b2btools_single_sequence: b2btools_single

author	iuc
date	Tue, 09 Aug 2022 12:29:40 +0000
parents
children

rev	line source
0 dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	1 <tool
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	2 id="b2btools_single_sequence"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	3 name="b2bTools: Biophysical predictors for single sequences"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	4 version="3.0.5+galaxy0"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	5 license="GPL-3.0"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	6 python_template_version="3.5"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	7 profile="21.05">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	8 <description>from their amino-acid sequences</description>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	9 <xrefs>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	10 <xref type="bio.tools">b2btools</xref>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	11 </xrefs>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	12 <requirements>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	13 <requirement type="package" version="3.0.5">b2btools</requirement>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	14 </requirements>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	15 <command detect_errors="exit_code"><![CDATA[
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	16 mkdir -p ./tabular ./plots &&
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	17 python '$__tool_directory__/script.py' --file '$input' --output ./tabular --json '$predictions_output'
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	18 $section_predictors.dynamine
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	19 $section_predictors.disomine
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	20 $section_predictors.efoldmine
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	21 $section_predictors.agmata
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	22 #if $section_plot.plot == '--plot' or $section_plot.plot_all == '--plot_all':
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	23 --plot-output ./plots
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	24 #end if
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	25 $section_plot.plot
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	26 $section_plot.plot_all
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	27 $section_plot.highlight
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	28 ]]></command>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	29 <inputs>
dc91f5626375 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"/>
dc91f5626375 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">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	32 <param
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	33 argument="--dynamine"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	34 type="boolean"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	35 checked="true"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	36 truevalue="--dynamine"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	37 falsevalue=""
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	38 label="DynaMine: Prediction of protein backbone dynamics from sequence only"
dc91f5626375 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." />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	40 <param
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	41 argument="--disomine"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	42 type="boolean"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	43 checked="true"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	44 truevalue="--disomine"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	45 falsevalue=""
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	46 label="DisoMine: Prediction of protein disorder from sequence only"
dc91f5626375 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."/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	48 <param
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	49 argument="--efoldmine"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	50 type="boolean"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	51 checked="true"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	52 truevalue="--efoldmine"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	53 falsevalue=""
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	54 label="EFoldMine: Prediction of protein early folding regions from sequence only"
dc91f5626375 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."/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	56 <param
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	57 argument="--agmata"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	58 type="boolean"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	59 checked="true"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	60 truevalue="--agmata"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	61 falsevalue=""
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	62 label="Agmata: Prediction of protein regions that are likely to cause beta-aggregation"
dc91f5626375 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."/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	64 </section>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	65 <section name="section_plot" title="Plot options" help="Configure plot output">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	66 <param
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	67 name="plot"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	68 argument="--plot"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	69 type="boolean"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	70 label="Plot predicted values by sequence"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	71 truevalue="--plot"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	72 falsevalue=""
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	73 help="This option plots predicted values in different files"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	74 <param
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	75 name="plot_all"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	76 argument="--plot_all"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	77 type="boolean"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	78 label="Plot all sequences together"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	79 truevalue="--plot_all"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	80 falsevalue=""
dc91f5626375 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"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	82 <param
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	83 name="highlight"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	84 argument="--highlight"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	85 type="boolean"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	86 label="Highlight regions of interest"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	87 truevalue="--highlight"
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	88 falsevalue=""
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	89 help="Highlight biophysical regions on the background of the plots"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	90 </section>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	91 </inputs>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	92 <outputs>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	93 <data name="predictions_output" label="Predictions in JSON format" format="json" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	94 <collection name="split_output" type="list" label="Tabular predictions by sequence">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	95 <discover_datasets pattern="__name_and_ext__" format="tabular" directory="tabular" visible="true" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	96 </collection>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	97 <collection name="split_output_plots" type="list" label="Plots">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	98 <discover_datasets pattern="__name_and_ext__" format="png" directory="plots" visible="true" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	99 </collection>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	100 </outputs>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	101 <tests>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	102 <!-- Test 1: All the predictors were selected, plotting both individual and aggregated charts -->
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	103 <test expect_exit_code="0" expect_num_outputs="3">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	104 <param name="input" value="input.fasta" ftype="fasta"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	105 <section name="section_predictors">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	106 <param name="dynamine" value="true"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	107 <param name="disomine" value="true"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	108 <param name="efoldmine" value="true"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	109 <param name="agmata" value="true"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	110 </section>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	111 <section name="section_plot">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	112 <param name="plot" value="true"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	113 <param name="plot_all" value="true"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	114 <param name="highlight" value="true"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	115 </section>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	116 <assert_command>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	117 <has_text text="--dynamine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	118 <has_text text="--disomine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	119 <has_text text="--agmata" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	120 <has_text text="--efoldmine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	121 <has_text text="--json" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	122 <has_text text="--plot_all" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	123 <has_text text="--highlight" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	124 <has_text text="--highlight" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	125 <has_text text="--output" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	126 <has_text text="--plot-output" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	127 </assert_command>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	128 <output name="predictions_output" value="test_output.json" ftype="json"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	129 <!-- 11 sequences = 11 TSV files -->
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	130 <output_collection name="split_output" type="list" count="11">
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	142 </output_collection>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	143 <!-- 9 predicted values x 11 sequences + 9 predicted values aggregated = (99 + 9) charts = 108 charts -->
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	144 <output_collection name="split_output_plots" type="list" count="108" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	145 </test>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	146 <!-- Test 2: Only one predictor was selected, plotting both individual and aggregated charts -->
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	147 <test expect_exit_code="0" expect_num_outputs="3">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	148 <param name="input" value="input.fasta" ftype="fasta"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	149 <section name="section_predictors">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	150 <param name="dynamine" value="true"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	151 <param name="disomine" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	152 <param name="efoldmine" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	153 <param name="agmata" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	154 </section>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	155 <section name="section_plot">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	156 <param name="plot" value="true"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	157 <param name="plot_all" value="true"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	158 <param name="highlight" value="true"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	159 </section>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	160 <assert_command>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	161 <has_text text="--dynamine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	162 <not_has_text text="--disomine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	163 <not_has_text text="--agmata" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	164 <not_has_text text="--efoldmine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	165 <has_text text="--json" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	166 <has_text text="--plot " />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	167 <has_text text="--plot_all" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	168 <has_text text="--highlight" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	169 <has_text text="--output" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	170 <has_text text="--plot-output" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	171 </assert_command>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	172 <output name="predictions_output" value="test_output_dynamine.json" ftype="json"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	173 <!-- 11 sequences = 11 TSV files -->
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	174 <output_collection name="split_output" type="list" count="11">
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	186 </output_collection>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	187 <!-- 6 predicted values x 11 sequences + 6 predicted values aggregated = (66 + 6) charts = 72 charts -->
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	188 <output_collection name="split_output_plots" type="list" count="72" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	189 </test>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	190 <!-- Test 3: Only one predictor was selected, plotting individual charts -->
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	191 <test expect_exit_code="0" expect_num_outputs="3">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	192 <param name="input" value="input.fasta" ftype="fasta"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	193 <section name="section_predictors">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	194 <param name="dynamine" value="true"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	195 <param name="disomine" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	196 <param name="efoldmine" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	197 <param name="agmata" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	198 </section>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	199 <section name="section_plot">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	200 <param name="plot" value="true"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	201 <param name="plot_all" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	202 <param name="highlight" value="true"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	203 </section>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	204 <assert_command>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	205 <has_text text="--dynamine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	206 <not_has_text text="--disomine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	207 <not_has_text text="--agmata" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	208 <not_has_text text="--efoldmine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	209 <has_text text="--json" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	210 <has_text text="--plot " />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	211 <not_has_text text="--plot_all" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	212 <has_text text="--highlight" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	213 <has_text text="--output" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	214 <has_text text="--plot-output" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	215 </assert_command>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	216 <output name="predictions_output" value="test_output_dynamine.json" ftype="json"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	217 <!-- 11 sequences = 11 TSV files -->
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	218 <output_collection name="split_output" type="list" count="11">
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	230 </output_collection>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	231 <!-- 6 predicted values x 11 sequences = 66 charts -->
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	232 <output_collection name="split_output_plots" type="list" count="66" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	233 </test>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	234 <!-- Test 4: Only one predictor was selected, plotting aggregated charts -->
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	235 <test expect_exit_code="0" expect_num_outputs="3">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	236 <param name="input" value="input.fasta" ftype="fasta"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	237 <section name="section_predictors">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	238 <param name="dynamine" value="true"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	239 <param name="disomine" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	240 <param name="efoldmine" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	241 <param name="agmata" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	242 </section>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	243 <section name="section_plot">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	244 <param name="plot" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	245 <param name="plot_all" value="true"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	246 <param name="highlight" value="true"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	247 </section>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	248 <assert_command>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	249 <has_text text="--dynamine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	250 <not_has_text text="--disomine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	251 <not_has_text text="--agmata" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	252 <not_has_text text="--efoldmine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	253 <has_text text="--json" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	254 <has_text text="--plot_all" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	255 <has_text text="--highlight" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	256 <not_has_text text="--plot " />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	257 <has_text text="--output" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	258 <has_text text="--plot-output" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	259 </assert_command>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	260 <output name="predictions_output" value="test_output_dynamine.json" ftype="json"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	261 <!-- 11 sequences = 11 TSV files -->
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	262 <output_collection name="split_output" type="list" count="11">
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	274 </output_collection>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	275 <!-- 6 predicted values aggregated = 6 charts -->
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	276 <output_collection name="split_output_plots" type="list" count="6" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	277 </test>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	278 <!-- Test 5: Only one predictor was selected, plotting aggregated charts with no highlighting -->
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	279 <test expect_exit_code="0" expect_num_outputs="3">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	280 <param name="input" value="input.fasta" ftype="fasta"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	281 <section name="section_predictors">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	282 <param name="dynamine" value="true"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	283 <param name="disomine" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	284 <param name="efoldmine" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	285 <param name="agmata" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	286 </section>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	287 <section name="section_plot">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	288 <param name="plot" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	289 <param name="plot_all" value="true"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	290 </section>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	291 <assert_command>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	292 <has_text text="--dynamine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	293 <has_text text="--json" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	294 <has_text text="--plot_all" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	295 <has_text text="--output" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	296 <has_text text="--plot-output" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	297 <not_has_text text="--disomine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	298 <not_has_text text="--agmata" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	299 <not_has_text text="--efoldmine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	300 <not_has_text text="--highlight" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	301 <not_has_text text="--plot " />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	302 </assert_command>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	303 <output name="predictions_output" value="test_output_dynamine.json" ftype="json"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	304 <!-- 11 sequences = 11 TSV files -->
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	305 <output_collection name="split_output" type="list" count="11">
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	317 </output_collection>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	318 <!-- 6 predicted values aggregated = 6 charts -->
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	319 <output_collection name="split_output_plots" type="list" count="6" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	320 </test>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	321 <!-- Test 6: Only one predictor was selected, plotting was disabled -->
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	322 <test expect_exit_code="0" expect_num_outputs="3">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	323 <param name="input" value="input.fasta" ftype="fasta"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	324 <section name="section_predictors">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	325 <param name="dynamine" value="true"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	326 <param name="disomine" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	327 <param name="efoldmine" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	328 <param name="agmata" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	329 </section>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	330 <section name="section_plot">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	331 <param name="plot" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	332 <param name="plot_all" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	333 <param name="highlight" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	334 </section>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	335 <assert_command>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	336 <has_text text="--dynamine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	337 <has_text text="--json" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	338 <has_text text="--output" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	339 <not_has_text text="--disomine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	340 <not_has_text text="--agmata" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	341 <not_has_text text="--efoldmine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	342 <not_has_text text="--plot " />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	343 <not_has_text text="--plot_all" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	344 <not_has_text text="--highlight" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	345 <not_has_text text="--plot-output" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	346 </assert_command>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	347 <output name="predictions_output" value="test_output_dynamine.json" ftype="json"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	348 <!-- 11 sequences = 11 TSV files -->
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	349 <output_collection name="split_output" type="list" count="11">
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 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"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	361 </output_collection>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	362 <output_collection name="split_output_plots" type="list" count="0" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	363 </test>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	364 <!-- Test 7: No predictor selected, it must fail -->
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	365 <test expect_failure="true" expect_exit_code="2">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	366 <param name="input" value="input.fasta" ftype="fasta"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	367 <section name="section_predictors">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	368 <param name="dynamine" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	369 <param name="disomine" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	370 <param name="efoldmine" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	371 <param name="agmata" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	372 </section>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	373 <section name="section_plot">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	374 <param name="plot" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	375 <param name="plot_all" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	376 <param name="highlight" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	377 </section>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	378 <assert_command>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	379 <not_has_text text="--dynamine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	380 <not_has_text text="--disomine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	381 <not_has_text text="--agmata" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	382 <not_has_text text="--efoldmine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	383 <not_has_text text="--plot-output" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	384 <not_has_text text="--plot " />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	385 <not_has_text text="--plot_all" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	386 <not_has_text text="--highlight" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	387 </assert_command>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	388 </test>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	389 <!-- Test 8: No input file, it must fail -->
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	390 <test expect_failure="true" expect_exit_code="1">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	391 <section name="section_predictors">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	392 <param name="dynamine" value="true"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	393 <param name="disomine" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	394 <param name="efoldmine" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	395 <param name="agmata" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	396 </section>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	397 <section name="section_plot">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	398 <param name="plot" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	399 <param name="plot_all" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	400 <param name="highlight" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	401 </section>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	402 <assert_command>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	403 <has_text text="--dynamine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	404 <not_has_text text="--disomine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	405 <not_has_text text="--agmata" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	406 <not_has_text text="--efoldmine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	407 <not_has_text text="--plot-output" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	408 <not_has_text text="--plot " />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	409 <not_has_text text="--plot_all" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	410 <not_has_text text="--highlight" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	411 </assert_command>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	412 </test>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	413 <!-- Test 9: No valid input file format, it must fail -->
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	414 <test expect_failure="true" expect_exit_code="1">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	415 <param name="input" value="wrong.fasta" ftype="fasta"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	416 <section name="section_predictors">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	417 <param name="dynamine" value="true"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	418 <param name="disomine" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	419 <param name="efoldmine" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	420 <param name="agmata" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	421 </section>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	422 <section name="section_plot">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	423 <param name="plot" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	424 <param name="plot_all" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	425 <param name="highlight" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	426 </section>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	427 <assert_command>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	428 <has_text text="--dynamine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	429 <not_has_text text="--disomine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	430 <not_has_text text="--agmata" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	431 <not_has_text text="--efoldmine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	432 <not_has_text text="--plot-output" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	433 <not_has_text text="--plot " />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	434 <not_has_text text="--plot_all" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	435 <not_has_text text="--highlight" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	436 </assert_command>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	437 </test>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	438 <!-- Test 10: Wrong input file type, it must fail -->
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	439 <test expect_failure="true" expect_exit_code="1">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	440 <param name="input" value="wrong.tsv" ftype="tabular"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	441 <section name="section_predictors">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	442 <param name="dynamine" value="true"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	443 <param name="disomine" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	444 <param name="efoldmine" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	445 <param name="agmata" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	446 </section>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	447 <section name="section_plot">
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	448 <param name="plot" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	449 <param name="plot_all" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	450 <param name="highlight" value="false"/>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	451 </section>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	452 <assert_command>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	453 <has_text text="--dynamine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	454 <not_has_text text="--disomine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	455 <not_has_text text="--agmata" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	456 <not_has_text text="--efoldmine" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	457 <not_has_text text="--plot-output" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	458 <not_has_text text="--plot " />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	459 <not_has_text text="--plot_all" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	460 <not_has_text text="--highlight" />
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	461 </assert_command>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	462 </test>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	463 </tests>
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	464 <help><![CDATA[
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	465 Single protein sequence analysis
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	466 --------------------------------
dc91f5626375 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.
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	468 It means that this tool receives amino-acid sequences in FASTA format and
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	469 will return the biophysical predictions depending on the predictors selected.
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	470
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	471 Input sequences
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	472 '''''''''''''''
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	473 The tool works with either single or multiple input files, just keeping in mind that
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	474 the file must be a valid FASTA containing at least one sequence of amino acids.
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	475
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	476 There is no limitation on the number of sequences per file, however, all
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	477 the sequences must have at least 5 residues.
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	478
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	479 Available biophysical predictors
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	480 ''''''''''''''''''''''''''''''''
dc91f5626375 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
dc91f5626375 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:
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	483
dc91f5626375 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.
dc91f5626375 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.
dc91f5626375 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.
dc91f5626375 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.
dc91f5626375 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.
dc91f5626375 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.
dc91f5626375 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.
dc91f5626375 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.
dc91f5626375 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.
dc91f5626375 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.
dc91f5626375 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.
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	495 - Agmata: Beta-sheet aggregation with the following predicted features:
dc91f5626375 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.
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	497
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	498 Expected results
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	499 ''''''''''''''''
dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75 iuc parents: diff changeset	500 From a single FASTA file with N sequences, the process will produce:

0

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1 <tool

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2 id="b2btools_single_sequence"

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

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4 version="3.0.5+galaxy0"

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5 license="GPL-3.0"

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6 python_template_version="3.5"

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7 profile="21.05">

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

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9 <xrefs>

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

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11 </xrefs>

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12 <requirements>

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

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14 </requirements>

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

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

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

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18 $section_predictors.dynamine

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19 $section_predictors.disomine

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20 $section_predictors.efoldmine

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21 $section_predictors.agmata

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

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23 --plot-output ./plots

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24 #end if

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25 $section_plot.plot

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26 $section_plot.plot_all

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27 $section_plot.highlight

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28 ]]></command>

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29 <inputs>

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

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

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32 <param

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33 argument="--dynamine"

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34 type="boolean"

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35 checked="true"

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36 truevalue="--dynamine"

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37 falsevalue=""

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parents:

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

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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." />

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parents:

diff changeset

40 <param

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41 argument="--disomine"

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42 type="boolean"

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parents:

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43 checked="true"

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parents:

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44 truevalue="--disomine"

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parents:

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45 falsevalue=""

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iuc

parents:

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

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iuc

parents:

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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."/>

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diff changeset

48 <param

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49 argument="--efoldmine"

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50 type="boolean"

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51 checked="true"

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52 truevalue="--efoldmine"

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53 falsevalue=""

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parents:

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

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parents:

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

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56 <param

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57 argument="--agmata"

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58 type="boolean"

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59 checked="true"

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60 truevalue="--agmata"

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61 falsevalue=""

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parents:

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

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parents:

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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."/>

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64 </section>

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

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66 <param

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67 name="plot"

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68 argument="--plot"

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69 type="boolean"

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70 label="Plot predicted values by sequence"

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71 truevalue="--plot"

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72 falsevalue=""

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

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74 <param

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75 name="plot_all"

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76 argument="--plot_all"

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77 type="boolean"

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78 label="Plot all sequences together"

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79 truevalue="--plot_all"

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80 falsevalue=""

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

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82 <param

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83 name="highlight"

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84 argument="--highlight"

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85 type="boolean"

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86 label="Highlight regions of interest"

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87 truevalue="--highlight"

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88 falsevalue=""

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

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90 </section>

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91 </inputs>

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92 <outputs>

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

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

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

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96 </collection>

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

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

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99 </collection>

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100 </outputs>

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101 <tests>

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102

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

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

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105 <section name="section_predictors">

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

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

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

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

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110 </section>

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111 <section name="section_plot">

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

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

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

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115 </section>

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116 <assert_command>

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

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

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

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

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

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

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

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

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

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

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127 </assert_command>

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

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129

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

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

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

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

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parents:

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

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

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

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parents:

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

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parents:

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

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

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

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

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142 </output_collection>

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143

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

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145 </test>

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146

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

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parents:

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

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149 <section name="section_predictors">

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

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

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

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

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154 </section>

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155 <section name="section_plot">

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

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

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

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159 </section>

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160 <assert_command>

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

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

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

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

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

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

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

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

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

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

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171 </assert_command>

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

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173

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

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

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

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

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

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

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

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

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

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

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

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

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186 </output_collection>

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187

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

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189 </test>

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190

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

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

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193 <section name="section_predictors">

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

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

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

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

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198 </section>

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199 <section name="section_plot">

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

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

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

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203 </section>

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204 <assert_command>

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

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

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

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

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

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

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

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

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

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

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215 </assert_command>

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

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217

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

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

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

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

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

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

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

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

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

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

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

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

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230 </output_collection>

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231

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

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233 </test>

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234

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

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

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237 <section name="section_predictors">

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

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

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

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

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242 </section>

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243 <section name="section_plot">

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

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

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

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247 </section>

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248 <assert_command>

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

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

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

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

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

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

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

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

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

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

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259 </assert_command>

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

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261

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

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

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

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

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

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

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

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

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

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

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

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

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274 </output_collection>

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275

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

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277 </test>

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278

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

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

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281 <section name="section_predictors">

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

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

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

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

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286 </section>

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287 <section name="section_plot">

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

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

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290 </section>

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291 <assert_command>

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

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

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

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

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

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

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

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

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

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

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302 </assert_command>

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

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304

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

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

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

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

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

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

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

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

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

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

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

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

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317 </output_collection>

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318

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

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320 </test>

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321

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

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

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324 <section name="section_predictors">

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

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

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

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

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329 </section>

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330 <section name="section_plot">

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

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

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

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334 </section>

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335 <assert_command>

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

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

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

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

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

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

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

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

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

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

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346 </assert_command>

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

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348

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

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

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

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

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

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

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

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

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

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

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

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

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361 </output_collection>

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

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363 </test>

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364

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

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

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367 <section name="section_predictors">

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

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

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

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

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372 </section>

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373 <section name="section_plot">

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

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

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

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377 </section>

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378 <assert_command>

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

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

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

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

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

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

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

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

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387 </assert_command>

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388 </test>

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389

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

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391 <section name="section_predictors">

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

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

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

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

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396 </section>

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397 <section name="section_plot">

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

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

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

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401 </section>

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402 <assert_command>

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

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

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

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

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

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

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

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

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411 </assert_command>

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412 </test>

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413

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

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

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416 <section name="section_predictors">

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

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

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

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

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421 </section>

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422 <section name="section_plot">

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

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

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

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426 </section>

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427 <assert_command>

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

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

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

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

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

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

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

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

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436 </assert_command>

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437 </test>

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438

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

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

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441 <section name="section_predictors">

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

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

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

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

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446 </section>

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447 <section name="section_plot">

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

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

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

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451 </section>

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452 <assert_command>

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

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

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

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

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

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

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

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

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461 </assert_command>

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462 </test>

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463 </tests>

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464 <help><![CDATA[

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465 Single protein sequence analysis

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

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

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

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

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470

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471 Input sequences

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

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

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

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475

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

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477 the sequences must have at least 5 residues.

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478

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479 Available biophysical predictors

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

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

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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:

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483

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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.

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

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

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

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

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

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

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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.

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

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

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

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

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

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497

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498 Expected results

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

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

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501

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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.

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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

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

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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

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506

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507 Example

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508 ~~~~~~~

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509

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510 Given this input in FASTA format with 11 sequences:

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511 ::

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512

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513 >random_sequence_01_consisting_of_40_residues

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514 MDRHDPVQKSMMMDRHDPVQKMDRHDPVQKSDRHDPVQKS

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515

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516 >random_sequence_02_consisting_of_40_residues

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517 MWSMWRAMWSSQRAMWSMWRAMWSMSQRAMWSMWRAMWSM

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518

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519 >random_sequence_03_consisting_of_30_residues

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520 YSWTHYELKAVWCELTYWRSWTHYELKAVV

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521

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522 >random_sequence_04_consisting_of_40_residues

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523 SWTHYEYSWTHYELKAVWCELTYWRSWTHYELKAVVLKAV

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524

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

525 >random_sequence_05_consisting_of_30_residues

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

526 NCPIEHHLCANKMDLHHHHLCAHHLPEDQY

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

527

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

528 >random_sequence_06_consisting_of_45_residues

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

529 YACLFQKPYIHHLCANKMDLHHNKMDLHHHHLCAHHLHHLCAHHL

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

530

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

531 >random_sequence_07_consisting_of_30_residues

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

532 FHHLCANKMDLHHHHLCAHHLVPGKQEPDS

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iuc

parents:

diff changeset

533

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

534 >random_sequence_08_consisting_of_40_residues

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

535 HHLCANKMDLHHHHLCAHHLCANKMDLNKMDLLCANKMDL

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iuc

parents:

diff changeset

536

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

537 >random_sequence_09_consisting_of_30_residues

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

538 GNKTPFMKMHGGNKTPFMKMHNKTPFMKMH

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

539

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

540 >random_sequence_10_consisting_of_65_residues

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

541 LDNSKMWQLDNPMPMSKMWQLDNSKMWQLDNLDNSKMWQLDNPMPMSKMWQLDNSKMWQLDNAAA

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

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parents:

diff changeset

542

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

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parents:

diff changeset

543 >random_sequence_11_consisting_of_30_residues

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

544 PMSKMWQLDNMSKMWQLDNPMSKMWQLDNA

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

545

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

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

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

547

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

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548 JSON result

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

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

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

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parents:

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

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

551 ::

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

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parents:

diff changeset

552

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

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553 {

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parents:

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554 "random_sequence_03_consisting_of_30_residues": {

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

555 "agmata": [

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

556 0.012,

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

557 0.08,

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

558 0.119,

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

559 0.154,

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

560 0.2,

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

561 0.34,

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

562 1.023,

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

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parents:

diff changeset

563 4.084,

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

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parents:

diff changeset

564 12.328,

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

565 20.723,

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

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parents:

diff changeset

566 25.866,

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parents:

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567 24.864,

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parents:

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568 17.509,

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iuc

parents:

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569 9.32,

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parents:

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570 3.591,

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iuc

parents:

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571 1.559,

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

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572 0.64,

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iuc

parents:

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573 0.221,

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iuc

parents:

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574 0.084,

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

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575 0.038,

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iuc

parents:

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576 0.031,

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parents:

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577 0.035,

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

578 0.052,

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iuc

parents:

diff changeset

579 0.159,

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parents:

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580 1.115,

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iuc

parents:

diff changeset

581 7.747,

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

diff changeset

582 8.329,

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

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parents:

diff changeset

583 8.214,

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

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parents:

diff changeset

584 7.259,

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

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parents:

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585 0.608

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

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parents:

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586 ],

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parents:

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587 "backbone": [

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iuc

parents:

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588 0.818,

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parents:

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589 0.833,

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

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590 0.87,

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iuc

parents:

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591 ...

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parents:

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592 ],

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parents:

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593 ...

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parents:

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594 },

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

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595 ...

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

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596 }

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parents:

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597

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parents:

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598 Tabular results

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

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

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

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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.

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parents:

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601

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

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602 ::

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parents:

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603

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

iuc

parents:

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

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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

dc91f5626375 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

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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

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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

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parents:

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

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iuc

parents:

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

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iuc

parents:

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

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iuc

parents:

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

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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

dc91f5626375 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

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

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iuc

parents:

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

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parents:

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

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parents:

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

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parents:

diff changeset

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

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

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

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

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

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

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iuc

parents:

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

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parents:

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

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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

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iuc

parents:

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

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

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iuc

parents:

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

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

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

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

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

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635

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636 Plots

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parents:

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637 .....

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638

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parents:

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

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iuc

parents:

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

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641

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parents:

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

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parents:

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

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parents:

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644 - ``sequence_01_agmata`` plot

dc91f5626375 planemo upload commit 599e1135baba020195b3f7576449d595bca9af75

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parents:

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645 - ``sequence_01_backbone`` plot

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parents:

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646 - ``sequence_01_coil`` plot

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parents:

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647 - ``sequence_01_disoMine`` plot

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648 - ``sequence_01_earlyFolding`` plot

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parents:

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649 - ``sequence_01_helix`` plot

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650 - ``sequence_01_ppII`` plot

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parents:

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651 - ``sequence_01_sheet`` plot

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parents:

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652 - ``sequence_01_sidechain`` plot

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parents:

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653 - ...

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parents:

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654 - ``sequence_11_sidechain`` plot

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655

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

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657 - 9 predicted features = 9 plots in PNG format

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

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

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

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

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

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

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

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

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

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667

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668 About Bio2Byte

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

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670

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

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672

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673 Proteins are the molecular machines that make cells work.

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

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

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

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677

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

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

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

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681

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

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683

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684 About Bio2Byte tools

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

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

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687

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688 **Useful links:**

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689

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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.

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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.

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692

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693 ]]>

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694 </help>

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695 <creator>

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

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

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

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

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

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