Mercurial > repos > galaxyp > openms_consensusid
diff macros_autotest.xml @ 17:abffdfee3021 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms"
| author | galaxyp |
|---|---|
| date | Mon, 22 Feb 2021 10:46:10 +0000 |
| parents | feebe2054e40 |
| children |
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--- a/macros_autotest.xml Fri Nov 06 19:49:28 2020 +0000 +++ b/macros_autotest.xml Mon Feb 22 10:46:10 2021 +0000 @@ -126,7 +126,6 @@ <param name="max_transitions" value="3"/> <param name="cosine_similarity_threshold" value="0.98"/> <param name="transition_threshold" value="5.0"/> - <param name="out_workspace_directory" value=""/> <section name="deisotoping"> <param name="use_deisotoper" value="false"/> <param name="fragment_tolerance" value="1.0"/> @@ -195,7 +194,6 @@ <param name="max_transitions" value="3"/> <param name="cosine_similarity_threshold" value="0.98"/> <param name="transition_threshold" value="5.0"/> - <param name="out_workspace_directory" value=""/> <section name="deisotoping"> <param name="use_deisotoper" value="false"/> <param name="fragment_tolerance" value="1.0"/> @@ -264,7 +262,6 @@ <param name="max_transitions" value="3"/> <param name="cosine_similarity_threshold" value="0.98"/> <param name="transition_threshold" value="5.0"/> - <param name="out_workspace_directory" value=""/> <section name="deisotoping"> <param name="use_deisotoper" value="false"/> <param name="fragment_tolerance" value="1.0"/> @@ -333,7 +330,6 @@ <param name="max_transitions" value="3"/> <param name="cosine_similarity_threshold" value="0.98"/> <param name="transition_threshold" value="5.0"/> - <param name="out_workspace_directory" value=""/> <section name="deisotoping"> <param name="use_deisotoper" value="false"/> <param name="fragment_tolerance" value="1.0"/> @@ -402,7 +398,6 @@ <param name="max_transitions" value="3"/> <param name="cosine_similarity_threshold" value="0.98"/> <param name="transition_threshold" value="5.0"/> - <param name="out_workspace_directory" value=""/> <section name="deisotoping"> <param name="use_deisotoper" value="false"/> <param name="fragment_tolerance" value="1.0"/> @@ -471,7 +466,6 @@ <param name="max_transitions" value="3"/> <param name="cosine_similarity_threshold" value="0.98"/> <param name="transition_threshold" value="3.0"/> - <param name="out_workspace_directory" value=""/> <section name="deisotoping"> <param name="use_deisotoper" value="false"/> <param name="fragment_tolerance" value="1.0"/> @@ -540,7 +534,6 @@ <param name="max_transitions" value="3"/> <param name="cosine_similarity_threshold" value="0.98"/> <param name="transition_threshold" value="3.0"/> - <param name="out_workspace_directory" value=""/> <section name="deisotoping"> <param name="use_deisotoper" value="false"/> <param name="fragment_tolerance" value="1.0"/> @@ -609,7 +602,6 @@ <param name="max_transitions" value="3"/> <param name="cosine_similarity_threshold" value="0.98"/> <param name="transition_threshold" value="3.0"/> - <param name="out_workspace_directory" value=""/> <section name="deisotoping"> <param name="use_deisotoper" value="false"/> <param name="fragment_tolerance" value="1.0"/> @@ -678,7 +670,6 @@ <param name="max_transitions" value="3"/> <param name="cosine_similarity_threshold" value="0.98"/> <param name="transition_threshold" value="3.0"/> - <param name="out_workspace_directory" value=""/> <section name="deisotoping"> <param name="use_deisotoper" value="false"/> <param name="fragment_tolerance" value="1.0"/> @@ -758,7 +749,6 @@ <param name="use_Y_ions" value="true"/> <param name="use_Z_ions" value="false"/> <param name="use_NL_ions" value="false"/> - <param name="second_enzyme" value=""/> <param name="digest_mass_range" value="600:5000"/> <param name="max_precursor_charge" value="5"/> <param name="spectrum_batch_size" value="1000"/> @@ -796,8 +786,8 @@ <param name="activation_method" value="ALL"/> <param name="max_fragment_charge" value="3"/> <param name="clip_nterm_methionine" value="false"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value=""/> + <param name="fixed_modifications" value="Carbamidomethyl (C)"/> + <param name="variable_modifications" value="Oxidation (M)"/> <param name="binary_modifications" value=""/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -816,7 +806,6 @@ <param name="use_Y_ions" value="true"/> <param name="use_Z_ions" value="false"/> <param name="use_NL_ions" value="false"/> - <param name="second_enzyme" value=""/> <param name="digest_mass_range" value="600:5000"/> <param name="max_precursor_charge" value="5"/> <param name="spectrum_batch_size" value="1000"/> @@ -854,8 +843,8 @@ <param name="activation_method" value="ALL"/> <param name="max_fragment_charge" value="3"/> <param name="clip_nterm_methionine" value="false"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value=""/> + <param name="fixed_modifications" value="Carbamidomethyl (C)"/> + <param name="variable_modifications" value="Oxidation (M)"/> <param name="binary_modifications" value=""/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -874,7 +863,6 @@ <param name="use_Y_ions" value="true"/> <param name="use_Z_ions" value="false"/> <param name="use_NL_ions" value="false"/> - <param name="second_enzyme" value=""/> <param name="digest_mass_range" value="600:5000"/> <param name="max_precursor_charge" value="5"/> <param name="spectrum_batch_size" value="20000"/> @@ -932,7 +920,6 @@ <param name="use_Y_ions" value="true"/> <param name="use_Z_ions" value="false"/> <param name="use_NL_ions" value="false"/> - <param name="second_enzyme" value=""/> <param name="digest_mass_range" value="600:1200"/> <param name="max_precursor_charge" value="5"/> <param name="spectrum_batch_size" value="20000"/> @@ -1007,8 +994,6 @@ <param name="number_of_hits" value="1"/> <param name="estimate_precursor_mz" value="true"/> <param name="number_of_prescoring_hits" value="250"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value=""/> <param name="residue_set" value="Natural19WithoutI"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> @@ -1046,8 +1031,6 @@ <param name="number_of_hits" value="1"/> <param name="estimate_precursor_mz" value="true"/> <param name="number_of_prescoring_hits" value="250"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value=""/> <param name="residue_set" value="Natural19WithoutI"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> @@ -4185,7 +4168,6 @@ <conditional name="adv_opts_cond"> <param name="adv_opts_selector" value="advanced"/> <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> <param name="log2_states_precalc" value="0"/> <param name="force" value="false"/> <param name="test" value="true"/> @@ -4214,7 +4196,6 @@ <conditional name="adv_opts_cond"> <param name="adv_opts_selector" value="advanced"/> <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> <param name="log2_states_precalc" value="0"/> <param name="force" value="false"/> <param name="test" value="true"/> @@ -4243,7 +4224,6 @@ <conditional name="adv_opts_cond"> <param name="adv_opts_selector" value="advanced"/> <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> <param name="log2_states_precalc" value="0"/> <param name="force" value="false"/> <param name="test" value="true"/> @@ -4272,7 +4252,6 @@ <conditional name="adv_opts_cond"> <param name="adv_opts_selector" value="advanced"/> <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> <param name="log2_states_precalc" value="0"/> <param name="force" value="false"/> <param name="test" value="true"/> @@ -4301,7 +4280,6 @@ <conditional name="adv_opts_cond"> <param name="adv_opts_selector" value="advanced"/> <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> <param name="log2_states_precalc" value="0"/> <param name="force" value="false"/> <param name="test" value="true"/> @@ -4330,7 +4308,6 @@ <conditional name="adv_opts_cond"> <param name="adv_opts_selector" value="advanced"/> <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> <param name="log2_states_precalc" value="0"/> <param name="force" value="false"/> <param name="test" value="true"/> @@ -5347,16 +5324,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -5453,16 +5425,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -5559,16 +5526,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -5665,16 +5627,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="true"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -5771,16 +5728,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -5877,16 +5829,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -5983,16 +5930,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -6089,16 +6031,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -6196,15 +6133,11 @@ <section name="spectra"> <param name="remove_zoom" value="false"/> <param name="remove_mode" value="SelectedIonMonitoring"/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -6301,16 +6234,12 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> <param name="remove_activation" value="Collision-induced dissociation"/> <param name="remove_collision_energy" value=":"/> <param name="remove_isolation_window_width" value=":"/> <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -6407,16 +6336,12 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> <param name="remove_activation" value="Plasma desorption"/> <param name="remove_collision_energy" value=":"/> <param name="remove_isolation_window_width" value=":"/> <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -6513,16 +6438,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -6619,16 +6539,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -6725,16 +6640,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -6831,16 +6741,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -6937,16 +6842,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -7043,16 +6943,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -7149,16 +7044,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -7255,16 +7145,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -7361,16 +7246,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -7467,16 +7347,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -7573,16 +7448,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -7679,16 +7549,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -7785,16 +7650,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -7891,16 +7751,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -7998,16 +7853,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -8105,16 +7955,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -8211,16 +8056,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -8317,16 +8157,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -8423,16 +8258,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> <param name="remove_collision_energy" value=":"/> <param name="remove_isolation_window_width" value=":2"/> <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -8529,16 +8359,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> <param name="select_collision_energy" value=":"/> <param name="select_isolation_window_width" value=":2"/> - <param name="select_polarity" value=""/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -8635,16 +8460,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> <param name="remove_collision_energy" value=":35"/> <param name="remove_isolation_window_width" value=":"/> <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -8741,16 +8561,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> <param name="select_collision_energy" value=":35"/> <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -8847,16 +8662,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -8953,16 +8763,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -9059,16 +8864,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -9165,16 +8965,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -9271,13 +9066,9 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> <param name="select_collision_energy" value=":"/> <param name="select_isolation_window_width" value=":"/> <param name="select_polarity" value="positive"/> @@ -9377,13 +9168,9 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> <param name="select_collision_energy" value=":"/> <param name="select_isolation_window_width" value=":"/> <param name="select_polarity" value="negative"/> @@ -9483,16 +9270,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -9589,16 +9371,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -9695,16 +9472,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -9801,16 +9573,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -9907,16 +9674,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -10013,16 +9775,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -10119,16 +9876,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="file" value="FileFilter_47_input_select.mzML"/> <param name="similarity_threshold" value="0.9"/> @@ -10226,16 +9978,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="file" value="FileFilter_47_input_select.mzML"/> <param name="similarity_threshold" value="0.9"/> @@ -10333,16 +10080,11 @@ </section> <section name="spectra"> <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> <section name="blackorwhitelist"> <param name="similarity_threshold" value="-1.0"/> <param name="rt" value="0.01"/> @@ -12230,12 +11972,10 @@ <param name="proteins" value="IDFilter_1_input.fas"/> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="enzyme" value="Trypsin"/> @@ -12297,13 +12037,11 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="peptides" value="IDFilter_3_2_input.idXML"/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="enzyme" value="Trypsin"/> @@ -12365,12 +12103,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="enzyme" value="Trypsin"/> @@ -12432,12 +12168,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="enzyme" value="Trypsin"/> @@ -12499,12 +12233,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="enzyme" value="Trypsin"/> @@ -12566,12 +12298,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="enzyme" value="Trypsin"/> @@ -12633,12 +12363,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="enzyme" value="Trypsin"/> @@ -12700,12 +12428,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="enzyme" value="Trypsin"/> @@ -12767,12 +12493,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="enzyme" value="Trypsin"/> @@ -12834,12 +12558,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="enzyme" value="Trypsin"/> @@ -12901,12 +12623,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="enzyme" value="Trypsin"/> @@ -12968,12 +12688,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="enzyme" value="Trypsin"/> @@ -13035,12 +12753,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="enzyme" value="Trypsin"/> @@ -13102,12 +12818,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="fasta" value="IDFilter_12_input.fasta"/> @@ -13170,12 +12884,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="fasta" value="IDFilter_13_input.fasta"/> @@ -13238,12 +12950,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="fasta" value="IDFilter_14_input.fasta"/> @@ -13306,12 +13016,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="fasta" value="IDFilter_15_input.fasta"/> @@ -13374,12 +13082,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="fasta" value="IDFilter_16_input.fasta"/> @@ -13442,12 +13148,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="enzyme" value="Trypsin"/> @@ -13509,12 +13213,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="enzyme" value="Trypsin"/> @@ -13576,12 +13278,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="enzyme" value="Trypsin"/> @@ -13643,12 +13343,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="enzyme" value="Trypsin"/> @@ -13710,12 +13408,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="enzyme" value="Trypsin"/> @@ -13777,12 +13473,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="enzyme" value="Trypsin"/> @@ -13844,12 +13538,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""Q9HP81""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="enzyme" value="Trypsin"/> @@ -13911,12 +13603,10 @@ <section name="whitelist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="blacklist"> <param name="protein_accessions" value=""/> <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> </section> <section name="in_silico_digestion"> <param name="enzyme" value="Trypsin"/> @@ -14648,7 +14338,7 @@ <param name="in" value="IsobaricAnalyzer_input_1.mzML"/> <output name="out" file="IsobaricAnalyzer_output_1.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> <section name="extraction"> - <param name="select_activation" value=""/> + <param name="select_activation" value="High-energy collision-induced dissociation"/> <param name="reporter_mass_shift" value="0.1"/> <param name="min_precursor_intensity" value="1.0"/> <param name="keep_unannotated_precursor" value="true"/> @@ -15139,8 +14829,6 @@ <param name="type" value="b_spline"/> <section name="linear"> <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> <param name="x_datum_min" value="1e-15"/> <param name="x_datum_max" value="1000000000000000.0"/> <param name="y_datum_min" value="1e-15"/> @@ -15195,8 +14883,6 @@ <param name="type" value="b_spline"/> <section name="linear"> <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> <param name="x_datum_min" value="1e-15"/> <param name="x_datum_max" value="1000000000000000.0"/> <param name="y_datum_min" value="1e-15"/> @@ -15250,8 +14936,6 @@ <param name="type" value="b_spline"/> <section name="linear"> <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> <param name="x_datum_min" value="1e-15"/> <param name="x_datum_max" value="1000000000000000.0"/> <param name="y_datum_min" value="1e-15"/> @@ -15305,8 +14989,6 @@ <param name="type" value="b_spline"/> <section name="linear"> <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> <param name="x_datum_min" value="1e-15"/> <param name="x_datum_max" value="1000000000000000.0"/> <param name="y_datum_min" value="1e-15"/> @@ -15360,8 +15042,6 @@ <param name="type" value="b_spline"/> <section name="linear"> <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> <param name="x_datum_min" value="1e-15"/> <param name="x_datum_max" value="1000000000000000.0"/> <param name="y_datum_min" value="1e-15"/> @@ -15416,8 +15096,6 @@ <param name="type" value="b_spline"/> <section name="linear"> <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> <param name="x_datum_min" value="1e-15"/> <param name="x_datum_max" value="1000000000000000.0"/> <param name="y_datum_min" value="1e-15"/> @@ -15473,8 +15151,6 @@ <param name="type" value="b_spline"/> <section name="linear"> <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> <param name="x_datum_min" value="1e-15"/> <param name="x_datum_max" value="1000000000000000.0"/> <param name="y_datum_min" value="1e-15"/> @@ -15748,8 +15424,6 @@ <param name="type" value="interpolated"/> <section name="linear"> <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> <param name="x_datum_min" value="1e-15"/> <param name="x_datum_max" value="1000000000000000.0"/> <param name="y_datum_min" value="1e-15"/> @@ -15796,8 +15470,6 @@ <param name="type" value="b_spline"/> <section name="linear"> <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> <param name="x_datum_min" value="1e-15"/> <param name="x_datum_max" value="1000000000000000.0"/> <param name="y_datum_min" value="1e-15"/> @@ -15851,8 +15523,6 @@ <param name="type" value="b_spline"/> <section name="linear"> <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> <param name="x_datum_min" value="1e-15"/> <param name="x_datum_max" value="1000000000000000.0"/> <param name="y_datum_min" value="1e-15"/> @@ -15906,8 +15576,6 @@ <param name="type" value="b_spline"/> <section name="linear"> <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> <param name="x_datum_min" value="1e-15"/> <param name="x_datum_max" value="1000000000000000.0"/> <param name="y_datum_min" value="1e-15"/> @@ -15981,8 +15649,6 @@ <param name="type" value="none"/> <section name="linear"> <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> <param name="x_datum_min" value="1e-15"/> <param name="x_datum_max" value="1000000000000000.0"/> <param name="y_datum_min" value="1e-15"/> @@ -16028,8 +15694,6 @@ <param name="type" value="none"/> <section name="linear"> <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> <param name="x_datum_min" value="1e-15"/> <param name="x_datum_max" value="1000000000000000.0"/> <param name="y_datum_min" value="1e-15"/> @@ -16074,8 +15738,6 @@ <param name="type" value="none"/> <section name="linear"> <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> <param name="x_datum_min" value="1e-15"/> <param name="x_datum_max" value="1000000000000000.0"/> <param name="y_datum_min" value="1e-15"/> @@ -16121,8 +15783,6 @@ <param name="type" value="none"/> <section name="linear"> <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> <param name="x_datum_min" value="1e-15"/> <param name="x_datum_max" value="1000000000000000.0"/> <param name="y_datum_min" value="1e-15"/> @@ -16168,8 +15828,6 @@ <param name="type" value="none"/> <section name="linear"> <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> <param name="x_datum_min" value="1e-15"/> <param name="x_datum_max" value="1000000000000000.0"/> <param name="y_datum_min" value="1e-15"/> @@ -16215,8 +15873,6 @@ <param name="type" value="none"/> <section name="linear"> <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> <param name="x_datum_min" value="1e-15"/> <param name="x_datum_max" value="1000000000000000.0"/> <param name="y_datum_min" value="1e-15"/> @@ -16273,8 +15929,6 @@ <param name="fragment_error_units" value="Da"/> <param name="charges" value="1,2,3"/> <param name="taxonomy" value="All entries"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value=""/> <param name="special_modifications" value="Cation:Na (DE),Deamidated (NQ),Oxidation (HW),Phospho (ST),Sulfo (ST)"/> <param name="mass_type" value="monoisotopic"/> <param name="number_of_hits" value="0"/> @@ -16286,7 +15940,7 @@ <section name="Mascot_server"> <param name="hostname" value="www.matrixscience.com"/> <param name="host_port" value="80"/> - <param name="server_path" value=""/> + <param name="server_path" value="mascot"/> <param name="timeout" value="1500"/> <param name="boundary" value="GZWgAaYKjHFeUaLOLEIOMq"/> <param name="use_proxy" value="false"/> @@ -16818,7 +16472,7 @@ <param name="max_mods" value="2"/> <param name="max_missed_cleavages" value="-1"/> <param name="tasks" value="0"/> - <param name="fixed_modifications" value=""/> + <param name="fixed_modifications" value="Carbamidomethyl (C)"/> <param name="variable_modifications" value="Oxidation (M)"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mzid_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -17082,13 +16736,12 @@ <param name="fragment_mass_tolerance" value="0.3"/> <param name="fragment_mass_tolerance_unit" value="Da"/> <param name="database" value="proteins.fasta"/> - <param name="fixed_modifications" value=""/> + <param name="fixed_modifications" value="Carbamidomethyl (C)"/> <param name="variable_modifications" value="Oxidation (M)"/> <param name="NumChargeStates" value="3"/> <param name="TicCutoffPercentage" value="0.98"/> <param name="MaxDynamicMods" value="2"/> <param name="MaxResultRank" value="5"/> - <param name="CleavageRules" value=""/> <param name="MinTerminiCleavages" value="2"/> <param name="MaxMissedCleavages" value="-1"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> @@ -17419,7 +17072,6 @@ <param name="ions" value="a-B,c,w,y"/> </section> <section name="modifications"> - <param name="variable" value=""/> <param name="variable_max_per_oligo" value="2"/> <param name="resolve_ambiguities" value="false"/> </section> @@ -17486,7 +17138,7 @@ <param name="database" value="proteins.fasta"/> <param name="min_precursor_charge" value="1"/> <param name="max_precursor_charge" value="3"/> - <param name="fixed_modifications" value=""/> + <param name="fixed_modifications" value="Carbamidomethyl (C)"/> <param name="variable_modifications" value="Oxidation (M)"/> <param name="v" value="1"/> <param name="enzyme" value="Trypsin"/> @@ -17528,8 +17180,6 @@ <param name="mass_tolerance_unit" value="ppm"/> </section> <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value=""/> <param name="variable_max_per_peptide" value="2"/> </section> <section name="peptide"> @@ -17603,7 +17253,7 @@ <param name="residue1" value=""D" "E" "C-term""/> <param name="residue2" value=""K" "S" "T" "Y" "N-term""/> <param name="mass" value="-18.010595"/> - <param name="mass_mono_link" value=""/> + <param name="mass_mono_link" value="156.07864431 155.094628715"/> <param name="name" value="DMTMM"/> </section> <section name="algorithm"> @@ -17658,8 +17308,6 @@ <param name="mass_tolerance_unit" value="Da"/> </section> <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value=""/> <param name="variable_max_per_peptide" value="2"/> </section> <section name="peptide"> @@ -19779,7 +19427,6 @@ </conditional> <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> <output name="out_features" file="OpenSwathWorkflow_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> <output name="out_chrom" file="OpenSwathWorkflow_1_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> <output name="out_qc" file="OpenSwathWorkflow_1_output.json" compare="sim_size" delta="5700" ftype="json"/> @@ -19937,7 +19584,6 @@ </conditional> <param name="in" value="OpenSwathWorkflow_2_input.mzXML"/> <param name="tr" value="OpenSwathWorkflow_2_input.TraML"/> - <param name="tr_type" value=""/> <output name="out_features" file="OpenSwathWorkflow_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> <output name="out_chrom" file="OpenSwathWorkflow_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> <param name="sonar" value="false"/> @@ -20094,7 +19740,6 @@ </conditional> <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> <param name="sonar" value="false"/> @@ -20251,7 +19896,6 @@ </conditional> <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> <output name="out_tsv" file="OpenSwathWorkflow_4.tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/> <output name="out_chrom" file="OpenSwathWorkflow_4.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> <param name="sonar" value="false"/> @@ -20408,7 +20052,6 @@ </conditional> <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> <param name="sonar" value="false"/> @@ -20565,7 +20208,6 @@ </conditional> <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> <param name="sonar" value="false"/> @@ -20722,7 +20364,6 @@ </conditional> <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> <param name="swath_windows_file" value="swath_windows.txt" ftype="txt"/> <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> @@ -20880,7 +20521,6 @@ </conditional> <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> <param name="swath_windows_file" value="swath_windows_overlap.txt" ftype="txt"/> <output name="out_features" file="OpenSwathWorkflow_10.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> <output name="out_chrom" file="OpenSwathWorkflow_10.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> @@ -21037,7 +20677,6 @@ </conditional> <param name="in" value="OpenSwathWorkflow_11_input.mzML"/> <param name="tr" value="OpenSwathWorkflow_11_input_2.TraML"/> - <param name="tr_type" value=""/> <param name="tr_irt" value="OpenSwathWorkflow_11_input.TraML"/> <output name="out_features" file="OpenSwathWorkflow_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> <output name="out_chrom" file="OpenSwathWorkflow_11_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> @@ -21509,7 +21148,6 @@ </conditional> <param name="in" value="OpenSwathWorkflow_15_input.mzML"/> <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> <output name="out_features" file="OpenSwathWorkflow_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> <output name="out_chrom" file="OpenSwathWorkflow_15_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> <param name="sonar" value="false"/> @@ -21666,7 +21304,6 @@ </conditional> <param name="in" value="OpenSwathWorkflow_16_input.sqMass"/> <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> <output name="out_features" file="OpenSwathWorkflow_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> <output name="out_chrom" file="OpenSwathWorkflow_16_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> <param name="sonar" value="false"/> @@ -21822,7 +21459,6 @@ </conditional> <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/> - <param name="tr_type" value=""/> <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> <param name="sonar" value="false"/> @@ -21978,7 +21614,6 @@ </conditional> <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/> - <param name="tr_type" value=""/> <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> <param name="sonar" value="false"/> @@ -22290,7 +21925,6 @@ </conditional> <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> <output name="out_features" file="OpenSwathWorkflow_18_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> <param name="sonar" value="false"/> <param name="rt_extraction_window" value="600.0"/> @@ -22445,7 +22079,6 @@ </conditional> <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> <output name="out_features" file="OpenSwathWorkflow_19_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> <param name="sonar" value="false"/> <param name="rt_extraction_window" value="600.0"/> @@ -22600,7 +22233,6 @@ </conditional> <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> <output name="out_features" file="OpenSwathWorkflow_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> <param name="sonar" value="false"/> <param name="rt_extraction_window" value="600.0"/> @@ -22755,7 +22387,6 @@ </conditional> <param name="in" value="OpenSwathWorkflow_21_input.mzML"/> <param name="tr" value="OpenSwathWorkflow_21_input.tsv" ftype="tabular"/> - <param name="tr_type" value=""/> <param name="tr_irt" value="OpenSwathWorkflow_21_input.irt.TraML"/> <output name="out_features" file="OpenSwathWorkflow_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> <output name="out_chrom" file="OpenSwathWorkflow_21_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> @@ -22913,7 +22544,6 @@ </conditional> <param name="in" value="OpenSwathWorkflow_22_input.mzML"/> <param name="tr" value="OpenSwathWorkflow_22_input.tsv" ftype="tabular"/> - <param name="tr_type" value=""/> <output name="out_features" file="OpenSwathWorkflow_22_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> <output name="out_chrom" file="OpenSwathWorkflow_22_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> <param name="sonar" value="false"/> @@ -24957,7 +24587,6 @@ <param name="mass_tolerance_unit" value="ppm"/> </section> <section name="modifications"> - <param name="fixed" value=""/> <param name="variable" value="Oxidation (M)"/> <param name="variable_max_per_peptide" value="2"/> </section> @@ -25016,7 +24645,6 @@ <param name="mass_tolerance_unit" value="ppm"/> </section> <section name="modifications"> - <param name="fixed" value=""/> <param name="variable" value="Oxidation (M)"/> <param name="variable_max_per_peptide" value="2"/> </section> @@ -25076,8 +24704,6 @@ <param name="mass_tolerance_unit" value="ppm"/> </section> <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value=""/> <param name="variable_max_per_peptide" value="2"/> </section> <section name="peptide"> @@ -25136,8 +24762,6 @@ <param name="mass_tolerance_unit" value="ppm"/> </section> <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value=""/> <param name="variable_max_per_peptide" value="2"/> </section> <section name="peptide"> @@ -25437,13 +25061,11 @@ <param name="mass_tolerance_unit" value="Da"/> </section> <section name="modifications"> - <param name="fixed" value=""/> + <param name="fixed" value="Carbamidomethyl (C)"/> <param name="variable" value="Oxidation (M)"/> <param name="variable_max_per_peptide" value="2"/> </section> - <section name="annotate"> - <param name="PSM" value=""/> - </section> + <section name="annotate"/> <section name="peptide"> <param name="min_size" value="7"/> <param name="max_size" value="40"/> @@ -25472,7 +25094,6 @@ </conditional> <param name="in" value="SiriusAdapter_1_input.mzML"/> <output name="out_sirius" file="SiriusAdapter_1_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="out_workspace_directory" value=""/> <section name="preprocessing"> <param name="filter_by_num_masstraces" value="1"/> <param name="precursor_mz_tolerance" value="0.005"/> @@ -25515,7 +25136,6 @@ <param name="in" value="SiriusAdapter_2_input.mzML"/> <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/> <output name="out_sirius" file="SiriusAdapter_2_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="out_workspace_directory" value=""/> <section name="preprocessing"> <param name="filter_by_num_masstraces" value="3"/> <param name="precursor_mz_tolerance" value="0.005"/> @@ -25558,7 +25178,6 @@ <param name="in" value="SiriusAdapter_3_input.mzML"/> <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/> <output name="out_sirius" file="SiriusAdapter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="out_workspace_directory" value=""/> <section name="preprocessing"> <param name="filter_by_num_masstraces" value="3"/> <param name="precursor_mz_tolerance" value="0.005"/> @@ -25601,7 +25220,6 @@ <param name="in" value="SiriusAdapter_3_input.mzML"/> <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/> <output name="out_ms" file="SiriusAdapter_5_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/> - <param name="out_workspace_directory" value=""/> <section name="preprocessing"> <param name="filter_by_num_masstraces" value="1"/> <param name="precursor_mz_tolerance" value="0.005"/> @@ -25644,7 +25262,6 @@ <param name="in" value="SiriusAdapter_4_input.mzML"/> <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/> <output name="out_ms" file="SiriusAdapter_6_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/> - <param name="out_workspace_directory" value=""/> <section name="preprocessing"> <param name="filter_by_num_masstraces" value="1"/> <param name="precursor_mz_tolerance" value="0.005"/> @@ -25687,7 +25304,6 @@ <param name="in" value="SiriusAdapter_4_input.mzML"/> <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/> <output name="out_sirius" file="SiriusAdapter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="out_workspace_directory" value=""/> <section name="preprocessing"> <param name="filter_by_num_masstraces" value="1"/> <param name="precursor_mz_tolerance" value="0.005"/> @@ -25731,7 +25347,6 @@ <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/> <output name="out_sirius" file="SiriusAdapter_4_output.tmp" compare="sim_size" delta="5700" ftype="mztab"/> <output name="out_fingerid" file="SiriusAdapter_4_foutput.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="out_workspace_directory" value=""/> <section name="preprocessing"> <param name="filter_by_num_masstraces" value="1"/> <param name="precursor_mz_tolerance" value="0.005"/> @@ -25798,8 +25413,6 @@ <param name="cut_peaks_below" value="1000"/> </section> <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value=""/> <param name="variable_max_per_peptide" value="2"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> @@ -27122,7 +26735,7 @@ <param name="fragment_error_units" value="Da"/> <param name="max_precursor_charge" value="0"/> <param name="no_isotope_error" value="false"/> - <param name="fixed_modifications" value=""/> + <param name="fixed_modifications" value="Carbamidomethyl (C)"/> <param name="variable_modifications" value="Oxidation (M)"/> <param name="minimum_fragment_mz" value="150.0"/> <param name="enzyme" value="Trypsin"/> @@ -27154,7 +26767,7 @@ <param name="fragment_error_units" value="Da"/> <param name="max_precursor_charge" value="0"/> <param name="no_isotope_error" value="false"/> - <param name="fixed_modifications" value=""/> + <param name="fixed_modifications" value="Carbamidomethyl (C)"/> <param name="variable_modifications" value="Oxidation (M)"/> <param name="minimum_fragment_mz" value="150.0"/> <param name="enzyme" value="Trypsin"/> @@ -27186,7 +26799,7 @@ <param name="fragment_error_units" value="Da"/> <param name="max_precursor_charge" value="0"/> <param name="no_isotope_error" value="false"/> - <param name="fixed_modifications" value=""/> + <param name="fixed_modifications" value="Carbamidomethyl (C)"/> <param name="variable_modifications" value="Oxidation (M)"/> <param name="minimum_fragment_mz" value="150.0"/> <param name="enzyme" value="Trypsin"/> @@ -27202,4 +26815,4 @@ </output> </test> </xml> -<xml name="autotest_PTPredict"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_RTPredict"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_IDDecoyProbability"/><xml name="autotest_InspectAdapter"/></macros> +<xml name="autotest_PTPredict"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_IDDecoyProbability"/><xml name="autotest_InspectAdapter"/><xml name="autotest_RTPredict"/><xml name="autotest_ProteomicsLFQ"/></macros>