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format with Galaxy VSC plugin, fix container usage
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@bgruening
bgruening committed Apr 13, 2024
1 parent f1ae938 commit 54b3bea
Showing 1 changed file with 63 additions and 88 deletions.
151 changes: 63 additions & 88 deletions tools/sirius_csifingerid/sirius_csifingerid.xml
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<tool id="sirius_csifingerid" name="SIRIUS-CSI:FingerID"
version="5.8.6+galaxy0" profile="22.05">
<description>is used to identify metabolites using single and
tandem mass spectrometry</description>
<tool id="sirius_csifingerid" name="SIRIUS-CSI:FingerID" version="@TOOL_VERSION@+galaxy0" profile="22.05">
<description>is used to identify metabolites using single and tandem mass spectrometry</description>
<macros>
<token name="@TOOL_VERSION@">5.8.6</token>
</macros>
<requirements>
<requirement type="package" version="5.8.6">sirius-csifingerid</requirement>
<requirement type="package" version="@TOOL_VERSION@">sirius-csifingerid</requirement>
<requirement type="package" version="3.11">python</requirement>
</requirements>
<version_command>sirius --version</version_command>
<command detect_errors="exit_code">
<![CDATA[
export _JAVA_OPTIONS=-Duser.home=\${TMPDIR:-.} &&
Expand Down Expand Up @@ -49,70 +52,51 @@
#end if
]]></command>
<inputs>
<param name="input" argument="--input_pth" type="data" format="msp"
label="MSP file (output from Create MSP tool)" />
<param argument="--database" type="select"
label="Select SIRIUS-CSI:FingerID Database" >
<option value="PUBCHEM" >PubChem</option>
<param name="input" argument="--input_pth" type="data" format="msp" label="MSP file (output from Create MSP tool)"/>
<param argument="--database" type="select" label="Select SIRIUS-CSI:FingerID Database">
<option value="PUBCHEM">PubChem</option>
<option value="HMDB">HMDB</option>
<option value="KEGG">KEGG</option>
<option value="KNAPSACK">KNApSAcK</option>
<option value="BIOCYC">BioCyc</option>
<option selected="true" value="BIO">Bio (all biological)</option>
<option value="ALL">All (use all databases)</option>
</param>
<param argument="--ppm_max" type="integer" value="10" min="0"
label="Mass deviation of the fragment peaks in ppm" />
<param argument="--candidates" type="integer" value="5" min="1"
label="Maximum number of candidates in the output" />
<param argument="--polarity" type="select" label="Ion mode" >
<param argument="--ppm_max" type="integer" value="10" min="0" label="Mass deviation of the fragment peaks in ppm"/>
<param argument="--candidates" type="integer" value="5" min="1" label="Maximum number of candidates in the output"/>
<param argument="--polarity" type="select" label="Ion mode">
<option value="positive" selected="true">Positive</option>
<option value="negative">Negative</option>
</param>
<param argument="--profile" type="select" label="Analysis used" >
</param>
<param argument="--profile" type="select" label="Analysis used">
<option value="orbitrap" selected="true">Orbitrap</option>
<option value="qtof">qTOF</option>
<option value="fticr">FT-ICR</option>
</param>
<param argument="--schema" type="select" label="Schema"
help="Schema used for the MSP file (auto will try to
determine the schema automatically)">
<param argument="--schema" type="select" label="Schema" help="Schema used for the MSP file (auto will try to determine the schema automatically)">
<option value="auto" selected="True">Auto</option>
<option value="msp" >Generic MSP</option>
<option value="msp">Generic MSP</option>
<option value="massbank">MassBank</option>
</param>
<param argument="--meta_select_col" type="select"
label="Choose how additional metadata columns are extracted"
help="The SIRIUS-CSI:Fingerid output can have additional
metadata columns added; these can be either extracted from all
MSP parameters or from the 'Name' and 'RECORD_TITLE' MSP
parameters. Additionally, columns can be added from the 'Name'
or 'RECORD_TITLE' parameters by splitting on | and : e.g.
'MZ:100.2 | RT:20 | xcms_grp_id:1' would create MZ,RT and
xcms_grp_id columns">
<param argument="--meta_select_col" type="select" label="Choose how additional metadata columns are extracted" help="The SIRIUS-CSI:Fingerid output can have additional metadata columns added; these can be either extracted from all MSP parameters or from the 'Name' and 'RECORD_TITLE' MSP parameters. Additionally, columns can be added from the 'Name' or 'RECORD_TITLE' parameters by splitting on | and : e.g. 'MZ:100.2 | RT:20 | xcms_grp_id:1' would create MZ,RT and xcms_grp_id columns">
<option value="name" selected="true">
Extra metadata columns from the Name or RECORD_TITLE</option>
<option value="name_split" >
<option value="name_split">
Extra metadata columns from the Name or
RECORD_TITLE (each column is split on "|" and ":" ) </option>
<option value="all">
Extra metadata columns from all MSP parameters</option>
</param>
<param argument="--min_MSMS_peaks" type="integer" min="0" value="0"
label="Minimum number of MS/MS peaks"/>

<param argument="--min_MSMS_peaks" type="integer" min="0" value="0" label="Minimum number of MS/MS peaks"/>
<conditional name="adducts_cond">
<param name="adducts_selector" type="select" label="How to handle adducts"
help="Choose whether to include a suspect list">
<param name="adducts_selector" type="select" label="How to handle adducts" help="Choose whether to include a suspect list">
<option value="msp" selected="True">Use adducts defined in MSP file</option>
<option value="select" >Select from list of adducts</option>
<option value="all" >Use pre-selected adducts for either pos or neg ionisation mode</option>
<option value="select">Select from list of adducts</option>
<option value="all">Use pre-selected adducts for either pos or neg ionisation mode</option>
</param>
<when value="msp">
</when>
<when value="msp"/>
<when value="select">
<param argument="--adducts" label="Select adducts"
type="select" help="" multiple="true" display="checkboxes">
<param argument="--adducts" label="Select adducts" type="select" help="" multiple="true" display="checkboxes">
<option value="[M+H]+" selected="True">[M+H]+ 1.007276</option>
<option value="[M+NH4]+">[M+NH4]+ 18.034374</option>
<option value="[M+Na]+">[M+Na]+ 22.989218</option>
Expand All @@ -121,7 +105,7 @@
<option value="[M+ACN+H]+">[M+ACN+H]+ 42.033823</option>
<option value="[M+ACN+Na]+">[M+ACN+Na]+ 64.015765</option>
<option value="[M+2ACN+H]+">[M+2ACN+H]+ 83.06037</option>
<option value="[M-H]-" >[M-H]- -1.007276</option>
<option value="[M-H]-">[M-H]- -1.007276</option>
<option value="[M+Cl]-">[M+Cl]- 34.969402</option>
<option value="[M+HCOO]-">[M+HCOO]- 44.99819</option>
<option value="[M+CH3COO]-">[M+CH3COO]- 59.01385</option>
Expand All @@ -130,69 +114,63 @@
<when value="all">
</when>
</conditional>

<!-- <param argument="&#45;&#45;rank_filter" type="integer" value="0"-->
<!-- label="Only show the top ranked annotations less than or equal-->
<!-- to this value (default to show all annotations)"/>-->

<!-- <param argument="&#45;&#45;confidence_filter" type="float" value="0"-->
<!-- label="Only show annotations greater than or or equal-->
<!-- to this value (default to show all annotations)"/>-->

<!-- <param argument="&#45;&#45;rank_filter" type="integer" value="0"-->
<!-- label="Only show the top ranked annotations less than or equal-->
<!-- to this value (default to show all annotations)"/>-->
<!-- <param argument="&#45;&#45;confidence_filter" type="float" value="0"-->
<!-- label="Only show annotations greater than or or equal-->
<!-- to this value (default to show all annotations)"/>-->
</inputs>
<outputs>
<data name="canopus_results" format="tsv" label="${tool.name} on ${on_string}: CANOPUS"
from_work_dir="canopus_all_summary.tsv"/>
<data name="annotation_results" format="tsv" label="${tool.name} on ${on_string}: Annotations"
from_work_dir="annotations_all_summary.tsv"/>
<data name="structure_results" format="tsv" label="${tool.name} on ${on_string}: All structures"
from_work_dir="structures_all_summary.tsv"/>
<data name="canopus_results" format="tabular" label="${tool.name} on ${on_string}: CANOPUS" from_work_dir="canopus_all_summary.tsv"/>
<data name="annotation_results" format="tabular" label="${tool.name} on ${on_string}: Annotations" from_work_dir="annotations_all_summary.tsv"/>
<data name="structure_results" format="tabular" label="${tool.name} on ${on_string}: All structures" from_work_dir="structures_all_summary.tsv"/>
</outputs>
<tests>
<test>
<test expect_num_outputs="3">
<!-- Test "massbank" style data format -->
<param name="input" value="ML006801.txt" ftype="msp"/>
<output name="annotation_results" file="annotation_ML006801.tsv"/>
<output name="canopus_results" file="canopus_ML006801.tsv"/>
<param name="input" value="ML006801.txt" ftype="msp"/>
<output name="annotation_results" file="annotation_ML006801.tsv" ftype="tabular"/>
<output name="canopus_results" file="canopus_ML006801.tsv" ftype="tabular"/>
<output name="structure_results" file="structures_ML006801.tsv" ftype="tabular"/>
</test>
<test>
<test expect_num_outputs="3">
<!-- Test "generic format" style data format -->
<param name="input" value="generic.msp" ftype="msp"/>
<output name="annotation_results" file="annotation_generic.tsv"/>
<output name="canopus_results" file="canopus_generic.tsv"/>
<output name="annotation_results" file="annotation_generic.tsv" ftype="tabular"/>
<output name="canopus_results" file="canopus_generic.tsv" ftype="tabular"/>
</test>
<test>
<test expect_num_outputs="3">
<!-- Test for glucose (qtof) MassBank data format -->
<param name="input" value="RP022611.txt" ftype="msp"/>
<param name="profile" value="qtof"/>
<output name="annotation_results" file="annotation_RP022611_result.tsv"/>
<output name="canopus_results" file="canopus_RP022611_result.tsv"/>
<output name="annotation_results" file="annotation_RP022611_result.tsv" ftype="tabular"/>
<output name="canopus_results" file="canopus_RP022611_result.tsv" ftype="tabular"/>
</test>
<test>
<test expect_num_outputs="3">
<!-- Test for glucose (q-exactive) GNPS, MoNA data format (and test canopus)-->
<param name="input" value="CCMSLIB00000578155.msp" ftype="msp"/>
<param name="profile" value="orbitrap"/>
<output name="annotation_results" file="annotation_CCMSLIB00000578155_result.tsv"/>
<output name="canopus_results" file="canopus_CCMSLIB00000578155_result.tsv"/>
<output name="annotation_results" file="annotation_CCMSLIB00000578155_result.tsv" ftype="tabular"/>
<output name="canopus_results" file="canopus_CCMSLIB00000578155_result.tsv" ftype="tabular"/>
</test>
<test>
<test expect_num_outputs="3">
<!-- Test invalid adduct -->
<param name="input" value="invalid_adduct.msp" ftype="msp"/>
<output name="annotation_results" file="annotation_invalid_adduct_result.tsv"/>
<output name="canopus_results" file="canopus_invalid_adduct_result.tsv"/>
<output name="annotation_results" file="annotation_invalid_adduct_result.tsv" ftype="tabular"/>
<output name="canopus_results" file="canopus_invalid_adduct_result.tsv" ftype="tabular"/>
</test>
<test>
<test expect_num_outputs="3">
<!-- Test all adducts -->
<param name="input" value="RP022611.txt" ftype="msp"/>
<param name="profile" value="qtof"/>
<param name="polarity" value="negative"/>
<conditional name="adducts_cond">
<param name="adducts_selector" value="all"/>
</conditional>
<output name="annotation_results" file="annotation_RP022611_result_all_adducts.tsv"/>
<output name="canopus_results" file="canopus_RP022611_result_all_adducts.tsv"/>
<output name="annotation_results" file="annotation_RP022611_result_all_adducts.tsv" ftype="tabular"/>
<output name="canopus_results" file="canopus_RP022611_result_all_adducts.tsv" ftype="tabular"/>
</test>

</tests>
<help>
----------------
Expand Down Expand Up @@ -263,18 +241,15 @@ options and scoring functions SIRIUS 3 will use for its analysis. For example,
the Orbitrap and FT-ICR profiles have tighter constraints for the allowed mass
deviation but do not rely so much on the intensity of isotope peaks.


Developers and contributors
---------------------------

- **Jordi Capellades ([email protected]) - Universitat Rovira i Virgili (SP)**
- **Thomas N Lawson ([email protected]) - University of Birmingham (UK)**
- **Simon Bray ([email protected]) - University of Freiburg (Germany)**
- **Ralf Weber ([email protected]) - University of Birmingham (UK)**

</help>
<creator>
<person givenName="Jordi" familyName="Capellades" email="[email protected]"/>
<person givenName="Thomas" familyName="Lawson" email="[email protected]"/>
<person givenName="Simon" familyName="Bray" email="[email protected]"/>
<person givenName="Ralf" familyName="Weber" email="[email protected]"/>
</creator>
<citations>
<citation type="doi">10.1073/pnas.1509788112</citation>
<citation type="doi">10.1093/bioinformatics/btu275</citation>
</citations>
</tool>
</tool>

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