Mercurial > repos > iuc > rrmscorer

annotate RRMScorer.xml @ 0:2e9c4504af91 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
author iuc
date Wed, 17 Sep 2025 14:53:19 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
1 <tool id="rrmscorer" name="RRM-Scorer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
2 <description>Predicts RNA Recognition Motif (RRM) scores</description>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
3 <macros>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
4 <import>macros.xml</import>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
5 </macros>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
6 <xrefs>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
7 <xref type="bio.tools">RRMScorer</xref>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
8 </xrefs>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
9 <expand macro="requirements"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
11 mkdir -p json tabular aligned plots &&
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
12 rrmscorer
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
13 --json 'json'
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
14 --csv 'tabular'
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
15 --window_size $tool_parameters.window_size
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
16 #if str($input_sequence.input_type_cond.input_type) == 'fasta'
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
17 --fasta '$input_sequence.input_type_cond.fasta_input'
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
18 #elif str($input_sequence.input_type_cond.input_type) == 'uniprot'
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
19 --uniprot '$input_sequence.input_type_cond.uniprot_id'
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
20 #end if
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
21
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
22 #if $output_options.generate_plots
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
23 --plot 'plots'
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
24 #end if
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
25
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
26 #if $output_options.generate_fasta
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
27 --aligned 'aligned'
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
28 #end if
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
29
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
30 #if $tool_parameters.target and not $output_options.top_scoring_rna
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
31 --rna '$tool_parameters.target'
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
32 #else
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
33 --top
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
34 #end if
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
35 ]]></command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
36 <inputs>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
37 <section name="input_sequence" title="Input sequence" expanded="true">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
38 <conditional name="input_type_cond">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
39 <param name="input_type" type="select" label="Select the type of sequence input" optional="false">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
40 <option value="fasta" selected="true">FASTA file containing the protein sequence(s)</option>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
41 <option value="uniprot">Protein identifier from UniProt</option>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
42 </param>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
43 <when value="fasta">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
44 <param name="fasta_input" type="data" format="fasta" optional="false" multiple="false" label="Protein sequence(s) in FASTA format" help="Provide a FASTA file containing the protein sequences.">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
45 <validator type="dataset_ok_validator"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
46 </param>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
47 </when>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
48 <when value="uniprot">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
49 <param name="uniprot_id" type="text" value="" optional="false" label="Protein identifier from UniProt" help="Provide a UniProt ID (e.g. P19339).">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
50 <validator type="empty_field" message="Missing UniProt ID"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
51 </param>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
52 </when>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
53 </conditional>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
54 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
55 <section name="tool_parameters" title="Tool parameters" help="Configure this section to select the predictions to be executed">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
56 <param name="target" type="text" optional="true" label="Target RNA sequence (min. 5 nucleotides)" help="Provide a valid target RNA sequence. Leave blank if not specifying a target RNA so that the predictor will use the top-scoring RNA by default.">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
57 <validator type="regex" message="The sequence must consist only of RNA nucleotides (A, U, G, C) or be left blank.">^([AUGCaugc]+)?$</validator>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
58 </param>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
59 <param name="window_size" type="select" label="The window size to test">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
60 <option value="5" selected="true">5</option>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
61 <option value="3">3</option>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
62 </param>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
63 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
64 <section name="output_options" title="Output parameters" help="Configure this section to define the tool output files">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
65 <param name="generate_plots" type="boolean" label="Generate score plots for all the RNA possible windows" help="Enable to generate score plots."/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
66 <param name="top_scoring_rna" type="boolean" label="Find the top-scoring RNA for the specified RRM(s)" help="Enable to find and plot the top-scoring RNA. Attention: This option overrides the target RNA if present."/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
67 <param name="generate_fasta" type="boolean" label="Generate a FASTA file for each input sequence aligned to the HMM" help="Enable to generate a FASTA file with aligned sequences."/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
68 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
69 </inputs>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
70 <outputs>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
71 <collection name="split_csv" type="list" label="Tabular predictions by sequence">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
72 <discover_datasets pattern="__designation_and_ext__" directory="tabular" visible="true"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
73 </collection>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
74 <collection name="split_json" type="list" label="Json predictions by sequence">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
75 <discover_datasets pattern="__designation_and_ext__" directory="json" visible="true"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
76 </collection>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
77 <collection name="split_aligned" type="list" label="Alignment in FASTA format by sequence">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
78 <discover_datasets pattern="__designation_and_ext__" directory="aligned" visible="true"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
79 </collection>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
80 <collection name="split_plots" type="list" label="Plots by sequence">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
81 <discover_datasets pattern="__designation_and_ext__" directory="plots" visible="true"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
82 </collection>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
83 </outputs>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
84 <tests>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
85 <!-- Test 1: UniProt ID P19339, Window Size 5, RNA AUGGCU -->
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
86 <test expect_num_outputs="4">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
87 <section name="input_sequence">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
88 <conditional name="input_type_cond">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
89 <param name="input_type" value="uniprot"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
90 <param name="uniprot_id" value="P19339"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
91 </conditional>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
92 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
93 <section name="tool_parameters">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
94 <param name="target" value="AUGGCU"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
95 <param name="window_size" value="5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
96 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
97 <assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
98 <has_text text="--uniprot 'P19339'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
99 <has_text text="--rna 'AUGGCU'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
100 <has_text text="--window_size 5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
101 <has_text text="--json 'json'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
102 <has_text text="--csv 'tabular'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
103 </assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
104 <output_collection name="split_json" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
105 <output_collection name="split_csv" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
106 <output_collection name="split_aligned" count="0"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
107 <output_collection name="split_plots" count="0"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
108 </test>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
109 <!-- Test 2: UniProt ID P19339, Window Size 3, RNA AUGGCU -->
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
110 <test expect_num_outputs="4">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
111 <section name="input_sequence">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
112 <conditional name="input_type_cond">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
113 <param name="input_type" value="uniprot"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
114 <param name="uniprot_id" value="P19339"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
115 </conditional>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
116 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
117 <section name="tool_parameters">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
118 <param name="target" value="AUGGCU"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
119 <param name="window_size" value="3"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
120 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
121 <assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
122 <has_text text="--uniprot 'P19339'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
123 <has_text text="--rna 'AUGGCU'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
124 <has_text text="--window_size 3"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
125 <has_text text="--json 'json'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
126 <has_text text="--csv 'tabular'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
127 </assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
128 <output_collection name="split_json" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
129 <output_collection name="split_csv" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
130 <output_collection name="split_aligned" count="0"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
131 <output_collection name="split_plots" count="0"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
132 </test>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
133 <!-- Test 3: UniProt ID P19339, Window Size 5, RNA AUGGCU, Aligned FASTA files -->
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
134 <test expect_num_outputs="4">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
135 <section name="input_sequence">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
136 <conditional name="input_type_cond">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
137 <param name="input_type" value="uniprot"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
138 <param name="uniprot_id" value="P19339"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
139 </conditional>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
140 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
141 <section name="tool_parameters">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
142 <param name="target" value="AUGGCU"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
143 <param name="window_size" value="5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
144 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
145 <section name="output_options">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
146 <param name="generate_fasta" value="true"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
147 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
148 <assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
149 <has_text text="--uniprot 'P19339'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
150 <has_text text="--rna 'AUGGCU'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
151 <has_text text="--window_size 5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
152 <has_text text="--json 'json'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
153 <has_text text="--csv 'tabular'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
154 <has_text text="--aligned 'aligned'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
155 </assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
156 <output_collection name="split_json" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
157 <output_collection name="split_csv" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
158 <output_collection name="split_aligned" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
159 <output_collection name="split_plots" count="0"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
160 </test>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
161 <!-- Test 4: UniProt ID P19339, Window Size 5, Top RNA, with Plots -->
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
162 <test expect_num_outputs="4">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
163 <section name="input_sequence">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
164 <conditional name="input_type_cond">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
165 <param name="input_type" value="uniprot"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
166 <param name="uniprot_id" value="P19339"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
167 </conditional>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
168 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
169 <section name="tool_parameters">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
170 <param name="window_size" value="5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
171 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
172 <section name="output_options">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
173 <param name="top_scoring_rna" value="true"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
174 <param name="generate_plots" value="true"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
175 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
176 <assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
177 <has_text text="--uniprot 'P19339'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
178 <has_text text="--window_size 5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
179 <has_text text="--json 'json'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
180 <has_text text="--csv 'tabular'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
181 <has_text text="--top"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
182 </assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
183 <output_collection name="split_json" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
184 <output_collection name="split_csv" count="0"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
185 <output_collection name="split_aligned" count="0"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
186 <output_collection name="split_plots" count="8"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
187 </test>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
188 <!-- Test 5: UniProt ID P19339, Window Size 5, Top RNA, with Plots, Aligned FASTA files -->
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
189 <test expect_num_outputs="4">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
190 <section name="input_sequence">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
191 <conditional name="input_type_cond">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
192 <param name="input_type" value="uniprot"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
193 <param name="uniprot_id" value="P19339"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
194 </conditional>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
195 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
196 <section name="tool_parameters">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
197 <param name="window_size" value="5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
198 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
199 <section name="output_options">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
200 <param name="top_scoring_rna" value="true"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
201 <param name="generate_plots" value="true"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
202 <param name="generate_fasta" value="true"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
203 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
204 <assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
205 <has_text text="--uniprot 'P19339'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
206 <has_text text="--window_size 5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
207 <has_text text="--json 'json'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
208 <has_text text="--csv 'tabular'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
209 <has_text text="--plot 'plots'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
210 <has_text text="--aligned 'aligned'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
211 <has_text text="--top"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
212 </assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
213 <output_collection name="split_json" type="list" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
214 <output_collection name="split_aligned" type="list" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
215 <output_collection name="split_plots" type="list" count="8"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
216 </test>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
217 <!-- Test 6: UniProt ID P19339, Window Size 5, RNA AUGGCU, with Plots -->
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
218 <test expect_num_outputs="4">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
219 <section name="input_sequence">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
220 <conditional name="input_type_cond">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
221 <param name="input_type" value="uniprot"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
222 <param name="uniprot_id" value="P19339"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
223 </conditional>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
224 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
225 <section name="tool_parameters">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
226 <param name="target" value="AUGGCU"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
227 <param name="window_size" value="5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
228 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
229 <section name="output_options">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
230 <param name="generate_plots" value="true"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
231 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
232 <assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
233 <has_text text="--uniprot 'P19339'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
234 <has_text text="--rna 'AUGGCU'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
235 <has_text text="--window_size 5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
236 <has_text text="--json 'json'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
237 <has_text text="--csv 'tabular'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
238 </assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
239 <output_collection name="split_json" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
240 <output_collection name="split_csv" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
241 <output_collection name="split_aligned" count="0"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
242 <output_collection name="split_plots" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
243 </test>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
244 <!-- Test 7: UniProt ID P19339, Window Size 5, RNA AUGGCU, with Plots, Aligned FASTA files -->
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
245 <test expect_num_outputs="4">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
246 <section name="input_sequence">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
247 <conditional name="input_type_cond">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
248 <param name="input_type" value="uniprot"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
249 <param name="uniprot_id" value="P19339"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
250 </conditional>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
251 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
252 <section name="tool_parameters">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
253 <param name="target" value="AUGGCU"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
254 <param name="window_size" value="5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
255 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
256 <section name="output_options">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
257 <param name="top_scoring_rna" value="false"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
258 <param name="generate_fasta" value="true"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
259 <param name="generate_plots" value="true"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
260 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
261 <assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
262 <has_text text="--uniprot 'P19339'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
263 <has_text text="--window_size 5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
264 <has_text text="--json 'json'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
265 <has_text text="--csv 'tabular'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
266 <has_text text="--plot 'plots'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
267 <not_has_text text="--top"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
268 </assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
269 <output_collection name="split_json" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
270 <output_collection name="split_csv" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
271 <output_collection name="split_aligned" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
272 <output_collection name="split_plots" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
273 </test>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
274 <!-- Test 8: Fasta file, Window Size 5, RNA AUGGCU, Aligned FASTA files -->
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
275 <test expect_num_outputs="4">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
276 <section name="input_sequence">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
277 <conditional name="input_type_cond">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
278 <param name="input_type" value="fasta"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
279 <param name="fasta_input" value="input.fasta" ftype="fasta"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
280 </conditional>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
281 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
282 <section name="tool_parameters">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
283 <param name="target" value="AUGGCU"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
284 <param name="window_size" value="5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
285 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
286 <section name="output_options">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
287 <param name="generate_fasta" value="true"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
288 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
289 <assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
290 <has_text text="--fasta"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
291 <has_text text="--rna 'AUGGCU'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
292 <has_text text="--window_size 5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
293 <has_text text="--json 'json'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
294 <has_text text="--csv 'tabular'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
295 </assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
296 <output_collection name="split_json" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
297 <output_collection name="split_csv" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
298 <output_collection name="split_aligned" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
299 <output_collection name="split_plots" type="list" count="0"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
300 </test>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
301 <!-- Test 9: Fasta file, Window Size 5, Top RNA, Aligned FASTA files -->
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
302 <test expect_num_outputs="4">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
303 <section name="input_sequence">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
304 <conditional name="input_type_cond">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
305 <param name="input_type" value="fasta"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
306 <param name="fasta_input" value="input.fasta" ftype="fasta"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
307 </conditional>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
308 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
309 <section name="tool_parameters">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
310 <param name="window_size" value="5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
311 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
312 <section name="output_options">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
313 <param name="top_scoring_rna" value="true"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
314 <param name="generate_fasta" value="true"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
315 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
316 <assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
317 <has_text text="--fasta"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
318 <not_has_text text="--rna 'AUGGCU'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
319 <has_text text="--window_size 5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
320 <has_text text="--json 'json'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
321 <has_text text="--csv 'tabular'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
322 <has_text text="--aligned 'aligned'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
323 <has_text text="--top"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
324 </assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
325 <output_collection name="split_csv" type="list" count="0"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
326 <output_collection name="split_json" type="list" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
327 <output_collection name="split_plots" type="list" count="0"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
328 <output_collection name="split_aligned" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
329 </test>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
330 <!-- Test 10: Fasta file, Window Size 5, Top RNA, with Plots, Aligned FASTA files -->
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
331 <test expect_num_outputs="4">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
332 <section name="input_sequence">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
333 <conditional name="input_type_cond">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
334 <param name="input_type" value="fasta"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
335 <param name="fasta_input" value="input.fasta" ftype="fasta"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
336 </conditional>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
337 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
338 <section name="tool_parameters">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
339 <param name="window_size" value="5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
340 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
341 <section name="output_options">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
342 <param name="top_scoring_rna" value="true"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
343 <param name="generate_fasta" value="true"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
344 <param name="generate_plots" value="true"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
345 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
346 <assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
347 <has_text text="--fasta"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
348 <not_has_text text="--rna 'AUGGCU'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
349 <has_text text="--window_size 5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
350 <has_text text="--json 'json'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
351 <has_text text="--csv 'tabular'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
352 <has_text text="--plot 'plots'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
353 <has_text text="--aligned 'aligned'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
354 <has_text text="--top"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
355 </assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
356 <output_collection name="split_csv" type="list" count="0"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
357 <output_collection name="split_json" type="list" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
358 <output_collection name="split_aligned" type="list" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
359 <output_collection name="split_plots" type="list" count="8"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
360 </test>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
361 <!-- Test 11: Fasta file, Window Size 5, RNA AUGGCU, Aligned FASTA files -->
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
362 <test expect_num_outputs="4">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
363 <section name="input_sequence">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
364 <conditional name="input_type_cond">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
365 <param name="input_type" value="fasta"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
366 <param name="fasta_input" value="input.fasta" ftype="fasta"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
367 </conditional>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
368 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
369 <section name="tool_parameters">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
370 <param name="window_size" value="5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
371 <param name="target" value="AUGGCU"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
372 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
373 <section name="output_options">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
374 <param name="top_scoring_rna" value="false"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
375 <param name="generate_fasta" value="true"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
376 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
377 <assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
378 <has_text text="--fasta"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
379 <has_text text="--rna 'AUGGCU'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
380 <has_text text="--window_size 5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
381 <has_text text="--json 'json'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
382 <has_text text="--csv 'tabular'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
383 <has_text text="--aligned 'aligned'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
384 <not_has_text text="--top"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
385 </assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
386 <output_collection name="split_csv" type="list" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
387 <output_collection name="split_json" type="list" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
388 <output_collection name="split_plots" type="list" count="0"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
389 <output_collection name="split_aligned" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
390 </test>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
391 <!-- Test 12: Fasta file, Window Size 5, RNA AUGGCU, with Plots, Aligned FASTA files -->
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
392 <test expect_num_outputs="4">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
393 <section name="input_sequence">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
394 <conditional name="input_type_cond">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
395 <param name="input_type" value="fasta"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
396 <param name="fasta_input" value="input.fasta" ftype="fasta"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
397 </conditional>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
398 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
399 <section name="tool_parameters">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
400 <param name="window_size" value="5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
401 <param name="target" value="AUGGCU"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
402 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
403 <section name="output_options">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
404 <param name="top_scoring_rna" value="false"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
405 <param name="generate_fasta" value="true"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
406 <param name="generate_plots" value="true"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
407 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
408 <assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
409 <has_text text="--fasta"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
410 <has_text text="--rna 'AUGGCU'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
411 <has_text text="--window_size 5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
412 <has_text text="--json 'json'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
413 <has_text text="--csv 'tabular'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
414 <has_text text="--plot 'plots'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
415 <has_text text="--aligned 'aligned'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
416 <not_has_text text="--top"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
417 </assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
418 <output_collection name="split_csv" type="list" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
419 <output_collection name="split_json" type="list" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
420 <output_collection name="split_plots" type="list" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
421 <output_collection name="split_aligned" count="2"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
422 </test>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
423 <!-- Test 13: Non-RRM-RNA protein (P05067) -->
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
424 <test>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
425 <section name="input_sequence">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
426 <conditional name="input_type_cond">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
427 <param name="input_type" value="uniprot"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
428 <param name="uniprot_id" value="P05067"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
429 </conditional>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
430 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
431 <section name="tool_parameters">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
432 <param name="target" value="AUGGCU"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
433 <param name="window_size" value="5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
434 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
435 <section name="output_options">
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
436 <param name="top_scoring_rna" value="false"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
437 <param name="generate_plots" value="false"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
438 <param name="generate_fasta" value="false"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
439 </section>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
440 <assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
441 <has_text text="--uniprot 'P05067'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
442 <has_text text="--rna 'AUGGCU'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
443 <has_text text="--window_size 5"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
444 <has_text text="--json 'json'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
445 <has_text text="--csv 'tabular'"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
446 </assert_command>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
447 <output_collection name="split_csv" type="list" count="0"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
448 <output_collection name="split_json" type="list" count="0"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
449 <output_collection name="split_plots" type="list" count="0"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
450 <output_collection name="split_aligned" type="list" count="0"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
451 </test>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
452 </tests>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
453 <creator>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
454 <organization name="Bio2Byte, Vrije Universiteit Brussel (VUB)" address="Interuniversity Institute Bioinformatics Brussels, Université Libre de Bruxelles, 1050 Ixelles, Brussels, Belgium" url="https://bio2byte.be/rrmscorer" email="bio2byte@vub.be" image="https://0.gravatar.com/avatar/2b51fb7600d876086669bcc85a941b763a81d1c2bb3c667b8c83a1aa892cf740"/>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
455 </creator>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
456 <help><![CDATA[
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
457 This tool allows you to predict RNA Recognition Motif (RRM) scores for protein
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
458 sequences provided in *FASTA* format or as *UniProt IDs*.
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
459
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
460 **RRMScorer** is designed to predict RNA binding preferences for proteins containing
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
461 RNA recognition motifs (RRMs), the most prevalent RNA binding domain in eukaryotes.
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
462
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
463 **Abstract:**
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
464
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
465 By carefully analysing a dataset of 187 RRM-RNA structural complexes, we calculated
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
466 residue-level binding scores using a probabilistic model derived from
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
467 amino acid-nucleotide interaction propensities, which are the basis of
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
468 **RRMScorer**.
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
469
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
470 With its ability to provide residue-level insights and accurate predictions,
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
471 **RRMScorer** serves as a valuable tool for researchers exploring the functional
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
472 landscape of RRM-RNA interactions.
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
473
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
474 **Methodology**:
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
475
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
476 The input sequence is scanned against our RRMScorer hidden Markov model (HMM)
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
477 to (i) identify whether the input sequence contains any RRM domain and (ii)
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
478 map to the 20 positions in the RRM protein sequence alignment that we use to compute
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
479 the RNA binding scores.
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
480
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
481 If one or more RRM domains are identified in the input sequence, RRMScorer computes
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
482 the score of the user-defined RNA sequence, or if absent, the scores for all the
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
483 1024 RNA possible sequences with a length of 5 nt. By utilizing a specific
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
484 RNA sequence, the user can inspect to which 5-nt windows the RRM is more likely
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
485 to bind.
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
486
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
487 **Input fields:**
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
488
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
489 * **Protein sequence(s) FASTA format:** Provide a *FASTA* file containing the protein sequences.
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
490 * **Protein identifier from Uniprot:** Provide a *UniProt ID* (e.g. P19339).
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
491 * **Custom RNA target:** Enable or disable the use of a custom RNA target for the predictions.
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
492 * **Target:** Provide a valid target RNA sequence (minimum 5 nucleotides) if Custom RNA target is enabled.
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
493 * **The window size to test:** Select the window size (either 3 or 5 nucleotides).
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
494 * **Plot options:** Configure plot output options.
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
495
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
496 **Output:**
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
497
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
498 The results are provided in comprehensive bar plots as well as in
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
499 CSV and JSON formats. When a custom RNA is not provided, the results will
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
500 include protein sequence logos for a range of top-scoring RNA sequences, as well
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
501 as the aforementioned CSV and JSON files with the scores.
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
502
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
503 **Funding:**
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
504 This project has received funding from the European Union's Horizon 2020 research
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
505 and innovation programme under the Marie Skłodowska-Curie grant
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
506 agreement No. 813239. This work was supported by the European Regional
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
507 Development Fund and Brussels-Capital Region-Innoviris within the framework of the
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
508 Operational Programme 2014-2020 (ERDF-2020 project ICITY-RDI.BRU)
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
509 ]]>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
510 </help>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
511 <citations>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
512 <citation type="doi">10.1371/journal.pcbi.1010859</citation>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
513 <citation type="doi">10.1093/nar/gkaf367</citation>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
514 </citations>
2e9c4504af91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer commit 1ed15985d486840a247b2803613c584c074e4744
iuc
parents:
diff changeset
515 </tool>