Mercurial > repos > tomnl > cameradims
view cameradims.xml @ 19:d4081e4160af draft
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 14435cfc042911bf1ee409f5a0d5ef908f5feec0-dirty
author | tomnl |
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date | Thu, 21 Jun 2018 08:47:44 -0400 |
parents | e798d637fbcd |
children | 8e33abdebc57 |
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<tool id="cameradims" name="CAMERA_DIMS" version="0.2.5"> <description>Modification of the R package CAMERA to work on DIMS data</description> <requirements> <requirement type="package" version="0.2.8">r-cameradims</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio> <command interpreter="Rscript"><![CDATA[ cameradims.R --in_file $peaks_file --out_dir . --ppm_adduct $ppm_adduct --ppm_iso $ppm_iso --mzabs_adduct $mzabs_adduct --mzabs_iso $mzabs_iso --maxiso $maxiso --maxcharge $maxcharge --maxmol $maxmol --polarity $polarity --rule_type $ruleset.ruleset #if $ruleset.ruleset == 'user' --rule_path $ruleset.rulesfile #end if #if $export_ruleset --export_ruleset #end if --intensity_filter=$intensity_filter ]]></command> <inputs> <param type="data" name="peaks_file" format="tabular,tsv" help="tsv or tabular file with mz and intensity columns"/> <param name="ppm_adduct" type="float" label="ppm (adduct)" value="5" help="general ppm error (adduct)"/> <param name="ppm_iso" type="float" label="ppm (iso)" value="5" help="general ppm error (iso)"/> <param name="mzabs_adduct" type="float" label="mzabs (adduct)" value="0.015" help="general absolute error in m/z"/> <param name="mzabs_iso" type="float" label="mzabs (iso)" value="0.015" help="general absolute error in m/z"/> <param name="maxmol" type="integer" label="maxmol" value="3" help="highest number(n) of allowed clusterion [nM+ion] (argument called multiplier in findAdducts())"/> <param name="maxiso" type="integer" label="maxiso" value="4" help="max number of expected isotopes"/> <param name="maxcharge" type="integer" label="maxcharge" value="3" help="max ion charge for finding isotopes"/> <param name="polarity" type="select" label="polarity" help="Which polarity mode was used for measuring of the ms sample" > <option value="pos" selected="true">positive</option> <option value="neg">negative</option> </param> <param name="intensity_filter" type="float" label="Intensity filter" value="5000" help="Filter out any peaks that have intensity less than this value. (Adduct calculation may take a very long time if peaks are not filtered before hand) "/> <conditional name="ruleset"> <param name="ruleset" type="select" label="Rules for adducts" > <option value="primary adducts" >Primary adducts ([M+Na]+, [M+K]+ and [M+NH4]+")</option> <option value="extended" selected="true" >Extended adducts</option> <option value="extended_large" >Extended adducts (large)</option> <option value="user" >Provide a csv file of the rules to use</option> </param> <when value="user"> <param type="data" name="rulesfile" format="tsv, tabular" help="User supplied rules file used to to calculate adducts, should contain the following columns name,nmol,charge,massdiff,oidscore,quasi,ips. If using the adducts to guide fragmentation then the frag_score column should be included. Where a score of 1 indicates the adduct is the best adduct form to fragment"/> </when> <when value="extended"> </when> <when value="primary adducts"> </when> </conditional> <param name="export_ruleset" type="boolean" label="Export the adduct ruleset used?" help=""/> </inputs> <outputs> <data name="camera_annotated_map" format="tsv" label="${tool.name} on ${on_string}: map" from_work_dir="camera_annotated_map.txt" /> <data name="camera_annotated_peaklist" label="${tool.name} on ${on_string}: peaklist" from_work_dir="camera_annotated_peaklist.txt" format="tsv"/> <data name="ruleset" label="${tool.name} on ${on_string}: ruleset" from_work_dir="ruleset.txt" format="tsv"> <filter>export_ruleset is True</filter> </data> </outputs> <tests> <test> <param name="peaks_file" value="peaklist_in.tsv" ftype="tsv"/> <output name="camera_annotated_peaklist" value="camera_annotated_peaklist.txt"/> <output name="camera_annotated_map" value="camera_annotated_map.txt"/> </test> </tests> <help><![CDATA[ cameraDIMS ]]></help> <citations> <citation type="doi">10.1021/ac202450g</citation> </citations> </tool>