Mercurial > repos > tduigou > straindesign_reduce_model
view reduce-model.xml @ 0:2af5552f2273 draft
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
author | tduigou |
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date | Mon, 15 May 2023 14:06:09 +0000 |
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children | 3119eda6ff48 |
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<tool id="straindesign_reduce_model" name="StrainDesign reduce-model" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@"> <description>Delete gene in a biological model</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <command detect_errors="exit_code"><![CDATA[ python -m straindesign reduce-model @CMD_INPUT_MODEL@ #if str($sd_strategy.sd_cond) == 'yes' --input-straindesign-file '$sd_strategy.sd_tsv' --parameter-strategy-str '$sd_strategy.sd_strategy_str' #end if --output-file-sbml '$output_sbml' #if str($input_gene_str) != '' --input-gene-str #echo $input_gene_str #end if ]]></command> <expand macro="env_variables"/> <inputs> <expand macro="input_model_sbml"/> <conditional name="sd_strategy"> <param name="sd_cond" type="select" label="Fill with the output of StrainDesign simulate-deletion"> <option value="no" selected="True">no</option> <option value="yes" >yes</option> </param> <when value="yes"> <param name="sd_tsv" type="data" format="tabular" label="StrainDesign simulate-deletion output" help="TSV input file"/> <param name="sd_strategy_str" type="select" label="Strategy" help="Choose which genes will be deleted automatically"> <option value="yield-max" selected="True">Yield Max</option> <option value="gene-max">Gene Max</option> <option value="gene-min"> Gene Min</option> </param> </when> <when value="no"/> </conditional> <param name="input_gene_str" type="text" value="" label="Gene IDs" help="Multiple genes are separated by space"> <validator type="regex" message="No special characters allowed">^(?:[ \w.-])*$</validator> </param> </inputs> <outputs> <data name="output_sbml" format="sbml" label="${tool.name}" /> </outputs> <tests> <test> <!-- test 1 --> <param name="model" ftype="sbml" value="iAF1260.xml.gz"/> <param name="input_gene_str" value="b4208 b4208 b3919"/> <output name="output_sbml" ftype="sbml"> <assert_contents> <is_valid_xml/> <not_has_text text="b4208"/> <not_has_text text="b3919"/> </assert_contents> </output> </test> <test> <!-- test 2 --> <param name="model" ftype="sbml" value="iAF1260.xml.gz"/> <param name="sd_cond" value="yes"/> <param name="sd_tsv" ftype="tabular" value="simulate_deletion.butanol.iAF1260.tsv"/> <output name="output_sbml" ftype="sbml"> <assert_contents> <is_valid_xml/> <not_has_text text="b3919"/> <not_has_text text="b0529"/> </assert_contents> </output> </test> <test> <!-- test 3 --> <param name="model" ftype="sbml" value="iAF1260.xml.gz"/> <param name="sd_cond" value="yes"/> <param name="sd_tsv" ftype="tabular" value="simulate_deletion.butanol.iAF1260.tsv"/> <param name="input_gene_str" value="b4208 b4208 b3919"/> <output name="output_sbml" ftype="sbml"> <assert_contents> <is_valid_xml/> <not_has_text text="b4208"/> <not_has_text text="b3919"/> <not_has_text text="b0529"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ @HELP_TITLE@ This tool deletes some genes provided either from **simulate-deletion¨** or provided by their ids, in a biological model (SBML format). If you provide a TSV file coming from the **simulate-deletion** commands either the file is cleanned by hand and contains one line or the program tries to identify which genes will be deleted by applying the suited strategy: * yield-max: the combination of genes with the maximum amount of yiel is taken * gene-max: the combination of genes with the maximum number of genes is taken * gene-min: the combination of genes with the minimum number of genes is taken @HELP_LINK@ ]]></help> <expand macro="creator"/> <expand macro="citation"/> </tool>