annotate MascotAdapter.xml @ 14:087b9d721a08 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906

<!--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: [Identification of Proteins/Peptides (SearchEngines)]-->
<tool id="MascotAdapter" name="MascotAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Annotates MS/MS spectra using Mascot</description>
  <macros>
    <token name="@EXECUTABLE@">MascotAdapter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@
#import re

## Preprocessing
mkdir in &&
cp '$in' 'in/${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($in.ext)'
-out
'out/output.${out_type}'

## Postprocessing
&& mv 'out/output.${out_type}' '$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[{"mascot_directory": "TODO", "temp_data_directory": "\$TMP_DIR", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param argument="-in" type="data" format="mascotxml,mzdata" label="input file in mzData format" help="Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read select mascotxml,mzdata data sets(s)"/>
    <param argument="-out_type" type="select" label="output file type (for TOPPAS)" help="">
      <option value="idXML">idxml</option>
      <option value="mgf">mgf</option>
      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
      <expand macro="list_string_san" name="out_type"/>
    </param>
    <param argument="-instrument" type="text" value="Default" label="the instrument that was used to measure the spectra" help="">
      <expand macro="list_string_san" name="instrument"/>
    </param>
    <param argument="-precursor_mass_tolerance" type="float" value="2.0" label="the precursor mass tolerance" help=""/>
    <param argument="-peak_mass_tolerance" type="float" value="1.0" label="the peak mass tolerance" help=""/>
    <param argument="-taxonomy" type="select" label="the taxonomy" help="">
      <option value="All entries" selected="true">All entries</option>
      <option value=". . Archaea (Archaeobacteria)">. . Archaea (Archaeobacteria)</option>
      <option value=". . Eukaryota (eucaryotes)">. . Eukaryota (eucaryotes)</option>
      <option value=". . . . Alveolata (alveolates)">. . . . Alveolata (alveolates)</option>
      <option value=". . . . . . Plasmodium falciparum (malaria parasite)">. . . . . . Plasmodium falciparum (malaria parasite)</option>
      <option value=". . . . . . Other Alveolata">. . . . . . Other Alveolata</option>
      <option value=". . . . Metazoa (Animals)">. . . . Metazoa (Animals)</option>
      <option value=". . . . . . Caenorhabditis elegans">. . . . . . Caenorhabditis elegans</option>
      <option value=". . . . . . Drosophila (fruit flies)">. . . . . . Drosophila (fruit flies)</option>
      <option value=". . . . . . Chordata (vertebrates and relatives)">. . . . . . Chordata (vertebrates and relatives)</option>
      <option value=". . . . . . . . bony vertebrates">. . . . . . . . bony vertebrates</option>
      <option value=". . . . . . . . . . lobe-finned fish and tetrapod clade">. . . . . . . . . . lobe-finned fish and tetrapod clade</option>
      <option value=". . . . . . . . . . . . Mammalia (mammals)">. . . . . . . . . . . . Mammalia (mammals)</option>
      <option value=". . . . . . . . . . . . . . Primates">. . . . . . . . . . . . . . Primates</option>
      <option value=". . . . . . . . . . . . . . . . Homo sapiens (human)">. . . . . . . . . . . . . . . . Homo sapiens (human)</option>
      <option value=". . . . . . . . . . . . . . . . Other primates">. . . . . . . . . . . . . . . . Other primates</option>
      <option value=". . . . . . . . . . . . . . Rodentia (Rodents)">. . . . . . . . . . . . . . Rodentia (Rodents)</option>
      <option value=". . . . . . . . . . . . . . . . Mus.">. . . . . . . . . . . . . . . . Mus.</option>
      <option value=". . . . . . . . . . . . . . . . . . Mus musculus (house mouse)">. . . . . . . . . . . . . . . . . . Mus musculus (house mouse)</option>
      <option value=". . . . . . . . . . . . . . . . Rattus">. . . . . . . . . . . . . . . . Rattus</option>
      <option value=". . . . . . . . . . . . . . . . Other rodentia">. . . . . . . . . . . . . . . . Other rodentia</option>
      <option value=". . . . . . . . . . . . . . Other mammalia">. . . . . . . . . . . . . . Other mammalia</option>
      <option value=". . . . . . . . . . . . Xenopus laevis (African clawed frog)">. . . . . . . . . . . . Xenopus laevis (African clawed frog)</option>
      <option value=". . . . . . . . . . . . Other lobe-finned fish and tetrapod clade">. . . . . . . . . . . . Other lobe-finned fish and tetrapod clade</option>
      <option value=". . . . . . . . . . Actinopterygii (ray-finned fishes)">. . . . . . . . . . Actinopterygii (ray-finned fishes)</option>
      <option value=". . . . . . . . . . . . Takifugu rubripes (Japanese Pufferfish)">. . . . . . . . . . . . Takifugu rubripes (Japanese Pufferfish)</option>
      <option value=". . . . . . . . . . . . Danio rerio (zebra fish)">. . . . . . . . . . . . Danio rerio (zebra fish)</option>
      <option value=". . . . . . . . . . . . Other Actinopterygii">. . . . . . . . . . . . Other Actinopterygii</option>
      <option value=". . . . . . . . Other Chordata">. . . . . . . . Other Chordata</option>
      <option value=". . . . . . Other Metazoa">. . . . . . Other Metazoa</option>
      <option value=". . . . Dictyostelium discoideum">. . . . Dictyostelium discoideum</option>
      <option value=". . . . Fungi">. . . . Fungi</option>
      <option value=". . . . . . Saccharomyces Cerevisiae (baker's yeast)">. . . . . . Saccharomyces Cerevisiae (baker's yeast)</option>
      <option value=". . . . . . Schizosaccharomyces pombe (fission yeast)">. . . . . . Schizosaccharomyces pombe (fission yeast)</option>
      <option value=". . . . . . Pneumocystis carinii">. . . . . . Pneumocystis carinii</option>
      <option value=". . . . . . Other Fungi">. . . . . . Other Fungi</option>
      <option value=". . . . Viridiplantae (Green Plants)">. . . . Viridiplantae (Green Plants)</option>
      <option value=". . . . . . Arabidopsis thaliana (thale cress)">. . . . . . Arabidopsis thaliana (thale cress)</option>
      <option value=". . . . . . Oryza sativa (rice)">. . . . . . Oryza sativa (rice)</option>
      <option value=". . . . . . Other green plants">. . . . . . Other green plants</option>
      <option value=". . . . Other Eukaryota">. . . . Other Eukaryota</option>
      <option value=". . Bacteria (Eubacteria)">. . Bacteria (Eubacteria)</option>
      <option value=". . . . Actinobacteria (class)">. . . . Actinobacteria (class)</option>
      <option value=". . . . . . Mycobacterium tuberculosis complex">. . . . . . Mycobacterium tuberculosis complex</option>
      <option value=". . . . . . Other Actinobacteria (class)">. . . . . . Other Actinobacteria (class)</option>
      <option value=". . . . Firmicutes (gram-positive bacteria)">. . . . Firmicutes (gram-positive bacteria)</option>
      <option value=". . . . . . Bacillus subtilis">. . . . . . Bacillus subtilis</option>
      <option value=". . . . . . Mycoplasma">. . . . . . Mycoplasma</option>
      <option value=". . . . . . Streptococcus Pneumoniae">. . . . . . Streptococcus Pneumoniae</option>
      <option value=". . . . . . Streptomyces coelicolor">. . . . . . Streptomyces coelicolor</option>
      <option value=". . . . . . Other Firmicutes">. . . . . . Other Firmicutes</option>
      <option value=". . . . Proteobacteria (purple bacteria)">. . . . Proteobacteria (purple bacteria)</option>
      <option value=". . . . . . Agrobacterium tumefaciens">. . . . . . Agrobacterium tumefaciens</option>
      <option value=". . . . . . Campylobacter jejuni">. . . . . . Campylobacter jejuni</option>
      <option value=". . . . . . Escherichia coli">. . . . . . Escherichia coli</option>
      <option value=". . . . . . Neisseria meningitidis">. . . . . . Neisseria meningitidis</option>
      <option value=". . . . . . Salmonella">. . . . . . Salmonella</option>
      <option value=". . . . . . Other Proteobacteria">. . . . . . Other Proteobacteria</option>
      <option value=". . . . Other Bacteria">. . . . Other Bacteria</option>
      <option value=". . Viruses">. . Viruses</option>
      <option value=". . . . Hepatitis C virus">. . . . Hepatitis C virus</option>
      <option value=". . . . Other viruses">. . . . Other viruses</option>
      <option value=". . Other (includes plasmids and artificial sequences)">. . Other (includes plasmids and artificial sequences)</option>
      <option value=". . unclassified">. . unclassified</option>
      <option value=". . Species information unavailable">. . Species information unavailable</option>
      <expand macro="list_string_san" name="taxonomy"/>
    </param>
    <param argument="-modifications" type="text" optional="true" value="" label="the modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
      <expand macro="list_string_val" name="modifications"/>
      <expand macro="list_string_san" name="modifications"/>
    </param>
    <param argument="-variable_modifications" type="text" optional="true" value="" label="the variable modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
      <expand macro="list_string_val" name="variable_modifications"/>
      <expand macro="list_string_san" name="variable_modifications"/>
    </param>
    <param argument="-charges" type="text" value="1+ 2+ 3+" label="the different charge states" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
      <expand macro="list_string_val" name="charges"/>
      <expand macro="list_string_san" name="charges"/>
    </param>
    <param argument="-db" type="text" value="MSDB" label="the database to search in" help="">
      <expand macro="list_string_san" name="db"/>
    </param>
    <param argument="-hits" type="text" value="AUTO" label="the number of hits to report" help="">
      <expand macro="list_string_san" name="hits"/>
    </param>
    <param argument="-cleavage" type="select" label="The enzyme descriptor to the enzyme used for digestion" help="(Trypsin is default, None would be best for peptide input or unspecific digestion, for more please refer to your mascot server)">
      <option value="Trypsin" selected="true">Trypsin</option>
      <option value="Arg-C">Arg-C</option>
      <option value="Asp-N">Asp-N</option>
      <option value="Asp-N_ambic">Asp-N_ambic</option>
      <option value="Chymotrypsin">Chymotrypsin</option>
      <option value="CNBr">CNBr</option>
      <option value="CNBr+Trypsin">CNBr+Trypsin</option>
      <option value="Formic_acid">Formic_acid</option>
      <option value="Lys-C">Lys-C</option>
      <option value="Lys-C/P">Lys-C/P</option>
      <option value="PepsinA">PepsinA</option>
      <option value="Tryp-CNBr">Tryp-CNBr</option>
      <option value="TrypChymo">TrypChymo</option>
      <option value="Trypsin/P">Trypsin/P</option>
      <option value="V8-DE">V8-DE</option>
      <option value="V8-E">V8-E</option>
      <option value="semiTrypsin">semiTrypsin</option>
      <option value="LysC+AspN">LysC+AspN</option>
      <option value="None">None</option>
      <expand macro="list_string_san" name="cleavage"/>
    </param>
    <param argument="-missed_cleavages" type="integer" min="0" value="0" label="number of allowed missed cleavages" help=""/>
    <param argument="-sig_threshold" type="float" value="0.05" label="significance threshold" help=""/>
    <param argument="-pep_homol" type="float" value="1.0" label="peptide homology threshold" help=""/>
    <param argument="-pep_ident" type="float" value="1.0" label="peptide ident threshold" help=""/>
    <param argument="-pep_rank" type="integer" value="1" label="peptide rank" help=""/>
    <param argument="-prot_score" type="float" value="1.0" label="protein score" help=""/>
    <param argument="-pep_score" type="float" value="1.0" label="peptide score" help=""/>
    <param argument="-pep_exp_z" type="integer" value="1" label="peptide expected charge" help=""/>
    <param argument="-show_unassigned" type="integer" value="1" label="show_unassigned" help=""/>
    <param argument="-first_dim_rt" type="float" value="0.0" label="additional information which is added to every peptide identification as metavalue if set &gt; 0" help=""/>
    <param argument="-boundary" type="text" optional="true" value="" label="MIME boundary for mascot output format" help="">
      <expand macro="list_string_san" name="boundary"/>
    </param>
    <param argument="-mass_type" type="select" label="mass type" help="">
      <option value="Monoisotopic" selected="true">Monoisotopic</option>
      <option value="Average">Average</option>
      <expand macro="list_string_san" name="mass_type"/>
    </param>
    <expand macro="adv_opts_macro">
      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
        <expand macro="list_string_san" name="test"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="idxml">
      <change_format>
        <when input="out_type" value="mgf" format="mgf"/>
      </change_format>
    </data>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <!-- TOPP_MascotAdapter_1 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="MascotAdapter_1_input.mzData"/>
      <output name="out" value="MascotAdapter_1_output.mascot_in" compare="sim_size" delta_frac="0.7"/>
      <param name="out_type" value="mgf"/>
      <param name="instrument" value="ESI-TRAP"/>
      <param name="precursor_mass_tolerance" value="1.3"/>
      <param name="peak_mass_tolerance" value="0.3"/>
      <param name="taxonomy" value=". . . . . . Chordata (vertebrates and relatives)"/>
      <param name="modifications" value="&quot;Carboxymethyl (C)&quot;"/>
      <param name="variable_modifications" value="&quot;Variable_Modifications_TEST_1&quot;"/>
      <param name="charges" value="&quot;1+&quot; &quot;2+&quot; &quot;3+&quot;"/>
      <param name="db" value="MSDB"/>
      <param name="hits" value="AUTO"/>
      <param name="cleavage" value="Trypsin"/>
      <param name="missed_cleavages" value="1"/>
      <param name="sig_threshold" value="0.05"/>
      <param name="pep_homol" value="1.0"/>
      <param name="pep_ident" value="1.0"/>
      <param name="pep_rank" value="1"/>
      <param name="prot_score" value="1.0"/>
      <param name="pep_score" value="1.0"/>
      <param name="pep_exp_z" value="1"/>
      <param name="show_unassigned" value="1"/>
      <param name="first_dim_rt" value="0.0"/>
      <param name="boundary" value="ABCDEFGHIJKMNOPQRSTUVWXYZ"/>
      <param name="mass_type" value="Monoisotopic"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_MascotAdapter_2 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="MascotAdapter_2_input.mascotXML"/>
      <output name="out" value="MascotAdapter_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
      <param name="out_type" value="idXML"/>
      <param name="instrument" value="Default"/>
      <param name="precursor_mass_tolerance" value="2.0"/>
      <param name="peak_mass_tolerance" value="1.0"/>
      <param name="taxonomy" value="All entries"/>
      <param name="charges" value="&quot;1+&quot; &quot;2+&quot; &quot;3+&quot;"/>
      <param name="db" value="MSDB"/>
      <param name="hits" value="AUTO"/>
      <param name="cleavage" value="Trypsin"/>
      <param name="missed_cleavages" value="0"/>
      <param name="sig_threshold" value="0.05"/>
      <param name="pep_homol" value="1.0"/>
      <param name="pep_ident" value="1.0"/>
      <param name="pep_rank" value="1"/>
      <param name="prot_score" value="1.0"/>
      <param name="pep_score" value="1.0"/>
      <param name="pep_exp_z" value="1"/>
      <param name="show_unassigned" value="1"/>
      <param name="first_dim_rt" value="0.0"/>
      <param name="boundary" value=""/>
      <param name="mass_type" value="Monoisotopic"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
  </tests>
  <help><![CDATA[Annotates MS/MS spectra using Mascot.


For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MascotAdapter.html]]></help>
  <expand macro="references"/>
</tool>