Mercurial > repos > iuc > swissmodel_modelling_api
changeset 1:f09a77e52ae5 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 13:17:07 +0000 |
| parents | 0c3f56c85e98 |
| children | |
| files | sm_api_wrapper.py swissmodel_api.xml |
| diffstat | 2 files changed, 25 insertions(+), 68 deletions(-) [+] |
line wrap: on
line diff
--- a/sm_api_wrapper.py Thu Dec 11 19:32:14 2025 +0000 +++ b/sm_api_wrapper.py Sat Jan 10 13:17:07 2026 +0000 @@ -286,14 +286,8 @@ metas = { "outdir": "<OUTPUT DIRECTORY>", "target_sequences": "<SEQUENCE[S]>", - "token": "<TOKEN>", } parser.add_argument( - "token", - help="Authentication token for SWISS-MODEL", - metavar=metas["token"], - ) - parser.add_argument( "outdir", help="Directory to store results in", metavar=metas["outdir"], @@ -377,12 +371,19 @@ """Run as script.""" opts = _parse_args() + token = os.getenv("SWISSMODEL_API_TOKEN") + if not token: + print( + "SWISS-MODEL token is not provided in credentials!", + file=sys.stderr, + ) + sys.exit(1) target_sequences = _defastarise_targets(opts.target_sequences) # determine class whsprr = None if opts.project_type.lower() == "automodel": whsprr = _AutoModelWhisperer( - target_sequences, opts.token, project_title=opts.project_title + target_sequences, token, project_title=opts.project_title ) elif opts.project_type.lower() == "alignment": template_sequence = _defastarise_targets([opts.template_sequence]) @@ -390,7 +391,7 @@ template_sequence = template_sequence[0] whsprr = _AlignmentWhisperer( target_sequences, - opts.token, + token, template_sequence, opts.template_seqres_offset, opts.pdb_id, @@ -401,7 +402,7 @@ elif opts.project_type.lower() == "usertemplate": whsprr = _UserTemplateWhisperer( target_sequences, - opts.token, + token, opts.template_file, project_title=opts.project_title, )
--- a/swissmodel_api.xml Thu Dec 11 19:32:14 2025 +0000 +++ b/swissmodel_api.xml Sat Jan 10 13:17:07 2026 +0000 @@ -1,13 +1,20 @@ -<tool name="SWISS-MODEL Modelling API" id="swissmodel_modelling_api" profile="21.05" version="2.0.0"> +<tool name="SWISS-MODEL Modelling API" id="swissmodel_modelling_api" profile="25.1" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description> Fully automated protein structure homology-modelling </description> + <macros> + <token name="@TOOL_VERSION@">2.0.0</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> <xrefs> <xref type="bio.tools">swiss_model</xref> </xrefs> <requirements> <requirement type="package" version="3.11">python</requirement> <requirement type="package" version="2.32.5">requests</requirement> + <credentials name="swissmodel_api_credentials" version="1.0" label="SWISS-MODEL API Credentials" description="Credentials for accessing SWISS-MODEL API"> + <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"/> + </credentials> </requirements> <command detect_errors="aggressive"><![CDATA[ mkdir -p 'output_dir/' @@ -27,7 +34,7 @@ --template-file '${template_file}' #end if '${project.project_type}' - '${token}' output_dir + output_dir #if $project_type == 'alignment' '${target_sequence}' #else @@ -39,12 +46,6 @@ ]]> </command> <inputs> - <param name="token" type="text" optional="false" label="API token"> - <help><![CDATA[ -Token to authenticate to the SWISS-MODEL API. Can be managed on your -<a href="https://swissmodel.expasy.org/login_page" target="_blank"> SWISS-MODEL account</a> page. - ]]></help> - </param> <param name="project_title" type="text" value="Untitled project" optional="true" label="Project title"/> <conditional name="project"> <param name="project_type" type="select" value="automodel" optional="false" label="Modelling setup" display="radio"> @@ -140,7 +141,7 @@ </assert_stderr> </test> <!-- with sequences, everything else empty, fail --> - <test expect_exit_code="2" expect_failure="true"> + <test expect_exit_code="1" expect_failure="true"> <conditional name="project"> <repeat name="target_list"> <param name="sequence" value="MVVKAVCVINGDAKGTVFFEQESSGTPVKVSGEVCGL"/> @@ -150,19 +151,7 @@ </repeat> </conditional> <assert_stderr> - <has_line line="Argument of '<TOKEN>' can not be an empty string"/> - </assert_stderr> - </test> - <!-- sequence and token (complete automodel job), fail (no real token) --> - <test expect_exit_code="1" expect_failure="true"> - <conditional name="project"> - <repeat name="target_list"> - <param name="sequence" value="MVVKAVCVINGDAKGTVFFEQESSGTPVKVSGEVCGL"/> - </repeat> - </conditional> - <param name="token" value="NOTAVALIDTOKEN"/> - <assert_stderr> - <has_line line="RuntimeError: Submitting modelling job failed (401)"/> + <has_line line="SWISS-MODEL token is not provided in credentials!"/> </assert_stderr> </test> <!-- alignment mode tests, as few params as possible, fail --> @@ -216,7 +205,7 @@ </assert_stderr> </test> <!-- alignment mode tests, with sequence, fail --> - <test expect_exit_code="2" expect_failure="true"> + <test expect_exit_code="1" expect_failure="true"> <conditional name="project"> <param name="assembly_id" value="0"/> <param name="auth_asym_id" value="A"/> @@ -227,23 +216,7 @@ <param name="template_sequence" value="MVVKAVCVINGDAKGTVFFEQESSGTPV"/> </conditional> <assert_stderr> - <has_line line="Argument of '<TOKEN>' can not be an empty string"/> - </assert_stderr> - </test> - <!-- alignment mode tests, with token, fail --> - <test expect_exit_code="1" expect_failure="true"> - <conditional name="project"> - <param name="assembly_id" value="0"/> - <param name="auth_asym_id" value="A"/> - <param name="pdb_id" value="1AKE"/> - <param name="project_type" value="alignment"/> - <param name="target_sequence" value="MVVKAVCVINGDAKGTVFFEQESSGTPVKVSG"/> - <param name="template_seqres_offset" value="0"/> - <param name="template_sequence" value="MVVKAVCVINGDAKGTVFFEQESSGTPV"/> - </conditional> - <param name="token" value="NOTAVALIDTOKEN"/> - <assert_stderr> - <has_line line="RuntimeError: Submitting modelling job failed (401)"/> + <has_line line="SWISS-MODEL token is not provided in credentials!"/> </assert_stderr> </test> <!-- usertemplate mode tests, as few params as possible, fail --> @@ -257,7 +230,7 @@ </assert_stderr> </test> <!-- usertemplate mode tests, with sequence, fail --> - <test expect_exit_code="2" expect_failure="true"> + <test expect_exit_code="1" expect_failure="true"> <conditional name="project"> <param name="project_type" value="usertemplate"/> <param name="template_file" value="model_01.pdb"/> @@ -269,24 +242,7 @@ </repeat> </conditional> <assert_stderr> - <has_line line="Argument of '<TOKEN>' can not be an empty string"/> - </assert_stderr> - </test> - <!-- usertemplate mode tests, with token, fail --> - <test expect_exit_code="1" expect_failure="true"> - <conditional name="project"> - <param name="project_type" value="usertemplate"/> - <param name="template_file" value="model_01.pdb"/> - <repeat name="target_list"> - <param name="sequence" value="MVVKAVCVINGDAKGTVFFEQESSGTPVKVSGEVCGL"/> - </repeat> - <repeat name="target_list"> - <param name="sequence" value="AKGLHGFHVHEFGDNTNGCMSSGPHFNPYGKE"/> - </repeat> - </conditional> - <param name="token" value="NOTAVALIDTOKEN"/> - <assert_stderr> - <has_line line="RuntimeError: Submitting modelling job failed (401)"/> + <has_line line="SWISS-MODEL token is not provided in credentials!"/> </assert_stderr> </test> </tests>