_has_text text="--efoldmine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	383 <not_has_text text="--plot-output" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	384 <not_has_text text="--plot " />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	385 <not_has_text text="--plot_all" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	386 <not_has_text text="--highlight" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	387 </assert_command>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	388 </test>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	389 <!-- Test 8: No input file, it must fail -->
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	390 <test expect_failure="true" expect_exit_code="1">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	391 <section name="section_predictors">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	392 <param name="dynamine" value="true"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	393 <param name="disomine" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	394 <param name="efoldmine" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	395 <param name="agmata" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	396 </section>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	397 <section name="section_plot">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	398 <param name="plot" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	399 <param name="plot_all" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	400 <param name="highlight" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	401 </section>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	402 <assert_command>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	403 <has_text text="--dynamine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	404 <not_has_text text="--disomine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	405 <not_has_text text="--agmata" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	406 <not_has_text text="--efoldmine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	407 <not_has_text text="--plot-output" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	408 <not_has_text text="--plot " />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	409 <not_has_text text="--plot_all" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	410 <not_has_text text="--highlight" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	411 </assert_command>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	412 </test>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	413 <!-- Test 9: No valid input file format, it must fail -->
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	414 <test expect_failure="true" expect_exit_code="1">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	415 <param name="input" value="wrong.fasta" ftype="fasta"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	416 <section name="section_predictors">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	417 <param name="dynamine" value="true"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	418 <param name="disomine" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	419 <param name="efoldmine" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	420 <param name="agmata" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	421 </section>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	422 <section name="section_plot">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	423 <param name="plot" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	424 <param name="plot_all" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	425 <param name="highlight" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	426 </section>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	427 <assert_command>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	428 <has_text text="--dynamine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	429 <not_has_text text="--disomine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	430 <not_has_text text="--agmata" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	431 <not_has_text text="--efoldmine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	432 <not_has_text text="--plot-output" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	433 <not_has_text text="--plot " />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	434 <not_has_text text="--plot_all" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	435 <not_has_text text="--highlight" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	436 </assert_command>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	437 </test>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	438 <!-- Test 10: Wrong input file type, it must fail -->
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	439 <test expect_failure="true" expect_exit_code="1">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	440 <param name="input" value="wrong.tsv" ftype="tabular"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	441 <section name="section_predictors">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	442 <param name="dynamine" value="true"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	443 <param name="disomine" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	444 <param name="efoldmine" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	445 <param name="agmata" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	446 </section>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	447 <section name="section_plot">
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	448 <param name="plot" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	449 <param name="plot_all" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	450 <param name="highlight" value="false"/>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	451 </section>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	452 <assert_command>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	453 <has_text text="--dynamine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	454 <not_has_text text="--disomine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	455 <not_has_text text="--agmata" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	456 <not_has_text text="--efoldmine" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	457 <not_has_text text="--plot-output" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	458 <not_has_text text="--plot " />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	459 <not_has_text text="--plot_all" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	460 <not_has_text text="--highlight" />
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	461 </assert_command>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	462 </test>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	463 </tests>
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	464 <help><![CDATA[
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	465 Single protein sequence analysis
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	466 --------------------------------
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	467 The current Galaxy Tool is the implementation of the Bio2Byte tools for single protein sequence analysis.
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	468 It means that this tool receives amino-acid sequences in FASTA format and
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	469 will return the biophysical predictions depending on the predictors selected.
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	470
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	471 Input sequences
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	472 '''''''''''''''
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	473 The tool works with either single or multiple input files, just keeping in mind that
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	474 the file must be a valid FASTA containing at least one sequence of amino acids.
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	475
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	476 There is no limitation on the number of sequences per file, however, all
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	477 the sequences must have at least 5 residues.
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	478
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	479 Available biophysical predictors
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	480 ''''''''''''''''''''''''''''''''
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	481 This is the list of the available Bio2Byte tools. As you can see, each prediction tool contains a subset of
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	482 predicted features, for instance, DynaMine produces six features which will appear as column in the tabular output and as keys in the JSON output:
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	483
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	484 - DynaMine: Fast predictor of protein backbone dynamics using only sequence information as input. The version here also predicts side-chain dynamics and secondary structure predictors using the same principle.
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	485 - Backbone dynamics: found as ``backbone`` inside either the tabular result, the JSON output file, or the plots in PNG format.
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	486 - Side chain dynamics: found as ``sidechain`` inside either the tabular result, the JSON output file, or the plots in PNG format.
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	487 - Helix propensity: found as ``helix`` inside either the tabular result, the JSON output file, or the plots in PNG format.
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	488 - Sheet propensity: found as ``sheet`` inside either the tabular result, the JSON output file, or the plots in PNG format.
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	489 - Coil propensity: found as ``coil`` inside either the tabular result, the JSON output file, or the plots in PNG format.
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	490 - Polyproline-II propensity: found as ``ppII`` inside either the tabular result, the JSON output file, or the plots in PNG format.
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	491 - DisoMine: Predicts protein disorder with recurrent neural networks not directly from the amino acid sequence, but instead from more generic predictions of key biophysical properties, here protein dynamics, secondary structure, and early folding.
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	492 - Disorder: found as ``disomine`` inside either the tabular result, the JSON output file, or the plots in PNG format.
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	493 - EFoldMine: Predicts from the primary amino acid sequence of a protein, which amino acids are likely involved in early folding events.
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	494 - Early folding: found as ``efoldmine`` inside either the tabular result, the JSON output file, or the plots in PNG format.
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	495 - Agmata: Beta-sheet aggregation with the following predicted features:
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	496 - Beta-sheet aggregation: found as ``agmata`` inside either the tabular result, the JSON output file, or the plots in PNG format.
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	497
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	498 Expected results
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	499 ''''''''''''''''
b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	500 From a single FASTA file with N sequences, the process will produce:

0

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

1 <tool

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

2 id="b2btools_single_sequence"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

3 name="b2bTools: Biophysical predictors for single sequences"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

4 version="3.0.5+galaxy0"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

5 license="GPL-3.0"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

6 python_template_version="3.5"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

7 profile="21.05">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

8 <description>from their amino-acid sequences</description>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

9 <xrefs>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

10 <xref type="bio.tools">b2btools</xref>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

11 </xrefs>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

12 <requirements>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

13 <requirement type="package" version="3.0.5">b2btools</requirement>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

14 </requirements>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

15 <command detect_errors="exit_code"><![CDATA[

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

16 mkdir -p ./tabular ./plots &&

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

17 python '$__tool_directory__/script.py' --file '$input' --output ./tabular --json '$predictions_output'

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

18 $section_predictors.dynamine

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

19 $section_predictors.disomine

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

20 $section_predictors.efoldmine

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

21 $section_predictors.agmata

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

22 #if $section_plot.plot == '--plot' or $section_plot.plot_all == '--plot_all':

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

23 --plot-output ./plots

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

24 #end if

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

25 $section_plot.plot

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

26 $section_plot.plot_all

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

27 $section_plot.highlight

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

28 ]]></command>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

29 <inputs>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

30 <param type="data" name="input" format="fasta" label="Protein sequences in FASTA format" help="FASTA file of protein sequences"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

31 <section name="section_predictors" title="Biophyisical predictors" help="Configure this section to select the predictions to be executed">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

32 <param

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

33 argument="--dynamine"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

34 type="boolean"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

35 checked="true"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

36 truevalue="--dynamine"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

37 falsevalue=""

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

38 label="DynaMine: Prediction of protein backbone dynamics from sequence only"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

39 help="Fast predictor of protein backbone dynamics using only sequence information as input. The version here also predicts side-chain dynamics and secondary structure predictors using the same principle." />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

40 <param

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

41 argument="--disomine"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

42 type="boolean"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

43 checked="true"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

44 truevalue="--disomine"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

45 falsevalue=""

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

46 label="DisoMine: Prediction of protein disorder from sequence only"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

47 help="Predicts protein disorder with recurrent neural networks not directly from the amino acid sequence, but instead from more generic predictions of key biophysical properties, here protein dynamics, secondary structure and early folding."/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

48 <param

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

49 argument="--efoldmine"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

50 type="boolean"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

51 checked="true"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

52 truevalue="--efoldmine"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

53 falsevalue=""

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

54 label="EFoldMine: Prediction of protein early folding regions from sequence only"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

55 help="Predicts from the primary amino acid sequence of a protein, which amino acids are likely involved in early folding events."/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

56 <param

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

57 argument="--agmata"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

58 type="boolean"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

59 checked="true"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

60 truevalue="--agmata"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

61 falsevalue=""

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

62 label="Agmata: Prediction of protein regions that are likely to cause beta-aggregation"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

63 help="Agmata is a single-sequence based predictor of protein regions that are likely to cause beta-aggregation. It is based on a model that uses the biophysical predictions of protein behaviour, not on amino acid codes directly."/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

64 </section>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

65 <section name="section_plot" title="Plot options" help="Configure plot output">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

66 <param

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

67 name="plot"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

68 argument="--plot"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

69 type="boolean"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

70 label="Plot predicted values by sequence"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

71 truevalue="--plot"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

72 falsevalue=""

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

73 help="This option plots predicted values in different files"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

74 <param

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

75 name="plot_all"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

76 argument="--plot_all"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

77 type="boolean"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

78 label="Plot all sequences together"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

79 truevalue="--plot_all"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

80 falsevalue=""

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

81 help="This option plots all sequences together in order to compare predicted values of different sequences"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

82 <param

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

83 name="highlight"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

84 argument="--highlight"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

85 type="boolean"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

86 label="Highlight regions of interest"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

87 truevalue="--highlight"

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

88 falsevalue=""

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

89 help="Highlight biophysical regions on the background of the plots"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

90 </section>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

91 </inputs>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

92 <outputs>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

93 <data name="predictions_output" label="Predictions in JSON format" format="json" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

94 <collection name="split_output" type="list" label="Tabular predictions by sequence">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

95 <discover_datasets pattern="__name_and_ext__" format="tabular" directory="tabular" visible="true" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

96 </collection>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

97 <collection name="split_output_plots" type="list" label="Plots">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

98 <discover_datasets pattern="__name_and_ext__" format="png" directory="plots" visible="true" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

99 </collection>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

100 </outputs>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

101 <tests>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

102

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

103 <test expect_exit_code="0" expect_num_outputs="3">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

104 <param name="input" value="input.fasta" ftype="fasta"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

105 <section name="section_predictors">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

106 <param name="dynamine" value="true"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

107 <param name="disomine" value="true"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

108 <param name="efoldmine" value="true"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

109 <param name="agmata" value="true"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

110 </section>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

111 <section name="section_plot">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

112 <param name="plot" value="true"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

113 <param name="plot_all" value="true"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

114 <param name="highlight" value="true"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

115 </section>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

116 <assert_command>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

117 <has_text text="--dynamine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

118 <has_text text="--disomine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

119 <has_text text="--agmata" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

120 <has_text text="--efoldmine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

121 <has_text text="--json" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

122 <has_text text="--plot_all" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

123 <has_text text="--highlight" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

124 <has_text text="--highlight" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

125 <has_text text="--output" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

126 <has_text text="--plot-output" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

127 </assert_command>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

128 <output name="predictions_output" value="test_output.json" ftype="json"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

129

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

130 <output_collection name="split_output" type="list" count="11">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

131 <element name="random_sequence_01_consisting_of_40_residues" file="random_sequence_01_consisting_of_40_residues.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

132 <element name="random_sequence_02_consisting_of_40_residues" file="random_sequence_02_consisting_of_40_residues.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

133 <element name="random_sequence_03_consisting_of_30_residues" file="random_sequence_03_consisting_of_30_residues.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

134 <element name="random_sequence_04_consisting_of_40_residues" file="random_sequence_04_consisting_of_40_residues.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

135 <element name="random_sequence_05_consisting_of_30_residues" file="random_sequence_05_consisting_of_30_residues.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

136 <element name="random_sequence_06_consisting_of_45_residues" file="random_sequence_06_consisting_of_45_residues.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

137 <element name="random_sequence_07_consisting_of_30_residues" file="random_sequence_07_consisting_of_30_residues.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

138 <element name="random_sequence_08_consisting_of_40_residues" file="random_sequence_08_consisting_of_40_residues.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

139 <element name="random_sequence_09_consisting_of_30_residues" file="random_sequence_09_consisting_of_30_residues.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

140 <element name="random_sequence_10_consisting_of_65_residues" file="random_sequence_10_consisting_of_65_residues.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

141 <element name="random_sequence_11_consisting_of_30_residues" file="random_sequence_11_consisting_of_30_residues.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

142 </output_collection>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

143

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

144 <output_collection name="split_output_plots" type="list" count="108" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

145 </test>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

146

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

147 <test expect_exit_code="0" expect_num_outputs="3">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

148 <param name="input" value="input.fasta" ftype="fasta"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

149 <section name="section_predictors">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

150 <param name="dynamine" value="true"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

151 <param name="disomine" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

152 <param name="efoldmine" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

153 <param name="agmata" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

154 </section>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

155 <section name="section_plot">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

156 <param name="plot" value="true"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

157 <param name="plot_all" value="true"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

158 <param name="highlight" value="true"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

159 </section>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

160 <assert_command>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

161 <has_text text="--dynamine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

162 <not_has_text text="--disomine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

163 <not_has_text text="--agmata" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

164 <not_has_text text="--efoldmine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

165 <has_text text="--json" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

166 <has_text text="--plot " />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

167 <has_text text="--plot_all" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

168 <has_text text="--highlight" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

169 <has_text text="--output" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

170 <has_text text="--plot-output" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

171 </assert_command>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

172 <output name="predictions_output" value="test_output_dynamine.json" ftype="json"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

173

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

174 <output_collection name="split_output" type="list" count="11">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

175 <element name="random_sequence_01_consisting_of_40_residues" file="random_sequence_01_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

176 <element name="random_sequence_02_consisting_of_40_residues" file="random_sequence_02_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

177 <element name="random_sequence_03_consisting_of_30_residues" file="random_sequence_03_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

178 <element name="random_sequence_04_consisting_of_40_residues" file="random_sequence_04_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

179 <element name="random_sequence_05_consisting_of_30_residues" file="random_sequence_05_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

180 <element name="random_sequence_06_consisting_of_45_residues" file="random_sequence_06_consisting_of_45_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

181 <element name="random_sequence_07_consisting_of_30_residues" file="random_sequence_07_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

182 <element name="random_sequence_08_consisting_of_40_residues" file="random_sequence_08_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

183 <element name="random_sequence_09_consisting_of_30_residues" file="random_sequence_09_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

184 <element name="random_sequence_10_consisting_of_65_residues" file="random_sequence_10_consisting_of_65_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

185 <element name="random_sequence_11_consisting_of_30_residues" file="random_sequence_11_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

186 </output_collection>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

187

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

188 <output_collection name="split_output_plots" type="list" count="72" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

189 </test>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

190

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

191 <test expect_exit_code="0" expect_num_outputs="3">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

192 <param name="input" value="input.fasta" ftype="fasta"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

193 <section name="section_predictors">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

194 <param name="dynamine" value="true"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

195 <param name="disomine" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

196 <param name="efoldmine" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

197 <param name="agmata" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

198 </section>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

199 <section name="section_plot">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

200 <param name="plot" value="true"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

201 <param name="plot_all" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

202 <param name="highlight" value="true"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

203 </section>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

204 <assert_command>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

205 <has_text text="--dynamine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

206 <not_has_text text="--disomine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

207 <not_has_text text="--agmata" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

208 <not_has_text text="--efoldmine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

209 <has_text text="--json" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

210 <has_text text="--plot " />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

211 <not_has_text text="--plot_all" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

212 <has_text text="--highlight" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

213 <has_text text="--output" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

214 <has_text text="--plot-output" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

215 </assert_command>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

216 <output name="predictions_output" value="test_output_dynamine.json" ftype="json"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

217

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

218 <output_collection name="split_output" type="list" count="11">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

219 <element name="random_sequence_01_consisting_of_40_residues" file="random_sequence_01_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

220 <element name="random_sequence_02_consisting_of_40_residues" file="random_sequence_02_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

221 <element name="random_sequence_03_consisting_of_30_residues" file="random_sequence_03_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

222 <element name="random_sequence_04_consisting_of_40_residues" file="random_sequence_04_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

223 <element name="random_sequence_05_consisting_of_30_residues" file="random_sequence_05_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

224 <element name="random_sequence_06_consisting_of_45_residues" file="random_sequence_06_consisting_of_45_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

225 <element name="random_sequence_07_consisting_of_30_residues" file="random_sequence_07_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

226 <element name="random_sequence_08_consisting_of_40_residues" file="random_sequence_08_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

227 <element name="random_sequence_09_consisting_of_30_residues" file="random_sequence_09_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

228 <element name="random_sequence_10_consisting_of_65_residues" file="random_sequence_10_consisting_of_65_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

229 <element name="random_sequence_11_consisting_of_30_residues" file="random_sequence_11_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

230 </output_collection>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

231

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

232 <output_collection name="split_output_plots" type="list" count="66" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

233 </test>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

234

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

235 <test expect_exit_code="0" expect_num_outputs="3">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

236 <param name="input" value="input.fasta" ftype="fasta"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

237 <section name="section_predictors">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

238 <param name="dynamine" value="true"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

239 <param name="disomine" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

240 <param name="efoldmine" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

241 <param name="agmata" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

242 </section>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

243 <section name="section_plot">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

244 <param name="plot" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

245 <param name="plot_all" value="true"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

246 <param name="highlight" value="true"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

247 </section>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

248 <assert_command>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

249 <has_text text="--dynamine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

250 <not_has_text text="--disomine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

251 <not_has_text text="--agmata" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

252 <not_has_text text="--efoldmine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

253 <has_text text="--json" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

254 <has_text text="--plot_all" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

255 <has_text text="--highlight" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

256 <not_has_text text="--plot " />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

257 <has_text text="--output" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

258 <has_text text="--plot-output" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

259 </assert_command>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

260 <output name="predictions_output" value="test_output_dynamine.json" ftype="json"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

261

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

262 <output_collection name="split_output" type="list" count="11">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

263 <element name="random_sequence_01_consisting_of_40_residues" file="random_sequence_01_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

264 <element name="random_sequence_02_consisting_of_40_residues" file="random_sequence_02_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

265 <element name="random_sequence_03_consisting_of_30_residues" file="random_sequence_03_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

266 <element name="random_sequence_04_consisting_of_40_residues" file="random_sequence_04_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

267 <element name="random_sequence_05_consisting_of_30_residues" file="random_sequence_05_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

268 <element name="random_sequence_06_consisting_of_45_residues" file="random_sequence_06_consisting_of_45_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

269 <element name="random_sequence_07_consisting_of_30_residues" file="random_sequence_07_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

270 <element name="random_sequence_08_consisting_of_40_residues" file="random_sequence_08_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

271 <element name="random_sequence_09_consisting_of_30_residues" file="random_sequence_09_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

272 <element name="random_sequence_10_consisting_of_65_residues" file="random_sequence_10_consisting_of_65_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

273 <element name="random_sequence_11_consisting_of_30_residues" file="random_sequence_11_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

274 </output_collection>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

275

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

276 <output_collection name="split_output_plots" type="list" count="6" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

277 </test>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

278

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

279 <test expect_exit_code="0" expect_num_outputs="3">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

280 <param name="input" value="input.fasta" ftype="fasta"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

281 <section name="section_predictors">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

282 <param name="dynamine" value="true"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

283 <param name="disomine" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

284 <param name="efoldmine" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

285 <param name="agmata" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

286 </section>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

287 <section name="section_plot">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

288 <param name="plot" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

289 <param name="plot_all" value="true"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

290 </section>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

291 <assert_command>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

292 <has_text text="--dynamine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

293 <has_text text="--json" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

294 <has_text text="--plot_all" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

295 <has_text text="--output" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

296 <has_text text="--plot-output" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

297 <not_has_text text="--disomine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

298 <not_has_text text="--agmata" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

299 <not_has_text text="--efoldmine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

300 <not_has_text text="--highlight" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

301 <not_has_text text="--plot " />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

302 </assert_command>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

303 <output name="predictions_output" value="test_output_dynamine.json" ftype="json"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

304

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

305 <output_collection name="split_output" type="list" count="11">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

306 <element name="random_sequence_01_consisting_of_40_residues" file="random_sequence_01_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

307 <element name="random_sequence_02_consisting_of_40_residues" file="random_sequence_02_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

308 <element name="random_sequence_03_consisting_of_30_residues" file="random_sequence_03_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

309 <element name="random_sequence_04_consisting_of_40_residues" file="random_sequence_04_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

310 <element name="random_sequence_05_consisting_of_30_residues" file="random_sequence_05_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

311 <element name="random_sequence_06_consisting_of_45_residues" file="random_sequence_06_consisting_of_45_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

312 <element name="random_sequence_07_consisting_of_30_residues" file="random_sequence_07_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

313 <element name="random_sequence_08_consisting_of_40_residues" file="random_sequence_08_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

314 <element name="random_sequence_09_consisting_of_30_residues" file="random_sequence_09_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

315 <element name="random_sequence_10_consisting_of_65_residues" file="random_sequence_10_consisting_of_65_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

316 <element name="random_sequence_11_consisting_of_30_residues" file="random_sequence_11_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

317 </output_collection>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

318

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

319 <output_collection name="split_output_plots" type="list" count="6" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

320 </test>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

321

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

322 <test expect_exit_code="0" expect_num_outputs="3">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

323 <param name="input" value="input.fasta" ftype="fasta"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

324 <section name="section_predictors">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

325 <param name="dynamine" value="true"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

326 <param name="disomine" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

327 <param name="efoldmine" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

328 <param name="agmata" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

329 </section>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

330 <section name="section_plot">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

331 <param name="plot" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

332 <param name="plot_all" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

333 <param name="highlight" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

334 </section>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

335 <assert_command>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

336 <has_text text="--dynamine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

337 <has_text text="--json" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

338 <has_text text="--output" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

339 <not_has_text text="--disomine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

340 <not_has_text text="--agmata" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

341 <not_has_text text="--efoldmine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

342 <not_has_text text="--plot " />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

343 <not_has_text text="--plot_all" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

344 <not_has_text text="--highlight" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

345 <not_has_text text="--plot-output" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

346 </assert_command>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

347 <output name="predictions_output" value="test_output_dynamine.json" ftype="json"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

348

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

349 <output_collection name="split_output" type="list" count="11">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

350 <element name="random_sequence_01_consisting_of_40_residues" file="random_sequence_01_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

351 <element name="random_sequence_02_consisting_of_40_residues" file="random_sequence_02_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

352 <element name="random_sequence_03_consisting_of_30_residues" file="random_sequence_03_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

353 <element name="random_sequence_04_consisting_of_40_residues" file="random_sequence_04_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

354 <element name="random_sequence_05_consisting_of_30_residues" file="random_sequence_05_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

355 <element name="random_sequence_06_consisting_of_45_residues" file="random_sequence_06_consisting_of_45_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

356 <element name="random_sequence_07_consisting_of_30_residues" file="random_sequence_07_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

357 <element name="random_sequence_08_consisting_of_40_residues" file="random_sequence_08_consisting_of_40_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

358 <element name="random_sequence_09_consisting_of_30_residues" file="random_sequence_09_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

359 <element name="random_sequence_10_consisting_of_65_residues" file="random_sequence_10_consisting_of_65_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

360 <element name="random_sequence_11_consisting_of_30_residues" file="random_sequence_11_consisting_of_30_residues_dynamine.tsv" ftype="tsv" compare="diff"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

361 </output_collection>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

362 <output_collection name="split_output_plots" type="list" count="0" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

363 </test>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

364

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

365 <test expect_failure="true" expect_exit_code="2">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

366 <param name="input" value="input.fasta" ftype="fasta"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

367 <section name="section_predictors">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

368 <param name="dynamine" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

369 <param name="disomine" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

370 <param name="efoldmine" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

371 <param name="agmata" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

372 </section>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

373 <section name="section_plot">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

374 <param name="plot" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

375 <param name="plot_all" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

376 <param name="highlight" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

377 </section>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

378 <assert_command>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

379 <not_has_text text="--dynamine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

380 <not_has_text text="--disomine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

381 <not_has_text text="--agmata" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

382 <not_has_text text="--efoldmine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

383 <not_has_text text="--plot-output" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

384 <not_has_text text="--plot " />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

385 <not_has_text text="--plot_all" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

386 <not_has_text text="--highlight" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

387 </assert_command>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

388 </test>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

389

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

390 <test expect_failure="true" expect_exit_code="1">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

391 <section name="section_predictors">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

392 <param name="dynamine" value="true"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

393 <param name="disomine" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

394 <param name="efoldmine" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

395 <param name="agmata" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

396 </section>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

397 <section name="section_plot">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

398 <param name="plot" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

399 <param name="plot_all" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

400 <param name="highlight" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

401 </section>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

402 <assert_command>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

403 <has_text text="--dynamine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

404 <not_has_text text="--disomine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

405 <not_has_text text="--agmata" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

406 <not_has_text text="--efoldmine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

407 <not_has_text text="--plot-output" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

408 <not_has_text text="--plot " />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

409 <not_has_text text="--plot_all" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

410 <not_has_text text="--highlight" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

411 </assert_command>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

412 </test>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

413

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

414 <test expect_failure="true" expect_exit_code="1">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

415 <param name="input" value="wrong.fasta" ftype="fasta"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

416 <section name="section_predictors">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

417 <param name="dynamine" value="true"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

418 <param name="disomine" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

419 <param name="efoldmine" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

420 <param name="agmata" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

421 </section>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

422 <section name="section_plot">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

423 <param name="plot" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

424 <param name="plot_all" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

425 <param name="highlight" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

426 </section>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

427 <assert_command>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

428 <has_text text="--dynamine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

429 <not_has_text text="--disomine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

430 <not_has_text text="--agmata" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

431 <not_has_text text="--efoldmine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

432 <not_has_text text="--plot-output" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

433 <not_has_text text="--plot " />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

434 <not_has_text text="--plot_all" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

435 <not_has_text text="--highlight" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

436 </assert_command>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

437 </test>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

438

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

439 <test expect_failure="true" expect_exit_code="1">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

440 <param name="input" value="wrong.tsv" ftype="tabular"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

441 <section name="section_predictors">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

442 <param name="dynamine" value="true"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

443 <param name="disomine" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

444 <param name="efoldmine" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

445 <param name="agmata" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

446 </section>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

447 <section name="section_plot">

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

448 <param name="plot" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

449 <param name="plot_all" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

450 <param name="highlight" value="false"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

451 </section>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

452 <assert_command>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

453 <has_text text="--dynamine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

454 <not_has_text text="--disomine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

455 <not_has_text text="--agmata" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

456 <not_has_text text="--efoldmine" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

457 <not_has_text text="--plot-output" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

458 <not_has_text text="--plot " />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

459 <not_has_text text="--plot_all" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

460 <not_has_text text="--highlight" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

461 </assert_command>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

462 </test>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

463 </tests>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

464 <help><![CDATA[

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

465 Single protein sequence analysis

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

466 --------------------------------

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

467 The **current Galaxy Tool** is the implementation of the Bio2Byte tools for **single protein sequence analysis**.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

468 It means that this tool receives amino-acid sequences in FASTA format and

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

469 will return the biophysical predictions depending on the predictors selected.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

470

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

471 Input sequences

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

472 '''''''''''''''

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

473 The tool works with either single or multiple input files, just keeping in mind that

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

474 the file must be a valid FASTA containing at least one sequence of amino acids.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

475

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

476 There is no limitation on the number of sequences per file, however, all

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

477 the sequences must have at least 5 residues.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

478

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

479 Available biophysical predictors

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

480 ''''''''''''''''''''''''''''''''

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

481 This is the list of the available Bio2Byte tools. As you can see, each prediction tool contains a subset of

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

482 predicted features, for instance, DynaMine produces six features which will appear as column in the tabular output and as keys in the JSON output:

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

483

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

484 - **DynaMine**: Fast predictor of protein backbone dynamics using only sequence information as input. The version here also predicts side-chain dynamics and secondary structure predictors using the same principle.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

485 - *Backbone dynamics*: found as ``backbone`` inside either the tabular result, the JSON output file, or the plots in PNG format.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

486 - *Side chain dynamics*: found as ``sidechain`` inside either the tabular result, the JSON output file, or the plots in PNG format.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

487 - *Helix propensity*: found as ``helix`` inside either the tabular result, the JSON output file, or the plots in PNG format.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

488 - *Sheet propensity*: found as ``sheet`` inside either the tabular result, the JSON output file, or the plots in PNG format.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

489 - *Coil propensity*: found as ``coil`` inside either the tabular result, the JSON output file, or the plots in PNG format.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

490 - *Polyproline-II propensity*: found as ``ppII`` inside either the tabular result, the JSON output file, or the plots in PNG format.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

491 - **DisoMine**: Predicts protein disorder with recurrent neural networks not directly from the amino acid sequence, but instead from more generic predictions of key biophysical properties, here protein dynamics, secondary structure, and early folding.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

492 - *Disorder*: found as ``disomine`` inside either the tabular result, the JSON output file, or the plots in PNG format.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

493 - **EFoldMine**: Predicts from the primary amino acid sequence of a protein, which amino acids are likely involved in early folding events.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

494 - *Early folding*: found as ``efoldmine`` inside either the tabular result, the JSON output file, or the plots in PNG format.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

495 - **Agmata**: Beta-sheet aggregation with the following predicted features:

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

496 - *Beta-sheet aggregation*: found as ``agmata`` inside either the tabular result, the JSON output file, or the plots in PNG format.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

497

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

498 Expected results

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

499 ''''''''''''''''

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

500 From a single FASTA file with N sequences, the process will produce:

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

501

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

502 - **single JSON output**: it will contain a key per sequence defined in the input FASTA file. Each key contains the predicted features* for that sequence.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

503 - **N tabular results**: Each tabular result is a table where the columns are the predicted features and the rows are each residue of the sequence

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

504 - **N predicted features plots** (in case the user checked the ``plot`` parameter): Each predicted feature is plotted for each sequence

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

505 - **predicted feature plots** (in case the user checked the ``plot_all`` parameter): For each predicted feature, there will be a plot containing a series per sequence, so all the sequences are plotted in one single png file for each predicted feature

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

506

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

507 Example

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

508 ~~~~~~~

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

509

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

510 Given this input in FASTA format with 11 sequences:

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

511 ::

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

512

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

513 >random_sequence_01_consisting_of_40_residues

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

514 MDRHDPVQKSMMMDRHDPVQKMDRHDPVQKSDRHDPVQKS

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

515

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

516 >random_sequence_02_consisting_of_40_residues

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

517 MWSMWRAMWSSQRAMWSMWRAMWSMSQRAMWSMWRAMWSM

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

518

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

519 >random_sequence_03_consisting_of_30_residues

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

520 YSWTHYELKAVWCELTYWRSWTHYELKAVV

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

521

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

522 >random_sequence_04_consisting_of_40_residues

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

523 SWTHYEYSWTHYELKAVWCELTYWRSWTHYELKAVVLKAV

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

524

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

525 >random_sequence_05_consisting_of_30_residues

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

526 NCPIEHHLCANKMDLHHHHLCAHHLPEDQY

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

527

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

528 >random_sequence_06_consisting_of_45_residues

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

529 YACLFQKPYIHHLCANKMDLHHNKMDLHHHHLCAHHLHHLCAHHL

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

530

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

531 >random_sequence_07_consisting_of_30_residues

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

532 FHHLCANKMDLHHHHLCAHHLVPGKQEPDS

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

533

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

534 >random_sequence_08_consisting_of_40_residues

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

535 HHLCANKMDLHHHHLCAHHLCANKMDLNKMDLLCANKMDL

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

536

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

537 >random_sequence_09_consisting_of_30_residues

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

538 GNKTPFMKMHGGNKTPFMKMHNKTPFMKMH

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

539

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

540 >random_sequence_10_consisting_of_65_residues

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

541 LDNSKMWQLDNPMPMSKMWQLDNSKMWQLDNLDNSKMWQLDNPMPMSKMWQLDNSKMWQLDNAAA

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

542

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

543 >random_sequence_11_consisting_of_30_residues

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

544 PMSKMWQLDNMSKMWQLDNPMSKMWQLDNA

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

545

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

546 There will be the next results if all the predictor tools (DynaMine, DisoMine, EFoldMine, and AgMata) are selected:

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

547

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

548 JSON result

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

549 ...........

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

550 Containing all the input sequences and their predicted features depending on the selected predictors.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

551 ::

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

552

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

553 {

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

554 "random_sequence_03_consisting_of_30_residues": {

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

555 "agmata": [

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

556 0.012,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

557 0.08,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

558 0.119,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

559 0.154,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

560 0.2,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

561 0.34,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

562 1.023,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

563 4.084,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

564 12.328,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

565 20.723,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

566 25.866,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

567 24.864,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

568 17.509,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

569 9.32,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

570 3.591,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

571 1.559,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

572 0.64,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

573 0.221,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

574 0.084,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

575 0.038,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

576 0.031,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

577 0.035,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

578 0.052,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

579 0.159,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

580 1.115,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

581 7.747,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

582 8.329,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

583 8.214,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

584 7.259,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

585 0.608

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

586 ],

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

587 "backbone": [

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

588 0.818,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

589 0.833,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

590 0.87,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

591 ...

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

592 ],

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

593 ...

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

594 },

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

595 ...

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

596 }

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

597

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

598 Tabular results

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

599 ...............

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

600 There will be a tabular files (.TSV) for each sequence where each row is a residue of the sequence and the columns are the predicted features depending on the selected predictors.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

601

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

602 ::

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

603

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

604 residue_index residue agmata backbone coil disoMine earlyFolding helix ppII sheet sidechain

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

605 0 Y 0.012 0.818 0.376 0.783 0.031 0.262 0.074 0.295 0.624

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

606 1 S 0.08 0.833 0.373 0.818 0.05 0.253 0.07 0.33 0.59

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

607 2 W 0.119 0.87 0.361 0.772 0.061 0.27 0.057 0.341 0.696

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

608 3 T 0.154 0.906 0.336 0.641 0.064 0.334 0.037 0.341 0.665

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

609 4 H 0.2 0.945 0.295 0.596 0.099 0.421 0.017 0.324 0.673

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

610 5 Y 0.34 0.969 0.261 0.583 0.15 0.47 0.015 0.339 0.644

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

611 6 E 1.023 0.967 0.251 0.534 0.187 0.494 0.024 0.354 0.438

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

612 7 L 4.084 0.959 0.247 0.441 0.291 0.481 0.025 0.382 0.677

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

613 8 K 12.328 0.972 0.237 0.355 0.294 0.464 0.024 0.429 0.449

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

614 9 A 20.723 0.974 0.239 0.273 0.274 0.442 0.026 0.436 0.685

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

615 10 V 25.866 0.984 0.233 0.231 0.336 0.415 0.028 0.45 0.684

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

616 11 W 24.864 1.016 0.222 0.193 0.408 0.412 0.023 0.471 0.722

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

617 12 C 17.51 1.014 0.229 0.174 0.426 0.396 0.016 0.479 0.747

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

618 13 E 9.32 0.997 0.241 0.155 0.261 0.434 0.016 0.456 0.403

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

619 14 L 3.591 0.99 0.255 0.142 0.259 0.443 0.012 0.422 0.704

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

620 15 T 1.559 0.977 0.277 0.138 0.278 0.45 0.019 0.379 0.72

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

621 16 Y 0.64 0.969 0.299 0.134 0.282 0.428 0.025 0.353 0.656

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

622 17 W 0.221 0.976 0.317 0.135 0.262 0.415 0.027 0.328 0.704

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

623 18 R 0.084 0.957 0.331 0.132 0.147 0.41 0.029 0.295 0.462

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

624 19 S 0.038 0.956 0.342 0.148 0.142 0.393 0.028 0.289 0.627

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

625 20 W 0.031 0.947 0.355 0.182 0.178 0.379 0.031 0.304 0.71

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

626 21 T 0.035 0.964 0.333 0.205 0.187 0.393 0.023 0.305 0.705

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

627 22 H 0.052 0.976 0.286 0.228 0.19 0.451 0.013 0.309 0.663

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

628 23 Y 0.159 0.967 0.268 0.229 0.185 0.503 0.016 0.296 0.635

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

629 24 E 1.115 0.949 0.26 0.226 0.187 0.528 0.022 0.319 0.385

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

630 25 L 7.747 0.929 0.243 0.215 0.261 0.519 0.023 0.358 0.649

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

631 26 K 8.329 0.924 0.225 0.253 0.247 0.487 0.023 0.405 0.399

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

632 27 A 8.214 0.906 0.22 0.313 0.25 0.452 0.031 0.451 0.606

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

633 28 V 7.259 0.89 0.218 0.405 0.076 0.443 0.042 0.455 0.607

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

634 29 V 0.608 0.871 0.242 0.605 0.029 0.418 0.051 0.426 0.596

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

635

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

636 Plots

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

637 .....

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

638

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

639 Depending on the options selected, there will be a plot (built using ``matplotlib``)

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

640 per prediction per sequence and/or a plot per prediction for all the sequences together.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

641

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

642 - Checking **Plot** parameter implies that predicted features will be plotted in different files by input sequence.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

643 - 11 input sequences x 9 predicted features = 99 plots in PNG format

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

644 - ``sequence_01_agmata`` plot

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

645 - ``sequence_01_backbone`` plot

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

646 - ``sequence_01_coil`` plot

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

647 - ``sequence_01_disoMine`` plot

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

648 - ``sequence_01_earlyFolding`` plot

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

649 - ``sequence_01_helix`` plot

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

650 - ``sequence_01_ppII`` plot

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

651 - ``sequence_01_sheet`` plot

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

652 - ``sequence_01_sidechain`` plot

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

653 - ...

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

654 - ``sequence_11_sidechain`` plot

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

655

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

656 - Checking **Plot all** parameter implies that all the input sequences will be plotted together in order to compare predicted features.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

657 - 9 predicted features = 9 plots in PNG format

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

658 - **agmata plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``)

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

659 - **backbone plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``)

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

660 - **coil plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``)

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

661 - **disoMine plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``)

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

662 - **earlyFolding plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``)

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

663 - **helix plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``)

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

664 - **ppII plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``)

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

665 - **sheet plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``)

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

666 - **sidechain plot** containing 11 series (``sequence_01``, ``sequence_02``, ..., ``sequence_11``)

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

667

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

668 About Bio2Byte

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

669 --------------

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

670

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

671 **We research the relation between protein sequence and biophysical behavior.**

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

672

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

673 Proteins are the molecular machines that make cells work.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

674 They perform a wide variety of functions through interactions with each other and many additional molecules.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

675 Traditionally, proteins are described in a single static state (a picture).

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

676 It is now increasingly recognized that many proteins can adopt multiple states and move between these conformational states dynamically (a movie).

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

677

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

678 We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

679 Underlying physical and chemical principles are computationally unraveled through data integration,

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

680 analysis and machine learning, so connecting them to biological events and improving our understanding of the way proteins work.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

681

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

682 Visit our website for further information: https://bio2byte.be

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

683

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

684 About Bio2Byte tools

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

685 ''''''''''''''''''''

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

686 The software suite "Bio2byte tools", known as ``b2btools`` offers a set of biophysical predictions for both single protein sequences and MSA input files.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

687

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

688 **Useful links:**

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

689

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

690 ``B2bTools`` is also available on the *Python Package Index* (``PyPI``) https://pypi.org/project/b2bTools/, as well as on *Bioconda* https://bioconda.github.io/recipes/b2btools/README.html.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

691 We also provide a set of online examples in Jupyter Notebook format that are available to run on the Google Colab platform on https://github.com/Bio2Byte/public_notebooks.

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

692

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

693 ]]>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

694 </help>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

695 <creator>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

696 <organization name="bio2Byte" url="https://bio2byte.be" email="Wim.Vranken@vub.be"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

697 <organization name="Vrije Universiteit Brussel" url="https://vub.be" alternateName="VUB"/>

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

698 <person honorificPrefix="Prof." givenName="Wim" familyName="Vranken" email="Wim.Vranken@vub.be" identifier="http://orcid.org/0000-0001-7470-4324" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

699 <person givenName="Jose" familyName="Gavalda-Garcia" email="Jose.Gavalda.Garcia@vub.be" identifier="http://orcid.org/0000-0001-6431-3442" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

700 <person givenName="Adrian" familyName="Diaz" email="Adrian.Diaz@vub.be" identifier="http://orcid.org/0000-0003-0165-1318" />

b694a77ca1e8 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc