comparison FeatureLinkerUnlabeledQT.xml @ 11:bd07412009d1 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"

10:55656563320d

<?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: [Map Alignment]-->
<tool id="FeatureLinkerUnlabeledQT" name="FeatureLinkerUnlabeledQT" version="2.3.0">
  <description>Groups corresponding features from multiple maps.</description>
  <macros>
    <token name="@EXECUTABLE@">FeatureLinkerUnlabeledQT</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[FeatureLinkerUnlabeledQT

-in
  #for token in $param_in:
    $token
  #end for
#if $param_out:
  -out $param_out
#end if
#if $param_design:
  -design $param_design
#end if
#if $param_keep_subelements:
  -keep_subelements
#end if
#if $param_algorithm_use_identifications:
  -algorithm:use_identifications
#end if
#if $param_algorithm_nr_partitions:
  -algorithm:nr_partitions $param_algorithm_nr_partitions
#end if
#if $param_algorithm_ignore_charge:
  -algorithm:ignore_charge
#end if
#if $param_algorithm_distance_RT_max_difference:
  -algorithm:distance_RT:max_difference $param_algorithm_distance_RT_max_difference
#end if
#if $param_algorithm_distance_MZ_max_difference:
  -algorithm:distance_MZ:max_difference $param_algorithm_distance_MZ_max_difference
#end if
#if $param_algorithm_distance_MZ_unit:
  -algorithm:distance_MZ:unit
  #if " " in str($param_algorithm_distance_MZ_unit):
    "$param_algorithm_distance_MZ_unit"
  #else
    $param_algorithm_distance_MZ_unit
  #end if
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_algorithm_distance_RT_exponent:
  -algorithm:distance_RT:exponent $adv_opts.param_algorithm_distance_RT_exponent
#end if
    #if $adv_opts.param_algorithm_distance_RT_weight:
  -algorithm:distance_RT:weight $adv_opts.param_algorithm_distance_RT_weight
#end if
    #if $adv_opts.param_algorithm_distance_MZ_exponent:
  -algorithm:distance_MZ:exponent $adv_opts.param_algorithm_distance_MZ_exponent
#end if
    #if $adv_opts.param_algorithm_distance_MZ_weight:
  -algorithm:distance_MZ:weight $adv_opts.param_algorithm_distance_MZ_weight
#end if
    #if $adv_opts.param_algorithm_distance_intensity_exponent:
  -algorithm:distance_intensity:exponent $adv_opts.param_algorithm_distance_intensity_exponent
#end if
    #if $adv_opts.param_algorithm_distance_intensity_weight:
  -algorithm:distance_intensity:weight $adv_opts.param_algorithm_distance_intensity_weight
#end if
    #if $adv_opts.param_algorithm_distance_intensity_log_transform:
  -algorithm:distance_intensity:log_transform
  #if " " in str($adv_opts.param_algorithm_distance_intensity_log_transform):
    "$adv_opts.param_algorithm_distance_intensity_log_transform"
  #else
    $adv_opts.param_algorithm_distance_intensity_log_transform
  #end if
#end if
#end if
]]></command>
  <inputs>
    <param name="param_in" type="data" format="featurexml,consensusxml" multiple="true" optional="False" size="30" label="input files separated by blanks" help="(-in) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_design" type="data" format="tabular" optional="True" label="input file containing the experimental design" help="(-design) "/>
    <param name="param_keep_subelements" display="radio" type="boolean" truevalue="-keep_subelements" falsevalue="" checked="false" optional="True" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help="(-keep_subelements) "/>
    <param name="param_algorithm_use_identifications" display="radio" type="boolean" truevalue="-algorithm:use_identifications" falsevalue="" checked="false" optional="True" label="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)" help="(-use_identifications) "/>
    <param name="param_algorithm_nr_partitions" type="integer" min="1" optional="True" value="100" label="How many partitions in m/z space should be used for the algorithm (more partitions means faster runtime and more memory efficient execution )" help="(-nr_partitions) "/>
    <param name="param_algorithm_ignore_charge" display="radio" type="boolean" truevalue="-algorithm:ignore_charge" falsevalue="" checked="false" optional="True" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help="(-ignore_charge) "/>
    <param name="param_algorithm_distance_RT_max_difference" type="float" min="0.0" optional="True" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help="(-max_difference) "/>
    <param name="param_algorithm_distance_MZ_max_difference" type="float" min="0.0" optional="True" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help="(-max_difference) "/>
    <param name="param_algorithm_distance_MZ_unit" display="radio" type="select" optional="False" value="Da" label="Unit of the 'max_difference' paramete" help="(-unit) ">
      <option value="Da" selected="true">Da</option>
      <option value="ppm">ppm</option>
    </param>
    <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_distance_RT_exponent" type="float" min="0.0" optional="True" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/>
      <param name="param_algorithm_distance_RT_weight" type="float" min="0.0" optional="True" value="1.0" label="Final RT distances are weighted by this facto" help="(-weight) "/>
      <param name="param_algorithm_distance_MZ_exponent" type="float" min="0.0" optional="True" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/>
      <param name="param_algorithm_distance_MZ_weight" type="float" min="0.0" optional="True" value="1.0" label="Final m/z distances are weighted by this facto" help="(-weight) "/>
      <param name="param_algorithm_distance_intensity_exponent" type="float" min="0.0" optional="True" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/>
      <param name="param_algorithm_distance_intensity_weight" type="float" min="0.0" optional="True" value="0.0" label="Final intensity distances are weighted by this facto" help="(-weight) "/>
      <param name="param_algorithm_distance_intensity_log_transform" display="radio" type="select" optional="False" value="disabled" label="Log-transform intensities?" help="(-log_transform) If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
        <option value="enabled">enabled</option>
        <option value="disabled" selected="true">disabled</option>
      </param>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="consensusxml"/>
  </outputs>
  <help>Groups corresponding features from multiple maps.


For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureLinkerUnlabeledQT.html</help>
</tool>

11:bd07412009d1

<?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: [Map Alignment]-->
<tool id="FeatureLinkerUnlabeledQT" name="FeatureLinkerUnlabeledQT" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
  <description>Groups corresponding features from multiple maps.</description>
  <macros>
    <token name="@EXECUTABLE@">FeatureLinkerUnlabeledQT</token>
    <import>macros.xml</import>
    <import>macros_autotest.xml</import>
    <import>macros_test.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@
#import re

## Preprocessing
mkdir in &&
${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
mkdir out &&
#if $design:
  mkdir design &&
  ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
#end if

## 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
${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
-out
'out/output.${gxy2omsext("consensusxml")}'
#if $design:
  -design
  'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)'
#end if

## Postprocessing
&& mv 'out/output.${gxy2omsext("consensusxml")}' '$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[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param name="in" argument="-in" type="data" format="consensusxml,featurexml" multiple="true" optional="false" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
    <param name="design" argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/>
    <param name="keep_subelements" argument="-keep_subelements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help=""/>
    <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
      <param name="use_identifications" argument="-algorithm:use_identifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)" help=""/>
      <param name="nr_partitions" argument="-algorithm:nr_partitions" type="integer" optional="true" min="1" value="100" label="How many partitions in m/z space should be used for the algorithm (more partitions means faster runtime and more memory efficient execution )" help=""/>
      <param name="ignore_charge" argument="-algorithm:ignore_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help=""/>
      <param name="ignore_adduct" argument="-algorithm:ignore_adduct" type="boolean" truevalue="true" falsevalue="false" checked="true" label="true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts" help=""/>
      <section name="distance_RT" title="Distance component based on RT differences" help="" expanded="false">
        <param name="max_difference" argument="-algorithm:distance_RT:max_difference" type="float" optional="true" min="0.0" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help=""/>
        <param name="exponent" argument="-algorithm:distance_RT:exponent" type="float" optional="true" min="0.0" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
        <param name="weight" argument="-algorithm:distance_RT:weight" type="float" optional="true" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/>
      </section>
      <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false">
        <param name="max_difference" argument="-algorithm:distance_MZ:max_difference" type="float" optional="true" min="0.0" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help=""/>
        <param name="unit" argument="-algorithm:distance_MZ:unit" display="radio" type="select" optional="false" label="Unit of the 'max_difference' paramete" help="">
          <option value="Da" selected="true">Da</option>
          <option value="ppm">ppm</option>
          <expand macro="list_string_san"/>
        </param>
        <param name="exponent" argument="-algorithm:distance_MZ:exponent" type="float" optional="true" min="0.0" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
        <param name="weight" argument="-algorithm:distance_MZ:weight" type="float" optional="true" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/>
      </section>
      <section name="distance_intensity" title="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)" help="" expanded="false">
        <param name="exponent" argument="-algorithm:distance_intensity:exponent" type="float" optional="true" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
        <param name="weight" argument="-algorithm:distance_intensity:weight" type="float" optional="true" min="0.0" value="0.0" label="Final intensity distances are weighted by this facto" help=""/>
        <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" display="radio" type="select" optional="false" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
          <option value="enabled">enabled</option>
          <option value="disabled" selected="true">disabled</option>
          <expand macro="list_string_san"/>
        </param>
      </section>
    </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="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <expand macro="autotest_FeatureLinkerUnlabeledQT"/>
    <expand macro="manutest_FeatureLinkerUnlabeledQT"/>
  </tests>
  <help><![CDATA[Groups corresponding features from multiple maps.


For more information, visit http://www.openms.de/documentation/TOPP_FeatureLinkerUnlabeledQT.html]]></help>
  <expand macro="references"/>
</tool>