annotate macros_discarded_auto.xml @ 11:75bb0f81cfa3 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"

<xml name="manutest_OpenSwathFileSplitter">
<test expect_num_outputs="2">
  <conditional name="adv_opts_cond">
    <param name="adv_opts_selector" value="advanced"/>
    <param name="force" value="false"/>
    <param name="test" value="true"/>
  </conditional>
  <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
  <output_collection name="outputDirectory" count=""/>
  <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>
  <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_qc_FLAG"/>
  <output name="ctd_out" ftype="xml">
    <assert_contents>
      <is_valid_xml/>
    </assert_contents>
  </output>
</test></xml>
<xml name="manutest_IDRipper">
<test expect_num_outputs="1">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDRipper_1_input.idXML"/>
      <output_collection name="out_path" count=""/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test><test expect_num_outputs="1">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDRipper_2_input.idXML"/>
      <output_collection name="out_path" count=""/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test><test expect_num_outputs="1">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDRipper_3_output.idXML"/>
      <output_collection name="out_path" count=""/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test></xml>
<xml name="manutest_MzMLSplitter">
<test expect_num_outputs="1">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="FileFilter_1_input.mzML"/>
      <output_collection name="out" count=""/>
      <param name="parts" value="2"/>
      <param name="size" value="0"/>
      <param name="unit" value="MB"/>
      <param name="no_chrom" value="false"/>
      <param name="no_spec" value="false"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test><test expect_num_outputs="1">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="FileFilter_1_input.mzML"/>
      <output_collection name="out" count=""/>
      <param name="parts" value="1"/>
      <param name="size" value="40"/>
      <param name="unit" value="KB"/>
      <param name="no_chrom" value="false"/>
      <param name="no_spec" value="false"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test></xml>
<xml name="manutest_MSFraggerAdapter">
<test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="java_heapmemory" value="2600"/>
      <param name="in" value="spectra.mzML"/>
      <output name="out" file="MSFraggerAdapter_7_out_tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <output name="opt_out" file="MSFraggerAdapter_7_opt_out_tmp.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
      <param name="database" value="proteins.fasta"/>
      <section name="tolerance">
        <param name="precursor_mass_tolerance" value="20.0"/>
        <param name="precursor_mass_unit" value="ppm"/>
        <param name="precursor_true_tolerance" value="0.0"/>
        <param name="precursor_true_unit" value="ppm"/>
        <param name="fragment_mass_tolerance" value="20.0"/>
        <param name="fragment_mass_unit" value="ppm"/>
        <param name="isotope_error" value="0"/>
      </section>
      <section name="digest">
        <param name="search_enzyme_name" value="Trypsin"/>
        <param name="search_enzyme_cutafter" value="KR"/>
        <param name="search_enzyme_nocutbefore" value="P"/>
        <param name="num_enzyme_termini" value="semi"/>
        <param name="allowed_missed_cleavage" value="2"/>
        <param name="min_length" value="7"/>
        <param name="max_length" value="64"/>
        <param name="mass_range_min" value="500.0"/>
        <param name="mass_range_max" value="5000.0"/>
      </section>
      <section name="varmod">
        <param name="clip_nterm_m" value="false"/>
        <param name="masses" value=""/>
        <param name="syntaxes" value=""/>
        <param name="enable_common" value="true"/>
        <param name="not_allow_multiple_variable_mods_on_residue" value="false"/>
        <param name="max_variable_mods_per_mod" value="2"/>
        <param name="max_variable_mods_combinations" value="5000"/>
      </section>
      <section name="spectrum">
        <param name="minimum_peaks" value="10"/>
        <param name="use_topn_peaks" value="50"/>
        <param name="minimum_ratio" value="0.0"/>
        <param name="clear_mz_range_min" value="0.0"/>
        <param name="clear_mz_range_max" value="0.0"/>
        <param name="max_fragment_charge" value="2"/>
        <param name="override_charge" value="false"/>
        <param name="precursor_charge_min" value="1"/>
        <param name="precursor_charge_max" value="4"/>
      </section>
      <section name="search">
        <param name="track_zero_topn" value="0"/>
        <param name="zero_bin_accept_expect" value="0.0"/>
        <param name="zero_bin_mult_expect" value="1.0"/>
        <param name="add_topn_complementary" value="0"/>
        <param name="min_fragments_modeling" value="3"/>
        <param name="min_matched_fragments" value="4"/>
        <param name="output_report_topn" value="1"/>
        <param name="output_max_expect" value="50.0"/>
      </section>
      <section name="statmod">
        <param name="add_cterm_peptide" value="0.0"/>
        <param name="add_nterm_peptide" value="0.0"/>
        <param name="add_cterm_protein" value="0.0"/>
        <param name="add_nterm_protein" value="0.0"/>
        <param name="add_G_glycine" value="0.0"/>
        <param name="add_A_alanine" value="0.0"/>
        <param name="add_S_serine" value="0.0"/>
        <param name="add_P_proline" value="0.0"/>
        <param name="add_V_valine" value="0.0"/>
        <param name="add_T_threonine" value="0.0"/>
        <param name="add_C_cysteine" value="57.021464"/>
        <param name="add_L_leucine" value="0.0"/>
        <param name="add_I_isoleucine" value="0.0"/>
        <param name="add_N_asparagine" value="0.0"/>
        <param name="add_D_aspartic_acid" value="0.0"/>
        <param name="add_Q_glutamine" value="0.0"/>
        <param name="add_K_lysine" value="0.0"/>
        <param name="add_E_glutamic_acid" value="0.0"/>
        <param name="add_M_methionine" value="0.0"/>
        <param name="add_H_histidine" value="0.0"/>
        <param name="add_F_phenylalanine" value="0.0"/>
        <param name="add_R_arginine" value="0.0"/>
        <param name="add_Y_tyrosine" value="0.0"/>
        <param name="add_W_tryptophan" value="0.0"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,opt_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test><test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="java_heapmemory" value="2600"/>
      <param name="in" value="spectra_comet.mzML"/>
      <output name="out" file="MSFraggerAdapter_8_out_tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="database" value="proteins.fasta"/>
      <section name="tolerance">
        <param name="precursor_mass_tolerance" value="20.0"/>
        <param name="precursor_mass_unit" value="ppm"/>
        <param name="precursor_true_tolerance" value="0.0"/>
        <param name="precursor_true_unit" value="ppm"/>
        <param name="fragment_mass_tolerance" value="20.0"/>
        <param name="fragment_mass_unit" value="ppm"/>
        <param name="isotope_error" value="0"/>
      </section>
      <section name="digest">
        <param name="search_enzyme_name" value="Trypsin"/>
        <param name="search_enzyme_cutafter" value="KR"/>
        <param name="search_enzyme_nocutbefore" value="P"/>
        <param name="num_enzyme_termini" value="semi"/>
        <param name="allowed_missed_cleavage" value="2"/>
        <param name="min_length" value="7"/>
        <param name="max_length" value="64"/>
        <param name="mass_range_min" value="500.0"/>
        <param name="mass_range_max" value="5000.0"/>
      </section>
      <section name="varmod">
        <param name="clip_nterm_m" value="false"/>
        <param name="masses" value=""/>
        <param name="syntaxes" value=""/>
        <param name="enable_common" value="true"/>
        <param name="not_allow_multiple_variable_mods_on_residue" value="false"/>
        <param name="max_variable_mods_per_mod" value="2"/>
        <param name="max_variable_mods_combinations" value="5000"/>
      </section>
      <section name="spectrum">
        <param name="minimum_peaks" value="10"/>
        <param name="use_topn_peaks" value="50"/>
        <param name="minimum_ratio" value="0.0"/>
        <param name="clear_mz_range_min" value="0.0"/>
        <param name="clear_mz_range_max" value="0.0"/>
        <param name="max_fragment_charge" value="2"/>
        <param name="override_charge" value="false"/>
        <param name="precursor_charge_min" value="1"/>
        <param name="precursor_charge_max" value="4"/>
      </section>
      <section name="search">
        <param name="track_zero_topn" value="0"/>
        <param name="zero_bin_accept_expect" value="0.0"/>
        <param name="zero_bin_mult_expect" value="1.0"/>
        <param name="add_topn_complementary" value="0"/>
        <param name="min_fragments_modeling" value="3"/>
        <param name="min_matched_fragments" value="4"/>
        <param name="output_report_topn" value="1"/>
        <param name="output_max_expect" value="50.0"/>
      </section>
      <section name="statmod">
        <param name="add_cterm_peptide" value="0.0"/>
        <param name="add_nterm_peptide" value="0.0"/>
        <param name="add_cterm_protein" value="0.0"/>
        <param name="add_nterm_protein" value="0.0"/>
        <param name="add_G_glycine" value="0.0"/>
        <param name="add_A_alanine" value="0.0"/>
        <param name="add_S_serine" value="0.0"/>
        <param name="add_P_proline" value="0.0"/>
        <param name="add_V_valine" value="0.0"/>
        <param name="add_T_threonine" value="0.0"/>
        <param name="add_C_cysteine" value="57.021464"/>
        <param name="add_L_leucine" value="0.0"/>
        <param name="add_I_isoleucine" value="0.0"/>
        <param name="add_N_asparagine" value="0.0"/>
        <param name="add_D_aspartic_acid" value="0.0"/>
        <param name="add_Q_glutamine" value="0.0"/>
        <param name="add_K_lysine" value="0.0"/>
        <param name="add_E_glutamic_acid" value="0.0"/>
        <param name="add_M_methionine" value="0.0"/>
        <param name="add_H_histidine" value="0.0"/>
        <param name="add_F_phenylalanine" value="0.0"/>
        <param name="add_R_arginine" value="0.0"/>
        <param name="add_Y_tyrosine" value="0.0"/>
        <param name="add_W_tryptophan" value="0.0"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test></xml>
<xml name="manutest_MaRaClusterAdapter">
<test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="verbose" value="2"/>
        <param name="precursor_tolerance" value="20.0"/>
        <param name="precursor_tolerance_units" value="ppm"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="MaRaClusterAdapter_1_in_1.mzML,MaRaClusterAdapter_1_in_2.mzML"/>
      <param name="id_in" value="MaRaClusterAdapter_1_in_3.idXML"/>
      <output name="out" file="MaRaClusterAdapter_2_out_1.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="pcut" value="-10.0"/>
      <param name="min_cluster_size" value="1"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test></xml>
<xml name="manutest_NovorAdapter">
<test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="NovorAdapter_in.mzML"/>
      <output name="out" file="NovorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="enzyme" value="Trypsin"/>
      <param name="fragmentation" value="CID"/>
      <param name="massAnalyzer" value="Trap"/>
      <param name="fragment_mass_tolerance" value="0.5"/>
      <param name="precursor_mass_tolerance" value="15.0"/>
      <param name="precursor_error_units" value="ppm"/>
      <param name="variable_modifications" value="Acetyl (K)"/>
      <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
      <param name="forbiddenResidues" value="I"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test></xml>
<xml name="manutest_SpectraSTSearchAdapter">
<test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="use_isotopically_averaged_mass" value="false"/>
        <param name="use_all_charge_states" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="spectra_files" value="SpectrastAdapter_1_hack.mzML"/>
      <param name="output_files_type" value="pep.xml"/>
      <output_collection name="output_files" count="1"/>
      <param name="library_file" value="testLib.splib" ftype="splib"/>
      <param name="sequence_database_type" value="AA"/>
      <param name="precursor_mz_tolerance" value="3.0"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test><test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="use_isotopically_averaged_mass" value="false"/>
        <param name="use_all_charge_states" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="spectra_files" value="SpectrastAdapter_1_hack.mzML"/>
      <param name="output_files_type" value="tsv"/>
      <output_collection name="output_files" count="1"/>
      <param name="library_file" value="testLib.splib" ftype="splib"/>
      <param name="sequence_database_type" value="AA"/>
      <param name="precursor_mz_tolerance" value="3.0"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test></xml>