Mercurial > repos > tomnl > lcms_interval_scheduling
diff lcms-interval-scheduling.xml @ 0:21a76537a900 draft
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
| author | tomnl |
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| date | Tue, 27 Mar 2018 06:53:12 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lcms-interval-scheduling.xml Tue Mar 27 06:53:12 2018 -0400 @@ -0,0 +1,151 @@ +<tool id="lcms_interval_scheduling" name="lcms_interval_scheduling" version="0.0.2"> + <requirements> + <requirement type="package" >r</requirement> + <requirement type="package" >r-optparse</requirement> + <requirement type="package" >r-xcmswrapper</requirement> + </requirements> + <description>Generate target lists from LC-MS features for a fragmentation experiment + </description> + + <stdio> + <exit_code range="1:" /> + </stdio> + <command interpreter="Rscript"><![CDATA[ + lcms-interval-scheduling.R + + --sample_peaklist=$sample_peaklist + --blank_peaklist=$blank_peaklist + --topn=$topn + --out_dir=. + --method=$method_select.method + #if $method_select.method=='metshot' + #if $method_select.fillgaps + --fillgaps + #end if + #elif $method_select.method=='simple' + --maxms2=$method_select.maxms2 + --ilimit=$method_select.ilimit + #else + --overlappingP=$method_select.overlappingP + #end if + --widthFactor=$widthFactor + --minWidth=$minWidth + --shift=$shift + --samplelistNm=$samplelistNm + #if $fullpw + --fullpw + #end if + --b_widthFactor=$b_widthFactor + --b_shift=$b_shift + --b_exclu_limit=$b_exclu_limit + --b_minWidth=$b_minWidth + --polarity=$polarity + #if $dma_nearline_cond.dma=='yes' + --blankClass=$dma_nearline_cond.blankClass + --filterS=$dma_nearline_cond.filterS + --dmaNearline + #end if + --intensityCN=$intensityCN + --sortCN=$sortCN + ]]></command> + <inputs> + <param type="data" name="sample_peaklist" label="Sample peaklist" format="tsv,tabular" + help="The peaklist from the samples to be scheduled for fragmentation"/> + + <param type="data" name="blank_peaklist" label="Blank peaklist" format="tsv,tabular" + help="The peaklist of blank features to avoid when performing fragmentation"/> + + <param type="data" name="topn" label="Topn blank peaklist" format="tsv,tabular" + help="The top (n) blank peaks determined from windows of the spectrum (i.e. not using XCMS)"/> + + <conditional name="method_select"> + <param name="method" type="select" label="Nearline method"> + <option value="simple" >Simple nearline (divide equally amongst runs) </option> + <option value="interval">Interval schedule with defined overlap</option> + <option value="interval_min_overlap" selected="true">Interval schedule with defined overlap. Overlap is also minimized</option> + <option value="metshot">Original metshot algorithm (No overlapping features)</option> + </param> + <when value="metshot"> + <param name="fillGaps" type="boolean" label="Fill gaps"/> + </when> + <when value="simple"> + <param name="maxms2" type="integer" label="Max MS2 per run" value="2000"/> + <param name="ilimit" type="float" label="Intensity (peak area) limit to be included" value="5000"/> + </when> + <when value="interval"> + <param name="overlappingP" type="integer" label="Max number of overlapping peaks" value="10"/> + </when> + <when value="interval_min_overlap"> + <param name="overlappingP" type="integer" label="Max number of overlapping peaks" value="10"/> + </when> + </conditional> + + <param name="widthFactor" type="float" label="Width factor" value="1" + help="Increase the width of the peaks by the chosen factor "/> + + <param name="minWidth" type="float" label="Minimum width of peak (sec)" value="5" + help="The time range will always be >= to this value (even if the prior peak width is calculated + to be smaller)"/> + + <param name="shift" type="float" label="Shift (sec)" value="0" help="Shift all the peaks by value to account for drift"/> + <param name="samplelistNm" type="integer" label="Number of MS2 runs to perform" value="4"/> + <param name="fullpw" type="boolean" label="Use full peak width?" help="" /> + <param name="b_widthFactor" type="float" label="Width factor (for blank)" value="2" + help="Increase the width of the peaks by the chosen factor "/> + + <param name="b_minWidth" type="float" label="Minimum width of peak (sec) (for blank)" value="5" + help="The time range will always be >= to this value (even if the prior peak width is calculated + to be smaller) (for blank)"/> + + + <param name="b_shift" type="float" label="Shift (for blank) (sec)" value="0" help="Shift all the peaks by value to account for drift"/> + <param name="b_exclu_limit" type="integer" label="Exclusion limit" value="5000" help="Limit of peaks to put on exclusion limit"/> + <param name="polarity" type="select" label="Polarity"> + <option value="positive" selected="true" >Positive</option> + <option value="negative" >Negative</option> + </param> + + <param name="sortCN" type="text" label="column of sample peaklist to order by" value="totalS" + help="default value corresponds if the tool 'deconrank' has been run prior. The 'total score' + column is based on multiple criteria (see deconrank tool). + If not using the deconrank tool, any other column can be used e.g. intensity (peak area)"/> + + <param name="intensityCN" type="text" label="column to use for intensity (peak area) for sample" value="i"/> + + + <conditional name="dma_nearline_cond"> + <param name="dma" type="select" label="Use as part of DMA nearline workflow?" + help="If using within the nearline LC-MS workflow then certain processing needs to be performed, + including filtering out peaks that are not to be scheduled"> + <option value="yes">Yes</option> + <option value="no" select="no">No</option> + </param> + <when value="yes"> + <param name="blankClass" type="text" label="Blank class" value="blank" + help="Note that this will have to change if the blank class has a different name. Uses the valid + column e.g. [blank_name]_valid. + If he value is 1 (we keep) if 0 (we do not use)" /> + <param name="filterS" type="text" label="Column name to filter sample on" value="excludedFinal" + help="This is a bit confusing.. But if this value is 1 then (we exclude) and if 0 (we keep for the + sample)"/> + </when> + </conditional> + + </inputs> + <outputs> + <collection name="inclusion_lists" type="list" label="${tool.name} on ${on_string}: inclusion lists"> + <discover_datasets pattern="(?P<designation>.+inclusion.+).csv" format="csv" directory="." /> + </collection> + <collection name="exclusion_lists" type="list" label="${tool.name} on ${on_string}: exclusion lists"> + <discover_datasets pattern="(?P<designation>.+exclusion.+).csv" format="csv" directory="." /> + </collection> + <data format="pdf" name="overlap_plots_positive" label="${tool.name} on ${on_string}: overlap plots" + from_work_dir="overlap_plots_positive.pdf"/> + + </outputs> + <tests> + </tests> + <help><![CDATA[ + + ]]></help> +</tool> \ No newline at end of file