swissmodel_modelling_api: swissmodel

annotate swissmodel_api.xml @ 1:3779090e153d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit d35c7d4dbe93451605d81b8e4fea8923e78b70ae

author	iuc
date	Sat, 10 Jan 2026 13:17:00 +0000
parents	fdee06ed645e
children

rev	line source
1 3779090e153d planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit d35c7d4dbe93451605d81b8e4fea8923e78b70ae iuc parents: 0 diff changeset	1 <tool name="SWISS-MODEL Modelling API" id="swissmodel_modelling_api" profile="25.1" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
0 fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	2 <description>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	3 Fully automated protein structure homology-modelling
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	4 </description>
1 3779090e153d planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit d35c7d4dbe93451605d81b8e4fea8923e78b70ae iuc parents: 0 diff changeset	5 <macros>
3779090e153d planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit d35c7d4dbe93451605d81b8e4fea8923e78b70ae iuc parents: 0 diff changeset	6 <token name="@TOOL_VERSION@">2.0.0</token>
3779090e153d planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit d35c7d4dbe93451605d81b8e4fea8923e78b70ae iuc parents: 0 diff changeset	7 <token name="@VERSION_SUFFIX@">0</token>
3779090e153d planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit d35c7d4dbe93451605d81b8e4fea8923e78b70ae iuc parents: 0 diff changeset	8 </macros>
0 fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	9 <xrefs>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	10 <xref type="bio.tools">swiss_model</xref>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	11 </xrefs>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	12 <requirements>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	13 <requirement type="package" version="3.11">python</requirement>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	14 <requirement type="package" version="2.32.5">requests</requirement>
1 3779090e153d planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit d35c7d4dbe93451605d81b8e4fea8923e78b70ae iuc parents: 0 diff changeset	15 <credentials name="swissmodel_api_credentials" version="1.0" label="SWISS-MODEL API Credentials" description="Credentials for accessing SWISS-MODEL API">
3779090e153d planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit d35c7d4dbe93451605d81b8e4fea8923e78b70ae iuc parents: 0 diff changeset	16 <secret name="swissmodel_api_token" inject_as_env="SWISSMODEL_API_TOKEN" optional="false" label="SWISS-MODEL API token" description="Token to authenticate to the SWISS-MODEL API. Can be managed on your https://swissmodel.expasy.org/login_page"/>
3779090e153d planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit d35c7d4dbe93451605d81b8e4fea8923e78b70ae iuc parents: 0 diff changeset	17 </credentials>
0 fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	18 </requirements>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	19 <command detect_errors="aggressive"><![CDATA[
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	20 mkdir -p 'output_dir/'
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	21 && python3 '$__tool_directory__/sm_api_wrapper.py'
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	22 $output_format.modelcif
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	23 $output_format.pdb
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	24 #if $project_title
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	25 --project-title '${project_title}'
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	26 #end if
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	27 #if $project_type == 'alignment'
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	28 --assembly-id '${assembly_id}'
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	29 --auth-asym-id '${auth_asym_id}'
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	30 --pdb-id '${pdb_id}'
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	31 --template-seqres-offset '${template_seqres_offset}'
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	32 --template-sequence '${template_sequence}'
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	33 #elif $project_type == 'usertemplate'
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	34 --template-file '${template_file}'
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	35 #end if
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	36 '${project.project_type}'
1 3779090e153d planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit d35c7d4dbe93451605d81b8e4fea8923e78b70ae iuc parents: 0 diff changeset	37 output_dir
0 fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	38 #if $project_type == 'alignment'
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	39 '${target_sequence}'
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	40 #else
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	41 #for $i in $target_list
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	42 '${i.sequence}'
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	43 #end for
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	44 #end if
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	45 && find output_dir -type f -name '*.gz' -exec gzip -d {} +
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	46 ]]>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	47 </command>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	48 <inputs>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	49 <param name="project_title" type="text" value="Untitled project" optional="true" label="Project title"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	50 <conditional name="project">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	51 <param name="project_type" type="select" value="automodel" optional="false" label="Modelling setup" display="radio">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	52 <option value="automodel" selected="true">Automodel mode</option>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	53 <option value="alignment">Alignment mode</option>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	54 <option value="usertemplate">User template mode</option>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	55 </param>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	56 <!-- AutoModel Mode Options -->
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	57 <when value="automodel">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	58 <repeat name="target_list" min="1"
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	59 help="Sequence(s) to be modelled. Add multiple sequences for hetero modelling." title="Target sequence">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	60 <param name="sequence" type="text" optional="false"
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	61 label="Sequence"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	62 </repeat>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	63 </when>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	64 <!-- Alignment Mode Options -->
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	65 <when value="alignment">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	66 <param name="target_sequence" type="text" optional="false"
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	67 label="Target sequence"
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	68 help="Target sequence as part of the alignment"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	69 <param name="pdb_id" type="text" optional="false"
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	70 label="PDB/ SMTL ID">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	71 <help><![CDATA[
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	72 PDB ID of the template SMTL entry as found in the
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	73 <a href="https://swissmodel.expasy.org/templates/" target="_blank"> SWISS-MODEL
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	74 Template Library</a>.
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	75 ]]></help>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	76 <validator type="regex" message="Only PDB-like IDs allowed, e.g. '1crn'.">^\d[A-Za-z0-9]{3}$</validator>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	77 </param>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	78 <param name="assembly_id" type="integer" min="0" value="0" optional="false"
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	79 label="Assembly ID">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	80 <help><![CDATA[
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	81 Assembly ID of the template as found in the
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	82 <a href="https://swissmodel.expasy.org/templates/" target="_blank"> SWISS-MODEL
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	83 Template Library</a>.
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	84 ]]></help>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	85 </param>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	86 <param name="auth_asym_id" type="text" optional="false"
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	87 label="Chain name">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	88 <help><![CDATA[
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	89 Chain name in the template assembly as found in the
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	90 <a href="https://swissmodel.expasy.org/templates/" target="_blank"> SWISS-MODEL
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	91 Template Library</a>.
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	92 ]]></help>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	93 </param>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	94 <param name="template_sequence" type="text" optional="false"
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	95 label="Template sequence"
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	96 help="Template sequence as part of the alignment"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	97 <param name="template_seqres_offset" type="integer" value="0" optional="false" label="Template sequence offset">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	98 <help><![CDATA[
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	99 Offset of the template sequence segment with respect to the full template
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	100 sequence.
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	101 ]]></help>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	102 </param>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	103 </when>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	104 <!-- User Template Mode Options -->
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	105 <when value="usertemplate">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	106 <repeat name="target_list" min="1"
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	107 help="Sequence(s) to be modelled. Add multiple sequences for hetero modelling." title="Target sequence">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	108 <param name="sequence" type="text" optional="false"
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	109 label="Sequence"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	110 </repeat>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	111 <param name="template_file" type="data" format="txt" optional="false" label="Template coordinates file"
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	112 help="File with template coordinaqtes in PDB legacy format."/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	113 </when>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	114 </conditional>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	115 <section name="output_format" title="Output format options">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	116 <param name="modelcif" type="boolean" truevalue="" falsevalue="--no-modelcif" checked="true" label="ModelCIF format"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	117 <param name="pdb" type="boolean" truevalue="--fetch-pdb" falsevalue="" checked="false" label="PDB legacy format"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	118 </section>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	119 </inputs>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	120 <outputs>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	121 <collection name="json_collection" type="list"
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	122 label="Metadata files for $project_title">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	123 <discover_datasets directory="output_dir/JSON" format="json" pattern="(?P<name>.+)\.json$"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	124 </collection>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	125 <collection name="pdb_collection" type="list"
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	126 label="PDB files for $project_title">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	127 <discover_datasets directory="output_dir/PDB" format="pdb" pattern="(?P<name>.+)\.pdb$"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	128 <filter>output_format['pdb'] == True</filter>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	129 </collection>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	130 <collection name="modelcif_collection" type="list"
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	131 label="ModelCIF files for $project_title">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	132 <discover_datasets directory="output_dir/ModelCIF" format="cif" pattern="(?P<name>.+)\.cif$"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	133 <filter>output_format['modelcif'] == True</filter>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	134 </collection>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	135 </outputs>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	136 <tests>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	137 <!-- w/o params, all will be empty strings, fail -->
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	138 <test expect_exit_code="2" expect_failure="true">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	139 <assert_stderr>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	140 <has_line line="Argument of '<SEQUENCE[S]>' can not be an empty"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	141 </assert_stderr>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	142 </test>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	143 <!-- with sequences, everything else empty, fail -->
1 3779090e153d planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit d35c7d4dbe93451605d81b8e4fea8923e78b70ae iuc parents: 0 diff changeset	144 <test expect_exit_code="1" expect_failure="true">
0 fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	145 <conditional name="project">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	146 <repeat name="target_list">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	147 <param name="sequence" value="MVVKAVCVINGDAKGTVFFEQESSGTPVKVSGEVCGL"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	148 </repeat>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	149 <repeat name="target_list">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	150 <param name="sequence" value="AKGLHGFHVHEFGDNTNGCMSSGPHFNPYGKE"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	151 </repeat>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	152 </conditional>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	153 <assert_stderr>
1 3779090e153d planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit d35c7d4dbe93451605d81b8e4fea8923e78b70ae iuc parents: 0 diff changeset	154 <has_line line="SWISS-MODEL token is not provided in credentials!"/>
0 fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	155 </assert_stderr>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	156 </test>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	157 <!-- alignment mode tests, as few params as possible, fail -->
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	158 <test expect_exit_code="2" expect_failure="true">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	159 <conditional name="project">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	160 <param name="project_type" value="alignment"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	161 <param name="assembly_id" value="0"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	162 <param name="template_seqres_offset" value="0"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	163 </conditional>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	164 <assert_stderr>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	165 <has_line line="Option '--auth-asym-id' can not be an empty string"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	166 </assert_stderr>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	167 </test>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	168 <!-- alignment mode tests, with auth_asym_id, fail -->
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	169 <test expect_exit_code="2" expect_failure="true">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	170 <conditional name="project">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	171 <param name="assembly_id" value="0"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	172 <param name="auth_asym_id" value="A"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	173 <param name="project_type" value="alignment"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	174 <param name="template_seqres_offset" value="0"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	175 </conditional>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	176 <assert_stderr>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	177 <has_line line="Option '--pdb-id' can not be an empty string"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	178 </assert_stderr>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	179 </test>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	180 <!-- alignment mode tests, with pdb_id, fail -->
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	181 <test expect_exit_code="2" expect_failure="true">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	182 <conditional name="project">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	183 <param name="assembly_id" value="0"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	184 <param name="auth_asym_id" value="A"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	185 <param name="pdb_id" value="1AKE"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	186 <param name="project_type" value="alignment"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	187 <param name="template_seqres_offset" value="0"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	188 </conditional>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	189 <assert_stderr>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	190 <has_line line="Option '--template-sequence' can not be an empty string"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	191 </assert_stderr>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	192 </test>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	193 <!-- alignment mode tests, with template_sequence, fail -->
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	194 <test expect_exit_code="2" expect_failure="true">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	195 <conditional name="project">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	196 <param name="assembly_id" value="0"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	197 <param name="auth_asym_id" value="A"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	198 <param name="pdb_id" value="1AKE"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	199 <param name="project_type" value="alignment"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	200 <param name="template_seqres_offset" value="0"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	201 <param name="template_sequence" value="MVVKAVCVINGDAKGTVFFEQESSGTPV"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	202 </conditional>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	203 <assert_stderr>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	204 <has_line line="Argument of '<SEQUENCE[S]>' can not be an empty"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	205 </assert_stderr>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	206 </test>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	207 <!-- alignment mode tests, with sequence, fail -->
1 3779090e153d planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit d35c7d4dbe93451605d81b8e4fea8923e78b70ae iuc parents: 0 diff changeset	208 <test expect_exit_code="1" expect_failure="true">
0 fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	209 <conditional name="project">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	210 <param name="assembly_id" value="0"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	211 <param name="auth_asym_id" value="A"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	212 <param name="pdb_id" value="1AKE"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	213 <param name="project_type" value="alignment"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	214 <param name="target_sequence" value="MVVKAVCVINGDAKGTVFFEQESSGTPVKVSG"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	215 <param name="template_seqres_offset" value="0"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	216 <param name="template_sequence" value="MVVKAVCVINGDAKGTVFFEQESSGTPV"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	217 </conditional>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	218 <assert_stderr>
1 3779090e153d planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit d35c7d4dbe93451605d81b8e4fea8923e78b70ae iuc parents: 0 diff changeset	219 <has_line line="SWISS-MODEL token is not provided in credentials!"/>
0 fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	220 </assert_stderr>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	221 </test>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	222 <!-- usertemplate mode tests, as few params as possible, fail -->
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	223 <test expect_exit_code="2" expect_failure="true">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	224 <conditional name="project">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	225 <param name="project_type" value="usertemplate"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	226 <param name="template_file" value="model_01.pdb"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	227 </conditional>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	228 <assert_stderr>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	229 <has_line line="Argument of '<SEQUENCE[S]>' can not be an empty"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	230 </assert_stderr>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	231 </test>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	232 <!-- usertemplate mode tests, with sequence, fail -->
1 3779090e153d planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit d35c7d4dbe93451605d81b8e4fea8923e78b70ae iuc parents: 0 diff changeset	233 <test expect_exit_code="1" expect_failure="true">
0 fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	234 <conditional name="project">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	235 <param name="project_type" value="usertemplate"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	236 <param name="template_file" value="model_01.pdb"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	237 <repeat name="target_list">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	238 <param name="sequence" value="MVVKAVCVINGDAKGTVFFEQESSGTPVKVSGEVCGL"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	239 </repeat>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	240 <repeat name="target_list">
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	241 <param name="sequence" value="AKGLHGFHVHEFGDNTNGCMSSGPHFNPYGKE"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	242 </repeat>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	243 </conditional>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	244 <assert_stderr>
1 3779090e153d planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit d35c7d4dbe93451605d81b8e4fea8923e78b70ae iuc parents: 0 diff changeset	245 <has_line line="SWISS-MODEL token is not provided in credentials!"/>
0 fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	246 </assert_stderr>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	247 </test>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	248 </tests>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	249 <help><![CDATA[
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	250 The SWISS-MODEL Modelling API tool gives you convenient access to homology models build by `SWISS-MODEL <https://swissmodel.expasy.org>`_ via our `API <https://swissmodel.expasy.org/docs/help#modelling_api>`_.
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	251
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	252 By default, the tool fetches model coordinates in ModelCIF format from the SWISS-MODEL API. SWISS-MODEL enriches its ModelCIF files with lots of extra information, essential for later reproduction of the computational experiment and enabling for easy deposition at archiving sites, like `Model Archive <https://modelarchive.org>`_. Output format can be toggled in the Output format options section for legacy PDB format, in case you are dealing with old-school tools in your workflows. Regardless of the format, output file names follow the pattern ``model_<N>.[cif\|pdb]``.
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	253
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	254 The SWISS-MODEL API provides three major modelling modes: Automodel, alignment and template upload mode.
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	255
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	256 Automodel mode
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	257 --------------
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	258
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	259 This mode corresponds to the "Sequence(s)" input mode and just hitting the "Build Model" button on our `web page <https://swissmodel.expasy.org/interactive>`_.
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	260
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	261 Automodel goes from sequence(s) to structural model. A single sequence for input leads to monomers or homomers. Multiple sequences for input produces heteromers, incorporating all target sequences. Multiple sequences input is sometimes mistaken for multi-model modelling tasks but its not, to produce models for more than one target sequence, you need to run the tool for each sequence separately.
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	262
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	263 Inside an automodel job, the following happens:
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	264
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	265 1. Template search in `PDB <https://www.rcsb.org>`_ and AlphaFold DB v4 sequences
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	266 2. Template selection by estimated quality and target sequence coverage
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	267
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	268 - gain high model confidence
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	269 - cover as much of the target sequence, maybe by different models per region
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	270 - employ models for equal regions if structurally diverse
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	271
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	272 3. Build models
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	273
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	274 Automodel options
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	275 ~~~~~~~~~~~~~~~~~
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	276
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	277 Only one or more sequences required, that's all! Single sequence produces monomers and/ or homomers. Multiple sequences produces heteromers.
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	278
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	279
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	280 Alignment mode
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	281 --------------
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	282
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	283 This mode corresponds to the "Target-Template Alignment" input mode on our `web page <https://swissmodel.expasy.org/interactive#alignment>`_.
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	284
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	285 The alignment mode still builds a model for a target sequence and a template from the `SWISS-MODEL template library <https://swissmodel.expasy.org/templates/>`_ (SMTL). But instead of creating the alignment from its own template search run, SWISS-MODEL will use an alignment provided by yourself. The alignment will be mapped onto the template sequence and then a structural model will be build.
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	286
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	287 To properly map a your alignment within the SMTL, you need to provide some extra information. SWISS-MODEL needs the identifier of the template. That's a common PDB ID, it just needs to exist in the SMTL. Then you need to identify the biological assembly of the entry you want your model to be based on... which can be easily done from the SMTL page. The assembly ID comes with the SMTL ID, its the number after the PDB ID and alternative assemblies of an entry can be found at the bottom of an entry page. The last component is the chain name you used for the alignment. Be aware, the SMTL uses its own chain names, so the original PDB chain name may not work. A mapping of chain names is provided on SMTL entry pages.
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	288
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	289 Alignment mode options
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	290 ~~~~~~~~~~~~~~~~~~~~~~
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	291
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	292 - Target sequence: first part of the alignment
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	293 - Template sequence: second sequence of the alignment
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	294 - Template sequence offset: position the template sequence starts at with respect to the full sequence; When using only a sub-sequence of the full sequence, it may be hard to automatically map to the right region in case of repeats, so you need to provide the offset
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	295 - PDB/ SMTL ID: PDB ID of the SMTL entry the alignment refers to
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	296 - Assembly ID: ID of the biological assembly to be used as template
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	297 - Chain name: ID of the chain to be used for modelling, needs to be the SMTL name, not the PDB name
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	298
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	299
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	300 User template mode
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	301 ------------------
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	302
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	303 This mode corresponds to the "User Template" input mode on our `web page <https://swissmodel.expasy.org/interactive#structure>`_.
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	304
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	305 The user template mode builds a model for a target sequence and template coordinates provided by you instead of using a SMTL entry for coordinates. The sequence alignment between target and template sequence is still calculated by SWISS-MODEL using HHblits and BLAST, or local alignment algorithm if both methods fail. With the alignment, a structural model is build based on the provided template coordinates.
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	306
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	307 Inside a user template job, the following happens:
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	308
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	309 1. Analyse uploaded coordinates
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	310 2. Calculate alignments with HHblits & BLAST
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	311 3. Choose "better" alignment or calculate Smith-Waterman alignment
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	312 4. Build model
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	313
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	314 User template mode options
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	315 ~~~~~~~~~~~~~~~~~~~~~~~~~~
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	316 - Target sequence: sequence to be modelled (post multiple for heteros)
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	317 - Template coordinate file: your template file, must be PDB formatted
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	318
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	319 Attribution/ License
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	320 ~~~~~~~~~~~~~~~~~~~~
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	321
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	322 Terms of use can be found at https://swissmodel.expasy.org/docs/terms_of_use
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	323
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	324 Modelling results of SWISS-MODEL are licensed under the
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	325 `CC BY-SA 4.0 Creative Commons Attribution-ShareAlike 4.0 International License <https://creativecommons.org/licenses/by-sa/4.0/legalcode>`_.
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	326
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	327 ]]>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	328 </help>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	329 <citations>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	330 <!-- SWISS-MODEL -->
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	331 <citation type="doi">10.1093/nar/gky427</citation>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	332 <!-- ProMod3 -->
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	333 <citation type="doi">10.1371/journal.pcbi.1008667</citation>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	334 <!-- QMEANDisCo -->
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	335 <citation type="doi">10.1093/bioinformatics/btz828</citation>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	336 <!-- Quaternary Structure Prediction/ QSQE -->
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	337 <citation type="doi">10.1038/s41598-017-09654-8</citation>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	338 <!-- lDDT -->
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	339 <citation type="doi">10.1093/bioinformatics/btt473</citation>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	340 </citations>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	341 <creator>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	342 <person email="stefan.bienert@unibas.ch" familyName="Bienert" givenName="Stefan"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	343 <organization name="Swiss Institute of Bioinformatics" alternateName="SIB" url="https://www.sib.swiss"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	344 <organization name="Biozentrum, University of Basel" alternateName="Biozentrum" url="https://www.biozentrum.unibas.ch"/>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	345 </creator>
fdee06ed645e planemo upload for repository https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api commit 43b5bef8757185b4c077effd0bad846f25d408db iuc parents: diff changeset	346 </tool>

Mercurial > repos > iuc > swissmodel_modelling_api

annotate swissmodel_api.xml @ 1:3779090e153d draft default tip