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Section #8

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Apr 7, 2017
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Section #8

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26ba6c5
add sections
lecorguille Apr 6, 2017
5c56ad0
more options in test
lecorguille Apr 6, 2017
2528307
simplifying of the form for the upload of the test-data
lecorguille Apr 6, 2017
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2 changes: 2 additions & 0 deletions .gitignore
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tool_test_output.html
tool_test_output.json
143 changes: 82 additions & 61 deletions galaxy/probmetab/ProbMetab.xml
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Expand Up @@ -41,18 +41,25 @@

#end if

#if $option_toexclude.option == "show":
toexclude $option_toexclude.toexclude
## Extraction of CAMERA annotation [get.annot]
allowMiss $getannot.allowMiss
#if $getannot.option_toexclude.option == "show":
toexclude $getannot.option_toexclude.toexclude
#end if
allowMiss $allowMiss
html $html
kegg_db $kegg_db
ppm_tol $ppm_tol
opt $opt
corths $corths
corprob $corprob
pcorprob $pcorprob
prob $prob

## Database matching [create.reactionM]
kegg_db $db.kegg_db
ppm_tol $db.ppm_tol

## Probability calculations matrix export [export.class.table]
prob $export.prob
html $export.html

## Calculate the correlations and partial correlations and cross reference then with reactions [reac2cor]
opt $reac2cor.opt
corprob $reac2cor.corprob
pcorprob $reac2cor.pcorprob
corths $reac2cor.corths

@COMMAND_LOG_EXIT@

Expand Down Expand Up @@ -80,6 +87,7 @@
</when>
</conditional>
-->
<expand macro="input_file_load"/>
</when>
<!-- Two acquisition modes-->
<when value="two">
Expand Down Expand Up @@ -111,77 +119,88 @@
-->
</when>
</conditional>
<expand macro="input_file_load" polarity="Positive"/>
<expand macro="input_file_load" polarity="Negative"/>
</when>
</conditional>

<param name="allowMiss" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Retrieves peaks with no eviendence of adduct or isotope" help=" [allowMiss] (ionAnnot function) Logical, annotate also the peaks as single charged molecules [M+/-H]." />
<conditional name="option_toexclude">
<param name="option" type="select" label="Exclude samples" >
<option value="show">show</option>
<option value="hide" selected="true">hide</option>
</param>
<when value="show">
<param name="toexclude" type="text" value="blank,medium,QC" label="samples to be excluded of peak counting to non-annotated peak selection." help="" />
</when>
<when value="hide" />
</conditional>
<!--
<conditional name="useIso_options">
<param name="option" type="select" label="Calculates the relative isotopic abundance ratio (Carbon 13)" >
<option value="show">Yes</option>
<option value="hide" selected="true">No</option>
<section name="getannot" title="Extraction of CAMERA annotation [get.annot]">
<param name="allowMiss" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Retrieves peaks with no eviendence of adduct or isotope" help=" [allowMiss] (ionAnnot function) Logical, annotate also the peaks as single charged molecules [M+/-H]." />
<conditional name="option_toexclude">
<param name="option" type="select" label="Exclude samples" >
<option value="show">show</option>
<option value="hide" selected="true">hide</option>
</param>
<when value="show">
<param name="toexclude" type="text" value="blank,medium,QC" label="Samples to be excluded of peak counting to non-annotated peak selection." help="[toexclude]" />
</when>
<when value="hide" />
</conditional>
</section>

<section name="db" title="Database matching [create.reactionM]">
<param name="kegg_db" type="text" size="40" label="Search on KEGG database or multiple organisms " help="Search on all KEGG organisms or multiple organisms (id1,id2,id3,...).By default,the value is KEGG which means searching on all KEGG organism. The list of KEGG IDs are available at http://rest.kegg.jp/list/organism" value="KEGG" >
<validator type="empty_field"/>
</param>
<when value="show">
<param name="var" type="select" label="var (incorporate.isotopes)" help="1 to use standard mean/sd estimators to carbon number prediction, 2 for median/mad estimators." >
<option value="1">1</option>
<option value="2" selected="true">2</option>
<param name="ppm_tol" type="integer" value="8" label="Parts per million mass tolerance allowed in the mass search" help="[ppm.tol]" />
<!--
<conditional name="useIso_options">
<param name="option" type="select" label="Calculates the relative isotopic abundance ratio (Carbon 13)" >
<option value="show">Yes</option>
<option value="hide" selected="true">No</option>
</param>
</when>
</conditional>
-->
<param name="html" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Logical, check if you want to generate a HTML ProbMetab report" help=" [html] (export.class.table function).This parameter uses the raw data to plot EICs and may be time consuming." />
<when value="show">
<param name="var" type="select" label="var (incorporate.isotopes)" help="1 to use standard mean/sd estimators to carbon number prediction, 2 for median/mad estimators." >
<option value="1">1</option>
<option value="2" selected="true">2</option>
</param>
</when>
</conditional>
-->
</section>

<param name="kegg_db" type="text" size="40" label="Search on KEGG database or multiple organisms " help="Search on all KEGG organisms or multiple organisms (id1,id2,id3,...).By default,the value is KEGG which means searching on all KEGG organism. The list of KEGG IDs are available at http://rest.kegg.jp/list/organism" value="KEGG" >
<validator type="empty_field"/>
</param>
<param name="ppm_tol" type="integer" value="8" label="Parts per million mass tolerance allowed in the mass search" help="[ppm.tol] (create.reactionMfunction) " />
<section name="export" title="Probability calculations matrix export [export.class.table]">
<param name="prob" type="select" label=" Calculation of the probability to attribute a mass to a compound" help="[prob] Default is 'count'. See the tool help for more details." >
<option value="count" selected="true">Count</option>
<option value="mean">Mean</option>
</param>

<param name="html" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Logical, check if you want to generate a HTML ProbMetab report" help="[html] This parameter uses the raw data to plot EICs and may be time consuming." />
</section>

<param name="opt" type="select" label="Correlation option" help="[opt] (reac2cor function) cor for correlation, and pcor for partial correlation." >
<option value="cor" selected="true">cor</option>
<option value="pcor">pcor</option>
</param>
<section name="reac2cor" title="Calculate the correlations and partial correlations and cross reference then with reactions [reac2cor]">
<param name="opt" type="select" label="Correlation option" help="[opt] cor for correlation, and pcor for partial correlation." >
<option value="cor" selected="true">cor</option>
<option value="pcor">pcor</option>
</param>

<param name="corprob" type="float" value="0.8" label="Probability that the correlation is considered significant" help="[corprob] (reac2cor function) " />
<param name="corprob" type="float" value="0.8" label="Probability that the correlation is considered significant" help="[corprob]" />

<param name="pcorprob" type="float" value="0.8" label="Probability that the partial correlation is considered significant." help="[pcorprob](reac2cor function)" />
<param name="corths" type="float" value="0.75" label="Correlation intensity threshold" help="[corths] (reac2cor function)" />
<param name="pcorprob" type="float" value="0.8" label="Probability that the partial correlation is considered significant." help="[pcorprob]" />
<param name="corths" type="float" value="0.75" label="Correlation intensity threshold" help="[corths]" />
</section>

<param name="prob" type="select" label=" Calculation of the probability to attribute a mass to a compound" help="[prob] (export.class.table function). Default is 'count'. See the tool help for more details." >
<option value="count" selected="true">Count</option>
<option value="mean">Mean</option>
</param>
<!--
<param name="organismId" type="text" size="40" value="NULL" label="organismIdorganismId" help="(create.pathway.node.attributes function) KEGG organism id (http://www.kegg.jp/kegg/catalog/org_list.html) to filter possible pathways for known pathways for that organism. Only works for KEGG database for now. Default is NULL (all KEGG organisms).
" />
<section name="cytoscape" title="CytoScape options">
<param name="organismId" type="text" size="40" value="NULL" label="organismIdorganismId" help="(create.pathway.node.attributes function) KEGG organism id (http://www.kegg.jp/kegg/catalog/org_list.html) to filter possible pathways for known pathways for that organism. Only works for KEGG database for now. Default is NULL (all KEGG organisms).
" />
</section>
-->

<expand macro="input_file_load"/>
<expand macro="input_file_load" polarity="Positive"/>
<expand macro="input_file_load" polarity="Negative"/>
</inputs>

<outputs>
<!-- <data name="output_image" format="rdata" from_work_dir="probmetab.RData" label="Probmetab.RData" /> -->
<data name="html_output" format="html" from_work_dir="AnalysisExample.html" label="Probmetab.Analysis_Report_html" >
<filter>(html)</filter>
<filter>(export['html'])</filter>
</data>
<data name="tsv_output" format="tabular" from_work_dir="Analysis_Report.tsv" label="Probmetab.CytoScape_output_Attribute_List.tsv" />
<data name="eics" format="zip" from_work_dir="Analysis_Report.zip" label="Probmetab.Analysis_Report_EICs_plots.zip" >
<filter>(html)</filter>
<filter>(export['html'])</filter>
</data>
<data name="sif_output" format="tabular" from_work_dir="sif.tsv" label="Probmetab.CytoScape_output.sif" />
<data name="variableMetadata" format="tabular" from_work_dir="variableMetadata.tsv" label="variableMetadata.tsv" >
<filter>(drop_new-file_path['mode'] == 'one')</filter>
<filter>(acquisition_options['mode'] == 'one')</filter>
</data>

<data name="CombineMolIon" format="tabular" from_work_dir="CombineMolIon.tsv" label="CombineMolIon.tsv" >
Expand All @@ -202,7 +221,7 @@
<param name="mode" value="one" />
<param name="image" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata" />
</conditional>
<param name="html" value="FALSE" />
<expand macro="test_commun"/>
<expand macro="test_file_load_zip"/>
<assert_stdout>
<has_text text="Step 1... determine cutoff point" />
Expand All @@ -216,7 +235,7 @@
<param name="mode" value="one" />
<param name="image" value="faahOK-single.xset.merged.group.retcor.group.fillPeaks.annotate.negative.Rdata" />
</conditional>
<param name="html" value="FALSE" />
<expand macro="test_commun"/>
<expand macro="test_file_load_single"/>
<assert_stdout>
<has_text text="Step 1... determine cutoff point" />
Expand Down Expand Up @@ -407,7 +426,9 @@ Probmetab.CytoScape_output.sif
Changelog/News
--------------

**Version 1.1.0 - 15/02/2017**
**Version 1.1.0 - 06/04/2017**

- IMPROVEMENT: add some sections within to separate the different parts of the process

- IMPROVEMENT: Probmetab is now compatible with merged individual data from xcms.xcmsSet

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66 changes: 35 additions & 31 deletions galaxy/probmetab/macros.xml
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Expand Up @@ -27,32 +27,30 @@
<!-- raw file load for planemo test -->
<token name="@COMMAND_FILE_LOAD_NEUTRAL@">
#if $file_load_section_selected.file_load_conditional.file_load_select == "yes":
#if $file_load_section_selected.file_load_conditional.inputs.input == "zip_file":
zipfile$polarity '$file_load_section_selected.file_load_conditional.inputs.zip_file'
#if $file_load_section_selected.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section_selected.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section_selected.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section_selected.file_load_conditional.input[0].is_of_type("netcdf"):
#set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section_selected.file_load_conditional.input ] )
#set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section_selected.file_load_conditional.input ] )
singlefile_galaxyPath$polarity '$singlefile_galaxyPath' singlefile_sampleName$polarity '$singlefile_sampleName'
#else
#set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section_selected.file_load_conditional.inputs.single_file ] )
#set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section_selected.file_load_conditional.inputs.single_file ] )

singlefile_galaxyPath$polarity '$singlefile_galaxyPath'
singlefile_sampleName$polarity '$singlefile_sampleName'
zipfile$polarity '$file_load_section_selected.file_load_conditional.input'
#end if
#end if
</token>

<token name="@COMMAND_FILE_LOAD_ONE@">
#set file_load_section_selected = $file_load_section
#set file_load_section_selected = $acquisition_options.file_load_section
#set polarity=""
@COMMAND_FILE_LOAD_NEUTRAL@
</token>

<token name="@COMMAND_FILE_LOAD_POSITIVE@">
#set file_load_section_selected = $file_load_sectionPositive
#set file_load_section_selected = $acquisition_options.file_load_sectionPositive
#set polarity="Positive"
@COMMAND_FILE_LOAD_NEUTRAL@
</token>

<token name="@COMMAND_FILE_LOAD_NEGATIVE@">
#set file_load_section_selected = $file_load_sectionNegative
#set file_load_section_selected = $acquisition_options.file_load_sectionNegative
#set polarity="Negative"
@COMMAND_FILE_LOAD_NEUTRAL@
</token>
Expand All @@ -67,31 +65,40 @@
<when value="no">
</when>
<when value="yes">
<conditional name="inputs">
<param name="input" type="select" label="Choose your inputs method" >
<option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option>
<option value="single_file">A mzXML or netCDF file from your history</option>
</param>
<when value="zip_file">
<param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
</when>
<when value="single_file">
<param name="single_file" type="data" format="mzxml,netcdf" label="Single file" multiple="true"/>
</when>
</conditional>
<param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />
</when>
</conditional>
</section>
</xml>

<xml name="test_commun">
<section name="getannot">
<param name="allowMiss" value="TRUE" />
<conditional name="option_toexclude">
<param name="option" value="hide" />
</conditional>
</section>
<section name="db">
<param name="kegg_db" value="KEGG" />
<param name="ppm_tol" value="8" />
</section>
<section name="export">
<param name="prob" value="count" />
<param name="html" value="FALSE" />
</section>
<section name="reac2cor">
<param name="opt" value="cor" />
<param name="corprob" value="0.8" />
<param name="pcorprob" value="0.8" />
<param name="corths" value="0.75" />
</section>
</xml>

<xml name="test_file_load_zip">
<section name="file_load_section">
<conditional name="file_load_conditional">
<param name="file_load_select" value="yes" />
<conditional name="inputs">
<param name="input" value="zip_file" />
<param name="zip_file" value="faahKO_reduce.zip" ftype="zip" />
</conditional>
<param name="input" value="faahKO_reduce.zip" ftype="zip" />
</conditional>
</section>
</xml>
Expand All @@ -100,10 +107,7 @@
<section name="file_load_section@POLARITY@">
<conditional name="file_load_conditional">
<param name="file_load_select" value="yes" />
<conditional name="inputs">
<param name="input" value="single_file" />
<param name="single_file" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
</conditional>
<param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
</conditional>
</section>
</xml>
Expand All @@ -118,7 +122,7 @@

.. class:: infomark

**Galaxy integration** Misharl Monsoor [email protected] ABIMS TEAM, Station biologique de Roscoff.
**Galaxy integration** Misharl Monsoor [email protected] (and Gildas Le Corguillé) from ABIMS TEAM, Station biologique de Roscoff.

| Contact [email protected] for any questions or concerns about the Galaxy implementation of this tool.

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