Mercurial > repos > galaxyp > openms_fidoadapter
diff FidoAdapter.xml @ 11:b552ec8456e7 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
| author | galaxyp |
|---|---|
| date | Wed, 09 Sep 2020 20:09:56 +0000 |
| parents | d4965c549fd9 |
| children | c3a5cd016963 |
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--- a/FidoAdapter.xml Fri May 17 09:56:49 2019 -0400 +++ b/FidoAdapter.xml Wed Sep 09 20:09:56 2020 +0000 @@ -1,100 +1,91 @@ <?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> <!--Proposed Tool Section: [ID Processing]--> -<tool id="FidoAdapter" name="FidoAdapter" version="2.3.0"> +<tool id="FidoAdapter" name="FidoAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Runs the protein inference engine Fido.</description> <macros> <token name="@EXECUTABLE@">FidoAdapter</token> <import>macros.xml</import> + <import>macros_autotest.xml</import> + <import>macros_test.xml</import> </macros> - <expand macro="references"/> - <expand macro="stdio"/> <expand macro="requirements"/> - <command detect_errors="aggressive"><![CDATA[FidoAdapter --fidocp_executable FidoChooseParameters --fido_executable Fido + <expand macro="stdio"/> + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re + +## Preprocessing +mkdir in && +ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +mkdir out && + +## Main program call + +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && +@EXECUTABLE@ -ini @EXECUTABLE@.ctd +-in +'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' +-out +'out/output.${gxy2omsext("idxml")}' -#if $param_in: - -in $param_in -#end if -#if $param_out: - -out $param_out -#end if -#if $param_separate_runs: - -separate_runs -#end if -#if $param_greedy_group_resolution: - -greedy_group_resolution -#end if -#if $param_no_cleanup: - -no_cleanup -#end if -#if $param_all_PSMs: - -all_PSMs -#end if -#if $param_group_level: - -group_level -#end if -#if $param_log2_states: - -log2_states $param_log2_states -#end if -#if $param_prob_protein: - -prob:protein $param_prob_protein -#end if -#if $param_prob_peptide: - -prob:peptide $param_prob_peptide -#end if -#if $param_prob_spurious: - -prob:spurious $param_prob_spurious -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_keep_zero_group: - -keep_zero_group -#end if - #if $adv_opts.param_accuracy: - -accuracy - #if " " in str($adv_opts.param_accuracy): - "$adv_opts.param_accuracy" - #else - $adv_opts.param_accuracy - #end if -#end if - #if $adv_opts.param_log2_states_precalc: - -log2_states_precalc $adv_opts.param_log2_states_precalc -#end if - #if $adv_opts.param_force: - -force -#end if -#end if -]]></command> +## Postprocessing +&& mv 'out/output.${gxy2omsext("idxml")}' '$out' +#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS + && mv '@EXECUTABLE@.ctd' '$ctd_out' +#end if]]></command> + <configfiles> + <inputs name="args_json" data_style="paths"/> + <configfile name="hardcoded_json"><![CDATA[{"fido_executable": "Fido", "fidocp_executable": "FidoChooseParameters", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> + </configfiles> <inputs> - <param name="param_in" type="data" format="idxml" optional="False" label="Input: identification results" help="(-in) "/> - <param name="param_separate_runs" display="radio" type="boolean" truevalue="-separate_runs" falsevalue="" checked="false" optional="True" label="Process multiple protein identification runs in the input separately, don't merge them" help="(-separate_runs) Merging results in loss of descriptive information of the single protein identification runs"/> - <param name="param_greedy_group_resolution" display="radio" type="boolean" truevalue="-greedy_group_resolution" falsevalue="" checked="false" optional="True" label="Post-process Fido output with greedy resolution of shared peptides based on the protein probabilities" help="(-greedy_group_resolution) Also adds the resolved ambiguity groups to output"/> - <param name="param_no_cleanup" display="radio" type="boolean" truevalue="-no_cleanup" falsevalue="" checked="false" optional="True" label="Omit clean-up of peptide sequences (removal of non-letter characters, replacement of I with L)" help="(-no_cleanup) "/> - <param name="param_all_PSMs" display="radio" type="boolean" truevalue="-all_PSMs" falsevalue="" checked="false" optional="True" label="Consider all PSMs of each peptide, instead of only the best one" help="(-all_PSMs) "/> - <param name="param_group_level" display="radio" type="boolean" truevalue="-group_level" falsevalue="" checked="false" optional="True" label="Perform inference on protein group level (instead of individual protein level)" help="(-group_level) This will lead to higher probabilities for (bigger) protein groups"/> - <param name="param_log2_states" type="integer" min="0" optional="True" value="0" label="Binary logarithm of the max" help="(-log2_states) number of connected states in a subgraph. For a value N, subgraphs that are bigger than 2^N will be split up, sacrificing accuracy for runtime. '0' uses the default (18)"/> - <param name="param_prob_protein" type="float" min="0.0" optional="True" value="0.0" label="Protein prior probability ('gamma' parameter)" help="(-protein) "/> - <param name="param_prob_peptide" type="float" min="0.0" optional="True" value="0.0" label="Peptide emission probability ('alpha' parameter)" help="(-peptide) "/> - <param name="param_prob_spurious" type="float" min="0.0" optional="True" value="0.0" label="Spurious peptide identification probability ('beta' parameter)" help="(-spurious) "/> - <expand macro="advanced_options"> - <param name="param_keep_zero_group" display="radio" type="boolean" truevalue="-keep_zero_group" falsevalue="" checked="false" optional="True" label="Keep the group of proteins with estimated probability of zero, which is otherwise removed (it may be very large)" help="(-keep_zero_group) "/> - <param name="param_accuracy" display="radio" type="select" optional="True" label="Accuracy level of start parameters" help="(-accuracy) There is a trade-off between accuracy and runtime. Empty uses the default ('best')"> + <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Input: identification results" help=" select idxml data sets(s)"/> + <param name="separate_runs" argument="-separate_runs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Process multiple protein identification runs in the input separately, don't merge them" help="Merging results in loss of descriptive information of the single protein identification runs"/> + <param name="greedy_group_resolution" argument="-greedy_group_resolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Post-process Fido output with greedy resolution of shared peptides based on the protein probabilities" help="Also adds the resolved ambiguity groups to output"/> + <param name="no_cleanup" argument="-no_cleanup" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Omit clean-up of peptide sequences (removal of non-letter characters, replacement of I with L)" help=""/> + <param name="all_PSMs" argument="-all_PSMs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Consider all PSMs of each peptide, instead of only the best one" help=""/> + <param name="group_level" argument="-group_level" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform inference on protein group level (instead of individual protein level)" help="This will lead to higher probabilities for (bigger) protein groups"/> + <param name="log2_states" argument="-log2_states" type="integer" optional="true" min="0" value="0" label="Binary logarithm of the max" help="number of connected states in a subgraph. For a value N, subgraphs that are bigger than 2^N will be split up, sacrificing accuracy for runtime. '0' uses the default (18)"/> + <section name="prob" title="Probability values for running Fido directly" help="i.e. without parameter estimation (in which case other settings, except 'log2_states', are ignored)" expanded="false"> + <param name="protein" argument="-prob:protein" type="float" optional="true" min="0.0" value="0.0" label="Protein prior probability ('gamma' parameter)" help=""/> + <param name="peptide" argument="-prob:peptide" type="float" optional="true" min="0.0" value="0.0" label="Peptide emission probability ('alpha' parameter)" help=""/> + <param name="spurious" argument="-prob:spurious" type="float" optional="true" min="0.0" value="0.0" label="Spurious peptide identification probability ('beta' parameter)" help=""/> + </section> + <expand macro="adv_opts_macro"> + <param name="keep_zero_group" argument="-keep_zero_group" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep the group of proteins with estimated probability of zero, which is otherwise removed (it may be very large)" help=""/> + <param name="accuracy" argument="-accuracy" display="radio" type="select" optional="true" label="Accuracy level of start parameters" help="There is a trade-off between accuracy and runtime. Empty uses the default ('best')"> + <option value="">default (nothing chosen)</option> <option value=""></option> <option value="best">best</option> <option value="relaxed">relaxed</option> <option value="sloppy">sloppy</option> + <expand macro="list_string_san"/> </param> - <param name="param_log2_states_precalc" type="integer" min="0" optional="True" value="0" label="Like 'log2_states', but allows to set a separate limit for the precalculation" help="(-log2_states_precalc) "/> - <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> + <param name="log2_states_precalc" argument="-log2_states_precalc" type="integer" optional="true" min="0" value="0" label="Like 'log2_states', but allows to set a separate limit for the precalculation" help=""/> + <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> + <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <expand macro="list_string_san"/> + </param> </expand> + <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> + <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> + </param> </inputs> <outputs> - <data name="param_out" format="idxml"/> + <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>Runs the protein inference engine Fido. + <tests> + <expand macro="autotest_FidoAdapter"/> + <expand macro="manutest_FidoAdapter"/> + </tests> + <help><![CDATA[Runs the protein inference engine Fido. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FidoAdapter.html</help> +For more information, visit http://www.openms.de/documentation/TOPP_FidoAdapter.html]]></help> + <expand macro="references"/> </tool>