Mercurial > repos > iuc > straindesign_simulate_deletion
diff macros.xml @ 0:33c6ffbd098f draft
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
author | iuc |
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date | Sun, 02 Oct 2022 19:26:40 +0000 |
parents | |
children | 1128f1e17c37 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun Oct 02 19:26:40 2022 +0000 @@ -0,0 +1,97 @@ +<macros> + <!-- GLOBAL --> + <token name="@TOOL_VERSION@">3.1.0</token> + <token name="@VERSION_SUFFIX@">1</token> + <token name="@LICENSE@">MIT</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">straindesign</requirement> + <yield/> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <regex match="WARNING" level="warning" /> + <regex match="ERROR" level="fatal" /> + </stdio> + </xml> + <xml name="citation"> + <citations> + <citation type="doi">10.1038/s41467-022-32661-x</citation> + </citations> + </xml> + <xml name="creator"> + <creator> + <organization name="BioRetroSynth" url="https://github.com/brsynth"/> + </creator> + </xml> + <xml name="env_variables"> + <environment_variables> + <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable> + <environment_variable name="USERNAME">\$__user_email__</environment_variable> + </environment_variables> + </xml> + + <!-- CMDLINE --> +<token name="@CMD_INPUT_MODEL@"><![CDATA[ +--input-model-file '$model' +]]></token> +<token name="@CMD_INPUT_PATHWAY@"><![CDATA[ +#if $pathway +--input-pathway-file '$pathway' +#end if +]]></token> +<token name="@CMD_INPUT_MEDIUM@"><![CDATA[ +#if $medium + --input-medium-file '$medium' +#end if +]]></token> +<token name="@CMD_BIOMASS_RXN_ID@"><![CDATA[ +--biomass-rxn-id '$biomass_rxn_id' +]]></token> +<token name="@CMD_TARGET_RXN_ID@"><![CDATA[ +--target-rxn-id '$target_rxn_id' +]]></token> + + <!-- INPUT --> + <xml name="input_model_sbml"> + <param name="model" type="data" format="sbml" label="Model" help="SBML input file, model"/> + </xml> + <xml name="input_pathway_sbml"> + <param name="pathway" type="data" format="sbml" optional="True" label="Pathway" help="SBML input file, containing heterologous pathway"/> + </xml> + <xml name="input_medium_tsv"> + <param name="medium" type="data" format="tabular" optional="True" label="Medium file" help="TSV input file, no header, with three columns: reaction_id, lower_bound, upper_bound"/> + </xml> + <xml name="input_biomass_rxn_id"> + <param name="biomass_rxn_id" type="text" value="" label="Biomass reaction ID" help="Reaction ID contains no special characters"> + <validator type="empty_field" message="Biomass reaction ID is required"/> + <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator> + </param> + </xml> + <xml name="input_target_rxn_id"> + <param name="target_rxn_id" type="text" value="" label="Target reaction ID" help="Reaction ID contains no special characters"> + <validator type="empty_field" message="Target reaction ID is required"/> + <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator> + </param> + </xml> + <xml name="input_substrate_rxn_id"> + <param name="substrate_rxn_id" type="text" value="" label="Substrate reaction ID" help="Reaction ID contains no special characters"> + <validator type="empty_field" message="Target reaction ID is required"/> + <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator> + </param> + </xml> + + <!-- HELP --> +<token name="@HELP_TITLE@"><![CDATA[ +StrainDesign +============ +]]></token> +<token name="@HELP_LINK@"><![CDATA[ +Project Links +------------- + +* `straindesign <https://github.com/brsynth/straindesign>`_ +* `cameo <https://github.com/biosustain/cameo>`_ +]]></token> +</macros>