Mercurial > repos > computational-metabolomics > mspurity_purityx
view purityX.xml @ 1:0f646a3e0a3f draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
author | computational-metabolomics |
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date | Thu, 05 Dec 2019 07:36:31 -0500 |
parents | a141be614e76 |
children | b16952cc06d2 |
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<tool id="mspurity_purityx" name="msPurity.purityX" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@"> <description>Calculate the anticipated precursor ion purity from a LC-MS XCMS dataset. </description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ Rscript '$__tool_directory__/purityX.R' --xset_path='$xset' --out_dir='.' --minOffset=$minoffset --maxOffset=$maxoffset --singleFile=$singleFile --purityType=$purityType --cores=\${GALAXY_SLOTS:-4} #if $xgroups.xgroups == "choose" --xgroups='$xgroups.xgroups_value' #end if --camera_xcms=$camera_xcms #if $camera_xcms == "camera" --rdata_name=xa #else --rdata_name=xset #end if --iwNorm=$iw_norm --ilim=$ilim #if $isotopes.isotopes == "exclude_default" --exclude_isotopes #elif $isotopes.isotopes == "user" --exclude_isotopes --isotope_matrix='$isotopes.im' #end if #if $file_load_conditional.file_load_select == 'yes' --galaxy_files=' #for $i in $file_load_conditional.input $i, #end for ' #end if #if $file_load_conditional.file_load_select == 'yes' --files=' #for $i in $file_load_conditional.input $i.name, #end for ' #end if #if $choose_class_cond.choose_class== 'choose' --choose_class=$choose_class_cond.class #end if #if $ignore_files_cond.ignore_files_choice== 'choose' --ignore_files=$ignore_files_cond.ignore_files #end if #if $raw_rt_columns --rtraw_columns #end if ]]></command> <inputs> <param argument="--xset" type="data" format="rdata" help="xcmsSet object saved as an RData file"/> <expand macro="offsets" /> <expand macro="general_params" /> <param argument="--singleFile" type="integer" label="singleFile" value="0" help="If just a single file for purity is to be calculated (rather than the grouped XCMS peaks). Uses the index of the files in xcmsSet object. If zero this is ignored"/> <conditional name="choose_class_cond"> <param name="choose_class" type="select" label="Choose class of XCMS set object to perform calculation on?" > <option value="choose">Choose class</option> <option value="all" selected="true">calculate average across all classes</option> </param> <when value="all"> </when> <when value="choose"> <param argument="--class" type="text" label="Choose class" help="Comma separated string of classes (found in the phenoData slot of xcmsSet object i.e. xset@phenoData). An average will across all the choosen classes." /> </when> </conditional> <conditional name="ignore_files_cond"> <param name="ignore_files_choice" type="select" label="Ignore files?" > <option value="choose">Choose files to ignore from calculation</option> <option value="none" selected="true" >Include all files of selected classes in calculation</option> </param> <when value="none"> </when> <when value="choose"> <param argument="--ignore_files" type="text" label="ignore files" help="Comma separated string of filenames to ignore (do not include the directory) eg. blank1.mzML,blank2.mzML,sample4.mzML" /> </when> </conditional> <conditional name="xgroups"> <param name="xgroups" type="select" label="xgroups" > <option value="choose">Choose XCMS grouped features to calculate precursor ion purity</option> <option value="all" selected="true">Calculate precursor ion purity for all XCMS grouped features</option> </param> <when value="choose"> <param name="xgroups_value" type="text" label="xgroup ids" help="Comma separated string of xcms groups to perform prediction on eg. 1,2,3,4" /> </when> <when value="all"/> </conditional> <param argument="--purityType" type="select" label="Method of averaging purity" help="Area and average used for the purity predictions. FWHM='Full width half maximum', FW='Full width'"> <option value="purityFWHMmedian" selected="true" >FWHM median</option> <option value="purityFWHMmean" >FWHM mean</option> <option value="purityFWmedian" >FW median</option> <option value="purityFWmean" >FW mean</option> </param> <expand macro="camera_xcms" /> <param argument="--raw_rt_columns" type="boolean" label="Has the raw retention time been tracked within the peaks?" help="Only applicable when using retention time correction with obiwarp. When obiwarp is used the retention time correction tracking is slightly different to the other correction methods. To ensure correct tracking with obiwarp an additional tool (track_rt_raw) should be performed prior to any retention time correction."/> <expand macro="fileload" /> </inputs> <outputs> <data name="purityX_tsv" format="tsv" label="${tool.name} on ${on_string}: tsv" from_work_dir="purityX.tsv" /> <data name="purityX_rdata" format="rdata" label="${tool.name} on ${on_string}: RData" from_work_dir="purityX.rdata" /> </outputs> <tests> <test> <conditional name="file_load_conditional"> <param name="file_load_select" value="yes"/> <param name="input" > <collection type="list"> <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/> <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/> <element name="LCMS_2.mzML" value="LCMS_2.mzML"/> <element name="LCMS_1.mzML" value="LCMS_1.mzML"/> </collection> </param> </conditional> <conditional name="xgroups"> <param name="xgroups" value="choose"/> <param name="xgroups_value" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15"/> </conditional> <param name="iw_norm" value="QE5" /> <param name="xset" value="xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData"/> <output name="purityX_tsv" value="purityX_output.tsv" /> <output name="purityX_rdata" value="purityX_output.Rdata" ftype="rdata" compare="sim_size"/> </test> </tests> <help><![CDATA[ =================================================================== Calculate anticipated precursor ion purity from LC-MS XCMS dataset =================================================================== ----------- Description ----------- Tool to calculate the anticipated precursor ion purity of selected precursor based on a prior LC-MS dataset. Based on XCMS determined features -------------- Output example -------------- Output consists of the mz and intensity of the XCMS features (id based on the XCMS group id) and various metrics regarding the anticipated precursor ion purity. ============= ============= ============= ================ ================ ================ ================ ================ ================ grpid mean median sd stde RSD pknm i mz ============= ============= ============= ================ ================ ================ ================ ================ ================ 1 1.00 1.00 0.0000 0.0000 0.0000 1 5404920 100.0758 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ---------------- 2 0.59 0.57 0.3016 0.1508 50.570 3 8793845 101.0084 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ---------------- 3 0.08 0.07 0.0784 0.0164 29.643 4 1526502 100.9781 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ---------------- 4 1.00 1.00 0.0000 0.0000 0.0000 1 42513139 102.0914 ============= ============= ============= ================ ================ ================ ================ ================ ================ ]]></help> <expand macro="citations" /> </tool>