Mercurial > repos > galaxyp > openms_multiplexresolver
diff MultiplexResolver.xml @ 9:381448b2db6d draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
| author | galaxyp |
|---|---|
| date | Wed, 09 Sep 2020 20:01:05 +0000 |
| parents | 8023d63040f6 |
| children | b3dcd2098472 |
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--- a/MultiplexResolver.xml Fri May 17 10:10:57 2019 -0400 +++ b/MultiplexResolver.xml Wed Sep 09 20:01:05 2020 +0000 @@ -1,119 +1,121 @@ <?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: [Utilities]--> -<tool id="MultiplexResolver" name="MultiplexResolver" version="2.3.0"> +<tool id="MultiplexResolver" name="MultiplexResolver" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Completes peptide multiplets and resolves conflicts within them.</description> <macros> <token name="@EXECUTABLE@">MultiplexResolver</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[MultiplexResolver + <expand macro="stdio"/> + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re -#if $param_in: - -in $param_in +## Preprocessing +mkdir in && +ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +#if $in_blacklist: + mkdir in_blacklist && + ln -s '$in_blacklist' 'in_blacklist/${re.sub("[^\w\-_]", "_", $in_blacklist.element_identifier)}.$gxy2omsext($in_blacklist.ext)' && #end if -#if $param_out: - -out $param_out -#end if -#if $param_out_conflicts: - -out_conflicts $param_out_conflicts -#end if -#if $param_algorithm_labels: - -algorithm:labels "$param_algorithm_labels" -#end if -#if $param_algorithm_missed_cleavages: - -algorithm:missed_cleavages $param_algorithm_missed_cleavages +mkdir out && +#if "out_conflicts_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + mkdir out_conflicts && #end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force -#end if - #if $adv_opts.param_algorithm_mass_tolerance: - -algorithm:mass_tolerance $adv_opts.param_algorithm_mass_tolerance -#end if - #if $adv_opts.param_labels_Arg6: - -labels:Arg6 $adv_opts.param_labels_Arg6 -#end if - #if $adv_opts.param_labels_Arg10: - -labels:Arg10 $adv_opts.param_labels_Arg10 + +## Main program call + +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__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)' +#if $in_blacklist: + -in_blacklist + 'in_blacklist/${re.sub("[^\w\-_]", "_", $in_blacklist.element_identifier)}.$gxy2omsext($in_blacklist.ext)' #end if - #if $adv_opts.param_labels_Lys4: - -labels:Lys4 $adv_opts.param_labels_Lys4 -#end if - #if $adv_opts.param_labels_Lys6: - -labels:Lys6 $adv_opts.param_labels_Lys6 +-out +'out/output.${gxy2omsext("consensusxml")}' +#if "out_conflicts_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + -out_conflicts + 'out_conflicts/output.${gxy2omsext("consensusxml")}' #end if - #if $adv_opts.param_labels_Lys8: - -labels:Lys8 $adv_opts.param_labels_Lys8 -#end if - #if $adv_opts.param_labels_Leu3: - -labels:Leu3 $adv_opts.param_labels_Leu3 -#end if - #if $adv_opts.param_labels_Dimethyl0: - -labels:Dimethyl0 $adv_opts.param_labels_Dimethyl0 +#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 + | tee '$stdout' #end if - #if $adv_opts.param_labels_Dimethyl4: - -labels:Dimethyl4 $adv_opts.param_labels_Dimethyl4 -#end if - #if $adv_opts.param_labels_Dimethyl6: - -labels:Dimethyl6 $adv_opts.param_labels_Dimethyl6 -#end if - #if $adv_opts.param_labels_Dimethyl8: - -labels:Dimethyl8 $adv_opts.param_labels_Dimethyl8 -#end if - #if $adv_opts.param_labels_ICPL0: - -labels:ICPL0 $adv_opts.param_labels_ICPL0 + +## Postprocessing +&& mv 'out/output.${gxy2omsext("consensusxml")}' '$out' +#if "out_conflicts_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + && mv 'out_conflicts/output.${gxy2omsext("consensusxml")}' '$out_conflicts' #end if - #if $adv_opts.param_labels_ICPL4: - -labels:ICPL4 $adv_opts.param_labels_ICPL4 -#end if - #if $adv_opts.param_labels_ICPL6: - -labels:ICPL6 $adv_opts.param_labels_ICPL6 -#end if - #if $adv_opts.param_labels_ICPL10: - -labels:ICPL10 $adv_opts.param_labels_ICPL10 -#end if -#end if -]]></command> +#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[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> + </configfiles> <inputs> - <param name="param_in" type="data" format="consensusxml" optional="False" label="Peptide multiplets with assigned sequence information" help="(-in) "/> - <param name="param_algorithm_labels" type="text" size="30" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="(-labels) [...] specifies the labels for a single sample. For example <br> <br>[][Lys8,Arg10] ... SILAC <br>[][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC <br>[Dimethyl0][Dimethyl6] ... Dimethyl <br>[Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl <br>[ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL"> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <param name="in" argument="-in" type="data" format="consensusxml" optional="false" label="Peptide multiplets with assigned sequence information" help=" select consensusxml data sets(s)"/> + <param name="in_blacklist" argument="-in_blacklist" type="data" format="mzml" optional="true" label="Optional input containing spectral peaks blacklisted during feature detection" help="Needed for generation of dummy features select mzml data sets(s)"/> + <section name="algorithm" title="Parameters for the algorithm" help="" expanded="false"> + <param name="labels" argument="-algorithm:labels" type="text" optional="true" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="[...] specifies the labels for a single sample. For example. . [][Lys8,Arg10] ... SILAC. [][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC. [Dimethyl0][Dimethyl6] ... Dimethyl. [Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl. [ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL"> + <expand macro="list_string_san"/> + </param> + <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" optional="true" min="0" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/> + <param name="mass_tolerance" argument="-algorithm:mass_tolerance" type="float" optional="true" value="0.1" label="Mass tolerance in Da for matching the mass shifts in the detected peptide multiplet to the theoretical mass shift pattern" help=""/> + <param name="mz_tolerance" argument="-algorithm:mz_tolerance" type="integer" optional="true" value="10" label="m/z tolerance in ppm for checking if dummy feature vicinity was blacklisted" help=""/> + <param name="rt_tolerance" argument="-algorithm:rt_tolerance" type="integer" optional="true" value="5" label="Retention time tolerance in seconds for checking if dummy feature vicinity was blacklisted" help=""/> + </section> + <section name="labels" title="Isotopic labels that can be specified in section 'algorithm:labels'" help="" expanded="false"> + <param name="Arg6" argument="-labels:Arg6" type="float" optional="true" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/> + <param name="Arg10" argument="-labels:Arg10" type="float" optional="true" min="0.0" value="10.0082686" label="Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267" help=""/> + <param name="Lys4" argument="-labels:Lys4" type="float" optional="true" min="0.0" value="4.0251069836" label="Label:2H(4) | H(-4) 2H(4) | unimod #481" help=""/> + <param name="Lys6" argument="-labels:Lys6" type="float" optional="true" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/> + <param name="Lys8" argument="-labels:Lys8" type="float" optional="true" min="0.0" value="8.0141988132" label="Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259" help=""/> + <param name="Leu3" argument="-labels:Leu3" type="float" optional="true" min="0.0" value="3.01883" label="Label:2H(3) | H(-3) 2H(3) | unimod #262" help=""/> + <param name="Dimethyl0" argument="-labels:Dimethyl0" type="float" optional="true" min="0.0" value="28.0313" label="Dimethyl | H(4) C(2) | unimod #36" help=""/> + <param name="Dimethyl4" argument="-labels:Dimethyl4" type="float" optional="true" min="0.0" value="32.056407" label="Dimethyl:2H(4) | 2H(4) C(2) | unimod #199" help=""/> + <param name="Dimethyl6" argument="-labels:Dimethyl6" type="float" optional="true" min="0.0" value="34.063117" label="Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510" help=""/> + <param name="Dimethyl8" argument="-labels:Dimethyl8" type="float" optional="true" min="0.0" value="36.07567" label="Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330" help=""/> + <param name="ICPL0" argument="-labels:ICPL0" type="float" optional="true" min="0.0" value="105.021464" label="ICPL | H(3) C(6) N O | unimod #365" help=""/> + <param name="ICPL4" argument="-labels:ICPL4" type="float" optional="true" min="0.0" value="109.046571" label="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" help=""/> + <param name="ICPL6" argument="-labels:ICPL6" type="float" optional="true" min="0.0" value="111.041593" label="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" help=""/> + <param name="ICPL10" argument="-labels:ICPL10" type="float" optional="true" min="0.0" value="115.0667" label="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" help=""/> + </section> + <expand macro="adv_opts_macro"> + <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="out_conflicts_FLAG">out_conflicts (ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866)</option> + <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> - <param name="param_algorithm_missed_cleavages" type="integer" min="0" optional="True" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(-missed_cleavages) (Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/> - <expand macro="advanced_options"> - <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> - <param name="param_algorithm_mass_tolerance" type="float" value="0.1" label="Mass tolerance in Da for matching the detected to the theoretical mass shifts" help="(-mass_tolerance) "/> - <param name="param_labels_Arg6" type="float" min="0.0" optional="True" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help="(-Arg6) "/> - <param name="param_labels_Arg10" type="float" min="0.0" optional="True" value="10.0082686" label="Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267" help="(-Arg10) "/> - <param name="param_labels_Lys4" type="float" min="0.0" optional="True" value="4.0251069836" label="Label:2H(4) | H(-4) 2H(4) | unimod #481" help="(-Lys4) "/> - <param name="param_labels_Lys6" type="float" min="0.0" optional="True" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help="(-Lys6) "/> - <param name="param_labels_Lys8" type="float" min="0.0" optional="True" value="8.0141988132" label="Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259" help="(-Lys8) "/> - <param name="param_labels_Leu3" type="float" min="0.0" optional="True" value="3.01883" label="Label:2H(3) | H(-3) 2H(3) | unimod #262" help="(-Leu3) "/> - <param name="param_labels_Dimethyl0" type="float" min="0.0" optional="True" value="28.0313" label="Dimethyl | H(4) C(2) | unimod #36" help="(-Dimethyl0) "/> - <param name="param_labels_Dimethyl4" type="float" min="0.0" optional="True" value="32.056407" label="Dimethyl:2H(4) | 2H(4) C(2) | unimod #199" help="(-Dimethyl4) "/> - <param name="param_labels_Dimethyl6" type="float" min="0.0" optional="True" value="34.063117" label="Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510" help="(-Dimethyl6) "/> - <param name="param_labels_Dimethyl8" type="float" min="0.0" optional="True" value="36.07567" label="Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330" help="(-Dimethyl8) "/> - <param name="param_labels_ICPL0" type="float" min="0.0" optional="True" value="105.021464" label="ICPL | H(3) C(6) N O | unimod #365" help="(-ICPL0) "/> - <param name="param_labels_ICPL4" type="float" min="0.0" optional="True" value="109.046571" label="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" help="(-ICPL4) "/> - <param name="param_labels_ICPL6" type="float" min="0.0" optional="True" value="111.041593" label="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" help="(-ICPL6) "/> - <param name="param_labels_ICPL10" type="float" min="0.0" optional="True" value="115.0667" label="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" help="(-ICPL10) "/> - </expand> </inputs> <outputs> - <data name="param_out" format="consensusxml"/> - <data name="param_out_conflicts" format="consensusxml"/> + <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/> + <data name="out_conflicts" label="${tool.name} on ${on_string}: out_conflicts" format="consensusxml"> + <filter>OPTIONAL_OUTPUTS is not None and "out_conflicts_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>Completes peptide multiplets and resolves conflicts within them. + <tests> + <expand macro="autotest_MultiplexResolver"/> + <expand macro="manutest_MultiplexResolver"/> + </tests> + <help><![CDATA[Completes peptide multiplets and resolves conflicts within them. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_MultiplexResolver.html</help> +For more information, visit http://www.openms.de/documentation/UTILS_MultiplexResolver.html]]></help> + <expand macro="references"/> </tool>