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Updates for beamspy 1.1.0 #3

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Updates for beamspy 1.1.0 #3

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26 changes: 21 additions & 5 deletions tools/beamspy/beamspy.xml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
<tool id="beamspy" name="BEAMSpy" version="1.0.0+galaxy0">
<tool id="beamspy" name="BEAMSpy" version="1.1.0">
<description> - Birmingham mEtabolite Annotation for Mass SpectroMetry</description>
<requirements>
<requirement type="package" version="1.0.0">beamspy</requirement>
<requirement type="package" version="1.1.0">beamspy</requirement>
</requirements>
<code file="get_databases.py" />
<command detect_errors="exit_code"><![CDATA[
Expand Down Expand Up @@ -35,13 +35,22 @@
--ppm $annotate_peak_patterns.condi.ppm
#if $annotate_peak_patterns.condi.annotate_adducts_flag == "true"
--adducts
#if $library_adducts
--adducts-library "$library_adducts"
#end if
#end if
#if $annotate_peak_patterns.condi.isotopes_condi.flag == "true"
--isotopes
#if $annotate_peak_patterns.condi.isotopes_condi.library_isotopes
--isotopes-library "$annotate_peak_patterns.condi.isotopes_condi.library_isotopes"
#end if
#end if
#if $annotate_peak_patterns.condi.neutral_losses_condi.flag == "true"
--neutral-losses
#if $annotate_peak_patterns.condi.neutral_losses_condi.library_neutral_losses
--neutral-losses-library "$annotate_peak_patterns.condi.neutral_losses_condi.library_neutral_losses"
#end if
#end if
#if $annotate_peak_patterns.condi.multiple_charged_ions_condi.flag == "true"
--multiple-charged-ions
#if $annotate_peak_patterns.condi.multiple_charged_ions_condi.library_multiple_charged_ions
Expand Down Expand Up @@ -174,6 +183,13 @@
</when>
<when value="false" />
</conditional>
<conditional name="neutral_losses_condi">
<param name="flag" type="boolean" checked="true" label="Annotate Neutral Losses" help="" truevalue="true" falsevalue="false" />
<when value="true">
<param name="library_neutral_losses" type="data" optional="true" format="tsv,tabular" label="Library Neutral Losses" help="" />
</when>
<when value="false" />
</conditional>
<conditional name="multiple_charged_ions_condi">
<param name="flag" type="boolean" checked="false" label="Annotate multiple charged ions" help="" truevalue="true" falsevalue="false" />
<when value="true">
Expand Down Expand Up @@ -225,7 +241,7 @@
</param>
<when value="databases">
<param name="db_name" type="select" label="Select databases" multiple="true" display="checkboxes" dynamic_options = "get_databases()" >
<validator type="no_options" message="Select at least one database." />
<validator type="no_options" message="Select at least one database." />
</param>
</when>
<when value="file">
Expand Down Expand Up @@ -301,7 +317,7 @@
<param name="annotate_compounds|condi|condi|source" value="databases"/>
<param name="annotate_compounds|condi|condi|db_name" value="hmdb_full_v4_0_v1"/>
<param name="annotate_compounds|condi|ppm" value="3.0"/>

<param name="summary|sr_mc" value="--single-row"/>
<param name="summary|rt_convert" value="skip"/>

Expand Down Expand Up @@ -408,4 +424,4 @@ Developers and contributors
</help>
<citations>
</citations>
</tool>
</tool>
43 changes: 21 additions & 22 deletions tools/beamspy/databases.txt
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Original file line number Diff line number Diff line change
@@ -1,24 +1,23 @@
description database_name
PlantCyc - ChlamyCyc (Chlamydomonas reinhardtii) | 2018-07-02 | v1 biocyc_chlamycyc_20180702_v1
CHEBI - Full database | rel169 | v1 chebi_full_rel169_v1
CHEBI - 3stars records | rel169 | v1 chebi_3star_rel169_v1
HMDB - The Urine Metabolome Database | v4.0 | v1 hmdb_urine_v4_0_v1
HMDB - The Serum Metabolome Database | v4.0 | v1 hmdb_serum_v4_0_v1
HMDB - The cerebrospinal fluid (CSF) Metabolome Database | v4.0 | v1 hmdb_csf_v4_0_v1
HMDB - The Saliva Metabolome Database | v4.0 | v1 hmdb_saliva_v4_0_v1
HMDB - The Fecal Metabolome Database | v4.0 | v1 hmdb_feces_v4_0_v1
HMDB - The Sweat Metabolome Database | v4.0 | v1 hmdb_sweat_v4_0_v1
HMDB - The Human Metabolome Database | v4.0 | v1 hmdb_full_v4_0_v1
KEGG - Daphnia pulex (dpx) | 2018-11-01 | v1 kegg_dpx_20181101_v1
KEGG - Human (hsa) | 2018-11-01 | v1 kegg_hsa_20181101_v1
KEGG - Full database | 2018-11-01 | v1 kegg_full_20181101_v1
LIPID_MAPS - FattyAcyls | 2018-12-17 | v1 lipidmaps_fattyacyls_20181217_v1
LIPID_MAPS - Glycerolipids | 2018-12-17 | v1 lipidmaps_glycerolipids_20181217_v1
LIPID_MAPS - Glycerophospholipids | 2018-12-17 | v1 lipidmaps_slycerophospholipids_20181217_v1
LIPID_MAPS - Polyketides | 2018-12-17 | v1 lipidmaps_solyketides_20181217_v1
LIPID_MAPS - PrenolLipids | 2018-12-17 | v1 lipidmaps_srenollipids_20181217_v1
LIPID_MAPS - Sacccharolipids | 2018-12-17 | v1 lipidmaps_sacccharolipids_20181217_v1
LIPID_MAPS - Sphingolipids | 2018-12-17 | v1 lipidmaps_sphingolipids_20181217_v1
LIPID_MAPS - SterolLipids | 2018-12-17 | v1 lipidmaps_sterollipids_20181217_v1
LIPID_MAPS - Full database | 2018-12-17 | v1 lipidmaps_full_20181217_v1
Yeast Metabolome Database (YMDB) | v2.0 | v1 ymdb_full_v2_0_v1
CHEBI - Complete database | rel195 | v1 chebi_complete_rel195_v1
CHEBI - Complete 3star records | rel195 | v1 chebi_complete_3star_rel195_v1
HMDB - The Urine Metabolome Database | v4.0 2020-09-10 | v1 hmdb_urine_v4_0_20200910_v1
HMDB - The Serum Metabolome Database | v4.0 2020-09-10 | v1 hmdb_serum_v4_0_20200910_v1
HMDB - The cerebrospinal fluid (CSF) Metabolome Database | v4.0 2020-09-10 | v1 hmdb_csf_v4_0_20200910_v1
HMDB - The Saliva Metabolome Database | v4.0 2020-09-10 | v1 hmdb_saliva_v4_0_20200910_v1
HMDB - The Fecal Metabolome Database | v4.0 2020-09-10 | v1 hmdb_feces_v4_0_20200910_v1
HMDB - The Sweat Metabolome Database | v4.0 2020-09-10 | v1 hmdb_sweat_v4_0_20200910_v1
HMDB - The Human Metabolome Database | v4.0 2020-09-09 | v1 hmdb_full_v4_0_20200909_v1
KEGG - Daphnia pulex (dpx) | 2021-01-11 | v1 kegg_dpx_20210111_v1
KEGG - Human (hsa) | 2021-01-11 | v1 kegg_hsa_20210111_v1
KEGG - Full database | 2021-01-11 | v1 kegg_full_20210111_v1
LIPID_MAPS - Fatty Acyls [FA] | 2020-10-01 | v1 lipidmaps_fattyacyls_20201001_v1
LIPID_MAPS - Glycerolipids [GL] | 2020-10-01 | v1 lipidmaps_glycerolipids_20201001_v1
LIPID_MAPS - Glycerophospholipids [GP] | 2020-10-01 | v1 lipidmaps_slycerophospholipids_20201001_v1
LIPID_MAPS - Polyketides [PK] | 2020-10-01 | v1 lipidmaps_solyketides_20201001_v1
LIPID_MAPS - Prenol Lipids [PR] | 2020-10-01 | v1 lipidmaps_srenollipids_20201001_v1
LIPID_MAPS - Sacccharolipids [SL]| 2020-10-01 | v1 lipidmaps_sacccharolipids_20201001_v1
LIPID_MAPS - Sphingolipids [SP] | 2020-10-01 | v1 lipidmaps_sphingolipids_20201001_v1
LIPID_MAPS - Sterol Lipids [ST] | 2020-10-01 | v1 lipidmaps_sterollipids_20201001_v1
LIPID_MAPS - Full database | 2020-10-01 | v1 lipidmaps_full_20201001_v1