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Changed indentation to 4 spaces and added profile=“23.0”
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@DamienCode404
DamienCode404 committed Oct 18, 2024
1 parent 9331cf5 commit 8595982
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192 changes: 96 additions & 96 deletions tools/camera/findAdducts.xml
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Original file line number Diff line number Diff line change
@@ -1,15 +1,15 @@
<tool id="CAMERA_findAdducts" name="CAMERA.findAdducts" version="0.1.0+camera@TOOL_VERSION@-galaxy@VERSION_SUFFIX@">
<tool id="CAMERA_findAdducts" name="CAMERA.findAdducts" version="0.1.0+camera@TOOL_VERSION@-galaxy@VERSION_SUFFIX@" profile="23.0">

<description>Annotate adducts (and fragments) for a xsAnnotate object. Returns a xsAnnotate object with annotated pseudospectra.</description>
<description>Annotate adducts (and fragments) for a xsAnnotate object. Returns a xsAnnotate object with annotated pseudospectra.</description>

<macros>
<import>macros.xml</import>
</macros>
<macros>
<import>macros.xml</import>
</macros>

<expand macro="requirements"/>
<expand macro="stdio"/>
<expand macro="requirements"/>
<expand macro="stdio"/>

<command detect_errors="exit_code"><![CDATA[
<command detect_errors="exit_code"><![CDATA[
@COMMAND_RSCRIPT@/CAMERA_findAdducts.R
'$image'
$findAdducts.ppm
Expand All @@ -24,91 +24,91 @@
$findAdducts.numDigitsMZ
$findAdducts.numDigitsRT
]]>
</command>
<inputs>
<param name="image" type="data" label="RData file" format="rdata" help="Output file from another function CAMERA (findIsotopes)" />

<section name="findAdducts" title="Annotate Adducts" expanded="True">
<param name="ppm" type="integer" value="5" label="General ppm error" />
<param name="mzabs" type="float" value="0.015" label="General absolute error in m/z" />
<param name="polarity" type="select" label="Which polarity mode was used for measuring of the MS sample">
<option value="positive">positive</option>
<option value="negative" selected="true">negative</option>
</param>

<conditional name="rules_block">
<param name="rules_select" type="select" label="Use a personal ruleset file">
<option value="TRUE">TRUE</option>
<option value="FALSE" selected="true">FALSE</option>
</param>
<when value="FALSE">
<param name="rules" type="text" value="NULL" label="No personal ruleset file (using default ruleset)" optional="true" />
</when>
<when value="TRUE">
<param name="rules" type="data" format="csv" label="User defined ruleset" />
</when>
</conditional>

<param name="intval" type="select" label="Choose intensity values">
<option value="into" selected="true">into</option>
<option value="maxo">maxo</option>
<option value="intb">intb</option>
</param>

<conditional name="advanced">
<param name="advanced_select" type="select" label="Advanced parameters">
<option value="TRUE">TRUE</option>
<option value="FALSE" selected="true">FALSE</option>
</param>
<when value="FALSE">
<param name="multiplier" type="integer" value="3" label="Highest number(n) of allowed clusterion [nM+ion]" optional="true" />
<param name="max_peaks" type="integer" value="100" label="How many peaks will be calculated in every thread (parallel mode)" optional="true" />
<param name="psg_list" type="text" value="NULL" label="No psg_list" optional="true" />
</when>
<when value="TRUE">
<param name="multiplier" type="integer" value="3" label="Highest number(n) of allowed clusterion [nM+ion]" />
<param name="max_peaks" type="integer" value="100" label="How many peaks will be calculated in every thread (parallel mode)" />

<conditional name="psg_list_block">
<param name="psg_list_select" type="select" label="Use a personal psg_list">
<option value="TRUE">TRUE</option>
<option value="FALSE" selected="true">FALSE</option>
</param>
<when value="FALSE">
<param name="psg_list" type="text" value="NULL" label="No psg_list" optional="true" />
</when>
<when value="TRUE">
<param name="psg_list" type="text" optional="true" label="Pseudospectra indices (optional)" help="Provide a comma-separated list of pseudospectra indices (e.g. 1,2,3)." />
</when>
</conditional>
</when>
</conditional>
<param name="convertRTMinute" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Convert seconds to minutes when exporting tsv" />
<param name="numDigitsMZ" type="integer" value="4" max="4" min="0" label="Number of digits for MZ values (namecustom)" />
<param name="numDigitsRT" type="integer" value="4" max="4" min="0" label="Number of digits for RT values (namecustom)" />
</section>
</inputs>
<outputs>
<data name="variableMetadata" format="tabular" label="${image.name[:-6]}.findAdducts.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" />
<data name="camera_findAdducts_rdata" format="rdata" label="${image.name[:-6]}.findAdducts.RData" from_work_dir="camera_findAdducts.RData" />
</outputs>
<tests>
<test>
<param name="image" value="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.RData" />
<param name="ppm" value="5" />
<param name="mzabs" value="0.015" />
<param name="polarity" value="positive" />
<param name="rules" value="NULL" />
<param name="intval" value="into" />
<param name="multiplier" value="3" />
<param name="max_peaks" value="100" />
<param name="psg_list" value="NULL" />

<output name="variableMetadata" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.findAdducts.variableMetadata.tsv" />
<output name="camera_findAdducts_rdata" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.findAdducts.RData" />
</test>
</tests>
<help><![CDATA[
</command>
<inputs>
<param name="image" type="data" label="RData file" format="rdata" help="Output file from another function CAMERA (findIsotopes)" />

<section name="findAdducts" title="Annotate Adducts" expanded="True">
<param name="ppm" type="integer" value="5" label="General ppm error" />
<param name="mzabs" type="float" value="0.015" label="General absolute error in m/z" />
<param name="polarity" type="select" label="Which polarity mode was used for measuring of the MS sample">
<option value="positive">positive</option>
<option value="negative" selected="true">negative</option>
</param>

<conditional name="rules_block">
<param name="rules_select" type="select" label="Use a personal ruleset file">
<option value="TRUE">TRUE</option>
<option value="FALSE" selected="true">FALSE</option>
</param>
<when value="FALSE">
<param name="rules" type="text" value="NULL" label="No personal ruleset file (using default ruleset)" optional="true" />
</when>
<when value="TRUE">
<param name="rules" type="data" format="csv" label="User defined ruleset" />
</when>
</conditional>

<param name="intval" type="select" label="Choose intensity values">
<option value="into" selected="true">into</option>
<option value="maxo">maxo</option>
<option value="intb">intb</option>
</param>

<conditional name="advanced">
<param name="advanced_select" type="select" label="Advanced parameters">
<option value="TRUE">TRUE</option>
<option value="FALSE" selected="true">FALSE</option>
</param>
<when value="FALSE">
<param name="multiplier" type="integer" value="3" label="Highest number(n) of allowed clusterion [nM+ion]" optional="true" />
<param name="max_peaks" type="integer" value="100" label="How many peaks will be calculated in every thread (parallel mode)" optional="true" />
<param name="psg_list" type="text" value="NULL" label="No psg_list" optional="true" />
</when>
<when value="TRUE">
<param name="multiplier" type="integer" value="3" label="Highest number(n) of allowed clusterion [nM+ion]" />
<param name="max_peaks" type="integer" value="100" label="How many peaks will be calculated in every thread (parallel mode)" />

<conditional name="psg_list_block">
<param name="psg_list_select" type="select" label="Use a personal psg_list">
<option value="TRUE">TRUE</option>
<option value="FALSE" selected="true">FALSE</option>
</param>
<when value="FALSE">
<param name="psg_list" type="text" value="NULL" label="No psg_list" optional="true" />
</when>
<when value="TRUE">
<param name="psg_list" type="text" optional="true" label="Pseudospectra indices (optional)" help="Provide a comma-separated list of pseudospectra indices (e.g. 1,2,3)." />
</when>
</conditional>
</when>
</conditional>
<param name="convertRTMinute" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Convert seconds to minutes when exporting tsv" />
<param name="numDigitsMZ" type="integer" value="4" max="4" min="0" label="Number of digits for MZ values (namecustom)" />
<param name="numDigitsRT" type="integer" value="4" max="4" min="0" label="Number of digits for RT values (namecustom)" />
</section>
</inputs>
<outputs>
<data name="variableMetadata" format="tabular" label="${image.name[:-6]}.findAdducts.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" />
<data name="camera_findAdducts_rdata" format="rdata" label="${image.name[:-6]}.findAdducts.RData" from_work_dir="camera_findAdducts.RData" />
</outputs>
<tests>
<test>
<param name="image" value="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.RData" />
<param name="ppm" value="5" />
<param name="mzabs" value="0.015" />
<param name="polarity" value="positive" />
<param name="rules" value="NULL" />
<param name="intval" value="into" />
<param name="multiplier" value="3" />
<param name="max_peaks" value="100" />
<param name="psg_list" value="NULL" />

<output name="variableMetadata" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.findAdducts.variableMetadata.tsv" />
<output name="camera_findAdducts_rdata" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.findAdducts.RData" />
</test>
</tests>
<help><![CDATA[
@HELP_AUTHORS@
Expand Down Expand Up @@ -180,8 +180,8 @@ Changelog/News
@HELP_CAMERA_SUITE@
]]></help>
]]> </help>

<expand macro="citation"/>
<expand macro="creator"/>
<expand macro="citation"/>
<expand macro="creator"/>
</tool>
107 changes: 54 additions & 53 deletions tools/camera/findIsotopes.xml
View file
Original file line number Diff line number Diff line change
@@ -1,15 +1,15 @@
<tool id="CAMERA_findIsotopes" name="CAMERA.findIsotopes" version="0.1.0+camera@TOOL_VERSION@-galaxy@VERSION_SUFFIX@">
<tool id="CAMERA_findIsotopes" name="CAMERA.findIsotopes" version="0.1.0+camera@TOOL_VERSION@-galaxy@VERSION_SUFFIX@" profile="23.0">

<description>Annotate isotope peaks for a xsAnnotate object. Returns a xsAnnotate object with annotated isotopes.</description>
<description>Annotate isotope peaks for a xsAnnotate object. Returns a xsAnnotate object with annotated isotopes.</description>

<macros>
<import>macros.xml</import>
</macros>
<macros>
<import>macros.xml</import>
</macros>

<expand macro="requirements"/>
<expand macro="stdio"/>
<expand macro="requirements"/>
<expand macro="stdio"/>

<command detect_errors="exit_code"><![CDATA[
<command detect_errors="exit_code"><![CDATA[
@COMMAND_RSCRIPT@/CAMERA_findIsotopes.R
'$image'
$findIsotopes.maxcharge
Expand All @@ -21,48 +21,49 @@
$findIsotopes.filter
$findIsotopes.convertRTMinute
$findIsotopes.numDigitsMZ
$findIsotopes.numDigitsRT
]]></command>

<inputs>
<param name="image" type="data" label="RData file" format="rdata" help="output file from another function CAMERA (groupFWHM)" />
<section name="findIsotopes" title="Annotate Isotopes" expanded="True">
<param name="maxcharge" type="integer" value="3" label="Max. ion charge" />
<param name="maxiso" type="integer" value="4" max="8" min="1" label="Max. number of expected isotopes" />
<param name="ppm" type="integer" value="5" label="ppm error for the search" />
<param name="mzabs" type="float" value="0.01" max="0.1" min="-0.1" label="allowed variance for the search" />
<param name="intval" type="select" label="choose intensity values for C12/C13 check. Allowed values are into, maxo, intb">
<option value="into" selected="true">into</option>
<option value="maxo">maxo</option>
<option value="intb">intb</option>
</param>
<param name="minfrac" type="float" value="0.5" max="1" min="0" label="The percentage number of samples, which must satisfy the C12/C13 rule for isotope annotation" />
<param name="filter" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Should C12/C13 filter be applied" />
<param name="convertRTMinute" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Convert seconds to minutes when exporting tsv" />
<param name="numDigitsMZ" type="integer" value="4" max="4" min="0" label="Number of digits for MZ values (namecustom)" />
<param name="numDigitsRT" type="integer" value="4" max="4" min="0" label="Number of digits for RT values (namecustom)" />
</section>
</inputs>
<outputs>
<data name="variableMetadata" format="tabular" label="${image.name[:-6]}.findIsotopes.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" />
<data name="camera_findIsotopes_rdata" format="rdata" label="${image.name[:-6]}.findIsotopes.RData" from_work_dir="camera_findIsotopes.RData" />
</outputs>
<tests>
<test>
<param name="image" value="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.RData" />
<param name="maxcharge" value="3" />
<param name="maxiso" value="4" />
<param name="ppm" value="5" />
<param name="mzabs" value="0.01" />
<param name="intval" value="into" />
<param name="minfrac" value="0.5" />
<param name="filter" value="FALSE" />

<output name="variableMetadata" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.variableMetadata.tsv" />
<output name="camera_findIsotopes_rdata" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.RData" />
</test>
</tests>
<help><![CDATA[
$findIsotopes.numDigitsRTF
]]>
</command>

<inputs>
<param name="image" type="data" label="RData file" format="rdata" help="output file from another function CAMERA (groupFWHM)" />
<section name="findIsotopes" title="Annotate Isotopes" expanded="True">
<param name="maxcharge" type="integer" value="3" label="Max. ion charge" />
<param name="maxiso" type="integer" value="4" max="8" min="1" label="Max. number of expected isotopes" />
<param name="ppm" type="integer" value="5" label="ppm error for the search" />
<param name="mzabs" type="float" value="0.01" max="0.1" min="-0.1" label="allowed variance for the search" />
<param name="intval" type="select" label="choose intensity values for C12/C13 check. Allowed values are into, maxo, intb">
<option value="into" selected="true">into</option>
<option value="maxo">maxo</option>
<option value="intb">intb</option>
</param>
<param name="minfrac" type="float" value="0.5" max="1" min="0" label="The percentage number of samples, which must satisfy the C12/C13 rule for isotope annotation" />
<param name="filter" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Should C12/C13 filter be applied" />
<param name="convertRTMinute" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Convert seconds to minutes when exporting tsv" />
<param name="numDigitsMZ" type="integer" value="4" max="4" min="0" label="Number of digits for MZ values (namecustom)" />
<param name="numDigitsRT" type="integer" value="4" max="4" min="0" label="Number of digits for RT values (namecustom)" />
</section>
</inputs>
<outputs>
<data name="variableMetadata" format="tabular" label="${image.name[:-6]}.findIsotopes.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" />
<data name="camera_findIsotopes_rdata" format="rdata" label="${image.name[:-6]}.findIsotopes.RData" from_work_dir="camera_findIsotopes.RData" />
</outputs>
<tests>
<test>
<param name="image" value="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.RData" />
<param name="maxcharge" value="3" />
<param name="maxiso" value="4" />
<param name="ppm" value="5" />
<param name="mzabs" value="0.01" />
<param name="intval" value="into" />
<param name="minfrac" value="0.5" />
<param name="filter" value="FALSE" />

<output name="variableMetadata" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.variableMetadata.tsv" />
<output name="camera_findIsotopes_rdata" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.RData" />
</test>
</tests>
<help><![CDATA[
@HELP_AUTHORS@
Expand Down Expand Up @@ -133,8 +134,8 @@ Changelog/News
@HELP_CAMERA_SUITE@
]]></help>
]]> </help>

<expand macro="citation"/>
<expand macro="creator"/>
<expand macro="citation"/>
<expand macro="creator"/>
</tool>
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