view NucleicAcidSearchEngine.xml @ 3:fe8d81be2564 draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 2adf8edc3de4e1cd3b299b26abb14544d17d0636"

<?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="NucleicAcidSearchEngine" name="NucleicAcidSearchEngine" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
  <description>Annotate nucleic acid identifications to MS/MS spectra.</description>
  <macros>
    <token name="@EXECUTABLE@">NucleicAcidSearchEngine</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 &&
ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
mkdir database &&
ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
mkdir out &&
#if "id_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir id_out &&
#end if
#if "lfq_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir lfq_out &&
#end if
#if "theo_ms2_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir theo_ms2_out &&
#end if
#if "exp_ms2_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir exp_ms2_out &&
#end if

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
@EXECUTABLE@ -ini @EXECUTABLE@.ctd
-in
'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
-database
'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)'
-out
'out/output.${gxy2omsext("mztab")}'
#if "id_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -id_out
  'id_out/output.${gxy2omsext("idxml")}'
#end if
#if "lfq_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -lfq_out
  'lfq_out/output.${gxy2omsext("tabular")}'
#end if
#if "theo_ms2_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -theo_ms2_out
  'theo_ms2_out/output.${gxy2omsext("mzml")}'
#end if
#if "exp_ms2_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -exp_ms2_out
  'exp_ms2_out/output.${gxy2omsext("mzml")}'
#end if
#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
  | tee '$stdout'
#end if

## Postprocessing
&& mv 'out/output.${gxy2omsext("mztab")}' '$out'
#if "id_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'id_out/output.${gxy2omsext("idxml")}' '$id_out'
#end if
#if "lfq_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'lfq_out/output.${gxy2omsext("tabular")}' '$lfq_out'
#end if
#if "theo_ms2_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'theo_ms2_out/output.${gxy2omsext("mzml")}' '$theo_ms2_out'
#end if
#if "exp_ms2_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'exp_ms2_out/output.${gxy2omsext("mzml")}' '$exp_ms2_out'
#end if
#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="mzml" optional="false" label="Input file: spectra" help=" select mzml data sets(s)"/>
    <param name="database" argument="-database" type="data" format="fasta" optional="false" label="Input file: sequence database" help=" select fasta data sets(s)"/>
    <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false">
      <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Precursor mass tolerance (+/- around uncharged precursor mass)" help=""/>
      <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
        <option value="Da">Da</option>
        <option value="ppm" selected="true">ppm</option>
        <expand macro="list_string_san"/>
      </param>
      <param name="min_charge" argument="-precursor:min_charge" type="integer" optional="true" value="-1" label="Minimum precursor charge to be considered" help=""/>
      <param name="max_charge" argument="-precursor:max_charge" type="integer" optional="true" value="-20" label="Maximum precursor charge to be considered" help=""/>
      <param name="include_unknown_charge" argument="-precursor:include_unknown_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include MS2 spectra with unknown precursor charge - try to match them in any possible charge between 'min_charge' and 'max_charge', at the risk of a higher error rate" help=""/>
      <param name="use_avg_mass" argument="-precursor:use_avg_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use average instead of monoisotopic precursor masses (appropriate for low-resolution instruments)" help=""/>
      <param name="use_adducts" argument="-precursor:use_adducts" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Consider possible salt adducts (see 'precursor:potential_adducts') when matching precursor masses" help=""/>
      <param name="potential_adducts" argument="-precursor:potential_adducts" type="text" optional="true" value="Na:+" label="Adducts considered to explain mass differences" help="Format: 'Element:Charge(+/-)', i.e. the number of '+' or '-' indicates the charge, e.g. 'Ca:++' indicates +2. Only used if 'precursor:use_adducts' is set (space separated list, in order to allow for spaces in list items surround them by single quotes)">
        <expand macro="list_string_val"/>
        <expand macro="list_string_san"/>
      </param>
      <param name="isotopes" argument="-precursor:isotopes" type="text" optional="true" value="0 1 2 3 4" label="Correct for mono-isotopic peak misassignments" help="E.g.: 1 = precursor may be misassigned to the first isotopic peak. Ignored if 'use_avg_mass' is set (space separated list, in order to allow for spaces in list items surround them by single quotes)">
        <expand macro="list_integer_valsan"/>
      </param>
    </section>
    <section name="fragment" title="Fragment (Product Ion) Options" help="" expanded="false">
      <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" optional="true" value="10.0" label="Fragment mass tolerance (+/- around fragment m/z)" help=""/>
      <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" display="radio" type="select" optional="false" label="Unit of fragment mass tolerance" help="">
        <option value="Da">Da</option>
        <option value="ppm" selected="true">ppm</option>
        <expand macro="list_string_san"/>
      </param>
      <param name="ions" argument="-fragment:ions" multiple="true" type="select" optional="true" label="Fragment ions to include in theoretical spectra" help="">
        <option value="a-B" selected="true">a-B</option>
        <option value="a" selected="true">a</option>
        <option value="b" selected="true">b</option>
        <option value="c" selected="true">c</option>
        <option value="d" selected="true">d</option>
        <option value="w" selected="true">w</option>
        <option value="x" selected="true">x</option>
        <option value="y" selected="true">y</option>
        <option value="z" selected="true">z</option>
        <expand macro="list_string_san"/>
      </param>
    </section>
    <section name="modifications" title="Modifications Options" help="" expanded="false">
      <param name="variable" argument="-modifications:variable" multiple="true" type="select" optional="true" label="Variable modifications" help="">
        <option value="">default (nothing chosen)</option>
        <option value="m1Am">m1Am</option>
        <option value="m1Gm">m1Gm</option>
        <option value="m1Im">m1Im</option>
        <option value="m1acp3Y">m1acp3Y</option>
        <option value="m1A">m1A</option>
        <option value="m1G">m1G</option>
        <option value="m1I">m1I</option>
        <option value="m1Y">m1Y</option>
        <option value="m28A">m28A</option>
        <option value="msms2i6A">msms2i6A</option>
        <option value="ges2U">ges2U</option>
        <option value="k2C">k2C</option>
        <option value="m2A">m2A</option>
        <option value="ms2ct6A">ms2ct6A</option>
        <option value="ms2io6A">ms2io6A</option>
        <option value="ms2hn6A">ms2hn6A</option>
        <option value="ms2i6A">ms2i6A</option>
        <option value="ms2m6A">ms2m6A</option>
        <option value="ms2t6A">ms2t6A</option>
        <option value="se2U">se2U</option>
        <option value="s2Um">s2Um</option>
        <option value="s2C">s2C</option>
        <option value="s2U">s2U</option>
        <option value="Am">Am</option>
        <option value="Cm">Cm</option>
        <option value="Gm">Gm</option>
        <option value="Im">Im</option>
        <option value="Ym">Ym</option>
        <option value="Um">Um</option>
        <option value="mcmo5Um">mcmo5Um</option>
        <option value="Ar(p)">Ar(p)</option>
        <option value="Gr(p)">Gr(p)</option>
        <option value="(pN)2'3'&gt;p">(pN)2'3'&gt;p</option>
        <option value="hm5Cm">hm5Cm</option>
        <option value="m3Um">m3Um</option>
        <option value="acp3D">acp3D</option>
        <option value="acp3Y">acp3Y</option>
        <option value="acp3U">acp3U</option>
        <option value="m3C">m3C</option>
        <option value="m3Y">m3Y</option>
        <option value="m3U">m3U</option>
        <option value="imG-14">imG-14</option>
        <option value="s4U">s4U</option>
        <option value="m5Cm">m5Cm</option>
        <option value="m5Um">m5Um</option>
        <option value="mchm5Um">mchm5Um</option>
        <option value="mchm5U">mchm5U</option>
        <option value="inm5s2U">inm5s2U</option>
        <option value="inm5Um">inm5Um</option>
        <option value="inm5U">inm5U</option>
        <option value="nm5ges2U">nm5ges2U</option>
        <option value="nm5se2U">nm5se2U</option>
        <option value="nm5s2U">nm5s2U</option>
        <option value="nm5U">nm5U</option>
        <option value="nchm5U">nchm5U</option>
        <option value="ncm5s2U">ncm5s2U</option>
        <option value="ncm5Um">ncm5Um</option>
        <option value="ncm5U">ncm5U</option>
        <option value="chm5U">chm5U</option>
        <option value="cm5s2U">cm5s2U</option>
        <option value="cmnm5ges2U">cmnm5ges2U</option>
        <option value="cmnm5se2U">cmnm5se2U</option>
        <option value="cmnm5s2U">cmnm5s2U</option>
        <option value="cmnm5Um">cmnm5Um</option>
        <option value="cmnm5U">cmnm5U</option>
        <option value="cm5U">cm5U</option>
        <option value="cnm5U">cnm5U</option>
        <option value="f5Cm">f5Cm</option>
        <option value="f5C">f5C</option>
        <option value="ho5C">ho5C</option>
        <option value="hm5C">hm5C</option>
        <option value="ho5U">ho5U</option>
        <option value="mcm5s2U">mcm5s2U</option>
        <option value="mcm5Um">mcm5Um</option>
        <option value="mcm5U">mcm5U</option>
        <option value="mo5U">mo5U</option>
        <option value="m5s2U">m5s2U</option>
        <option value="mnm5ges2U">mnm5ges2U</option>
        <option value="mnm5se2U">mnm5se2U</option>
        <option value="mnm5s2U">mnm5s2U</option>
        <option value="mnm5U">mnm5U</option>
        <option value="m5C">m5C</option>
        <option value="m5D">m5D</option>
        <option value="m5U">m5U</option>
        <option value="tm5s2U">tm5s2U</option>
        <option value="tm5U">tm5U</option>
        <option value="CoA(pN)">CoA(pN)</option>
        <option value="acCoA(pN)">acCoA(pN)</option>
        <option value="malonyl-CoA(pN)">malonyl-CoA(pN)</option>
        <option value="succinyl-CoA(pN)">succinyl-CoA(pN)</option>
        <option value="p(pN)">p(pN)</option>
        <option value="5'-OH-N">5'-OH-N</option>
        <option value="(pN)">(pN)</option>
        <option value="NAD(pN)">NAD(pN)</option>
        <option value="pp(pN)">pp(pN)</option>
        <option value="yW-86">yW-86</option>
        <option value="yW-72">yW-72</option>
        <option value="yW-58">yW-58</option>
        <option value="preQ1tRNA">preQ1tRNA</option>
        <option value="preQ0tRNA">preQ0tRNA</option>
        <option value="m7G">m7G</option>
        <option value="m7Gpp(pN)">m7Gpp(pN)</option>
        <option value="m8A">m8A</option>
        <option value="m2Gm">m2Gm</option>
        <option value="m27Gm">m27Gm</option>
        <option value="m27G">m27G</option>
        <option value="m27Gpp(pN)">m27Gpp(pN)</option>
        <option value="m22Gm">m22Gm</option>
        <option value="m227G">m227G</option>
        <option value="m227Gpp(pN)">m227Gpp(pN)</option>
        <option value="m22G">m22G</option>
        <option value="m2G">m2G</option>
        <option value="m4Cm">m4Cm</option>
        <option value="m44Cm">m44Cm</option>
        <option value="m44C">m44C</option>
        <option value="ac4Cm">ac4Cm</option>
        <option value="ac4C">ac4C</option>
        <option value="m4C">m4C</option>
        <option value="m6Am">m6Am</option>
        <option value="m66Am">m66Am</option>
        <option value="m66A">m66A</option>
        <option value="io6A">io6A</option>
        <option value="ac6A">ac6A</option>
        <option value="f6A">f6A</option>
        <option value="g6A">g6A</option>
        <option value="hm6A">hm6A</option>
        <option value="hn6A">hn6A</option>
        <option value="i6A">i6A</option>
        <option value="m6t6A">m6t6A</option>
        <option value="m6A">m6A</option>
        <option value="t6A">t6A</option>
        <option value="Qbase">Qbase</option>
        <option value="C+">C+</option>
        <option value="mm(pN)">mm(pN)</option>
        <option value="m(pN)">m(pN)</option>
        <option value="G+">G+</option>
        <option value="ct6A">ct6A</option>
        <option value="D">D</option>
        <option value="oQ">oQ</option>
        <option value="galQ">galQ</option>
        <option value="mpp(pN)">mpp(pN)</option>
        <option value="gluQ">gluQ</option>
        <option value="pG(pN)">pG(pN)</option>
        <option value="Gpp(pN)">Gpp(pN)</option>
        <option value="ht6A">ht6A</option>
        <option value="OHyW">OHyW</option>
        <option value="I">I</option>
        <option value="imG2">imG2</option>
        <option value="manQ">manQ</option>
        <option value="OHyWy">OHyWy</option>
        <option value="mimG">mimG</option>
        <option value="o2yW">o2yW</option>
        <option value="preQ0base">preQ0base</option>
        <option value="preQ1base">preQ1base</option>
        <option value="Y">Y</option>
        <option value="Q">Q</option>
        <option value="OHyWx">OHyWx</option>
        <option value="Xm">Xm</option>
        <option value="xX">xX</option>
        <option value="xA">xA</option>
        <option value="xC">xC</option>
        <option value="xG">xG</option>
        <option value="xU">xU</option>
        <option value="N">N</option>
        <option value="cmo5U">cmo5U</option>
        <option value="mcmo5U">mcmo5U</option>
        <option value="yW">yW</option>
        <option value="imG">imG</option>
        <option value="3'-p">3'-p</option>
        <option value="5'-p">5'-p</option>
        <option value="mA">mA</option>
        <option value="mC">mC</option>
        <option value="mG">mG</option>
        <option value="mU">mU</option>
        <option value="sU">sU</option>
        <option value="mmA">mmA</option>
        <option value="mAm">mAm</option>
        <option value="mCm">mCm</option>
        <option value="mGm">mGm</option>
        <option value="mUm">mUm</option>
        <option value="cmo5U/chm5U">cmo5U/chm5U</option>
        <option value="mchm5U/mcmo5U">mchm5U/mcmo5U</option>
        <option value="mchm5Um/mcmo5Um">mchm5Um/mcmo5Um</option>
        <option value="m6t6A/hn6A">m6t6A/hn6A</option>
        <option value="galQ/manQ">galQ/manQ</option>
        <option value="mA?">mA?</option>
        <option value="mC?">mC?</option>
        <option value="mG?">mG?</option>
        <option value="mU?">mU?</option>
        <option value="mI?">mI?</option>
        <option value="msU?">msU?</option>
        <option value="mmA?">mmA?</option>
        <option value="mmC?">mmC?</option>
        <option value="mmG?">mmG?</option>
        <option value="mmmG?">mmmG?</option>
        <option value="ac4C/f5Cm?">ac4C/f5Cm?</option>
        <option value="acp3U/cmnm5Um?">acp3U/cmnm5Um?</option>
        <expand macro="list_string_san"/>
      </param>
      <param name="variable_max_per_oligo" argument="-modifications:variable_max_per_oligo" type="integer" optional="true" value="2" label="Maximum number of residues carrying a variable modification per candidate oligonucleotide" help=""/>
      <param name="resolve_ambiguities" argument="-modifications:resolve_ambiguities" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Attempt to resolve ambiguous modifications" help="(e.g. 'mA?' for 'mA'/'Am') based on a-B ions.. This incurs a performance cost because two modifications have to be considered for each case.. Requires a-B ions to be enabled in parameter 'fragment:ions'"/>
    </section>
    <section name="oligo" title="Oligonucleotide Options" help="" expanded="false">
      <param name="min_size" argument="-oligo:min_size" type="integer" optional="true" value="5" label="Minimum size an oligonucleotide must have after digestion to be considered in the search" help=""/>
      <param name="max_size" argument="-oligo:max_size" type="integer" optional="true" value="0" label="Maximum size an oligonucleotide must have after digestion to be considered in the search, leave at 0 for no limit" help=""/>
      <param name="missed_cleavages" argument="-oligo:missed_cleavages" type="integer" optional="true" value="1" label="Number of missed cleavages" help=""/>
      <param name="enzyme" argument="-oligo:enzyme" type="select" optional="false" label="The enzyme used for RNA digestion" help="">
        <option value="RNase_T1">RNase_T1</option>
        <option value="cusativin">cusativin</option>
        <option value="RNase_U2">RNase_U2</option>
        <option value="RNase_A">RNase_A</option>
        <option value="RNase_MC1">RNase_MC1</option>
        <option value="RNase_H">RNase_H</option>
        <option value="no cleavage" selected="true">no cleavage</option>
        <option value="unspecific cleavage">unspecific cleavage</option>
        <expand macro="list_string_san"/>
      </param>
    </section>
    <section name="report" title="Reporting Options" help="" expanded="false">
      <param name="top_hits" argument="-report:top_hits" type="integer" optional="true" min="0" value="1" label="Maximum number of top-scoring hits per spectrum that are reported ('0' for all hits)" help=""/>
    </section>
    <section name="fdr" title="False Discovery Rate Options" help="" expanded="false">
      <param name="decoy_pattern" argument="-fdr:decoy_pattern" type="text" optional="true" value="" label="String used as part of the accession to annotate decoy sequences" help="(e.g. 'DECOY_'). Leave empty to skip the FDR/q-value calculation">
        <expand macro="list_string_san"/>
      </param>
      <param name="cutoff" argument="-fdr:cutoff" type="float" optional="true" min="0.0" max="1.0" value="1.0" label="Cut-off for FDR filtering; search hits with higher q-values will be removed" help=""/>
      <param name="remove_decoys" argument="-fdr:remove_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not score hits to decoy sequences and remove them when filtering" help=""/>
    </section>
    <expand macro="adv_opts_macro">
      <param name="decharge_ms2" argument="-decharge_ms2" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Decharge the MS2 spectra for scoring" help=""/>
      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides 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" optional="true" multiple="true" label="Optional outputs">
      <option value="id_out_FLAG">id_out (Output file: idXML (for visualization in TOPPView))</option>
      <option value="lfq_out_FLAG">lfq_out (Output file: Targets for label-free quantification using FeatureFinderMetaboIdent ('id' input))</option>
      <option value="theo_ms2_out_FLAG">theo_ms2_out (Output file: theoretical MS2 spectra for precursor mass matches)</option>
      <option value="exp_ms2_out_FLAG">exp_ms2_out (Output file: experimental MS2 spectra for precursor mass matches)</option>
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/>
    <data name="id_out" label="${tool.name} on ${on_string}: id_out" format="idxml">
      <filter>OPTIONAL_OUTPUTS is not None and "id_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
    <data name="lfq_out" label="${tool.name} on ${on_string}: lfq_out" format="tabular">
      <filter>OPTIONAL_OUTPUTS is not None and "lfq_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
    <data name="theo_ms2_out" label="${tool.name} on ${on_string}: theo_ms2_out" format="mzml">
      <filter>OPTIONAL_OUTPUTS is not None and "theo_ms2_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
    <data name="exp_ms2_out" label="${tool.name} on ${on_string}: exp_ms2_out" format="mzml">
      <filter>OPTIONAL_OUTPUTS is not None and "exp_ms2_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <expand macro="autotest_NucleicAcidSearchEngine"/>
    <expand macro="manutest_NucleicAcidSearchEngine"/>
  </tests>
  <help><![CDATA[Annotate nucleic acid identifications to MS/MS spectra.


For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_NucleicAcidSearchEngine.html]]></help>
  <expand macro="references"/>
</tool>