Mercurial > repos > tomnl > mspurity_flagremove
diff flagRemove.xml @ 15:b71677d4f958 draft default tip
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
| author | tomnl |
|---|---|
| date | Wed, 27 Nov 2019 12:31:10 +0000 |
| parents | 7e4a5ce0877d |
| children |
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--- a/flagRemove.xml Fri Sep 27 09:12:41 2019 -0400 +++ b/flagRemove.xml Wed Nov 27 12:31:10 2019 +0000 @@ -2,98 +2,92 @@ <description>Tool to flag and remove XCMS grouped peaks from the xcmsSet object based on various thresholds (e.g. RSD of intensity and retention time). </description> - <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> - - <stdio> - <exit_code range="1:" /> - </stdio> - <command interpreter="Rscript"><![CDATA[ - flagRemove.R - --xset_path=$xset_path + <command detect_errors="exit_code"><![CDATA[ + Rscript '$__tool_directory__/flagRemove.R' + --xset_path='$xset_path' --out_dir=. #if $sample_flag.sample_flag=='update' - --rsd_i_sample=$sample_flag.rsd_i_sample - --minfrac_sample=$sample_flag.minfrac_sample - --ithres_sample=$sample_flag.ithres_sample + --rsd_i_sample='$sample_flag.rsd_i_sample' + --minfrac_sample='$sample_flag.minfrac_sample' + --ithres_sample='$sample_flag.ithres_sample' #end if #if $blank_flag.blank_flag=='update' - --rsd_i_blank=$blank_flag.rsd_i_blank - --minfrac_blank=$blank_flag.minfrac_blank - --ithres_blank=$blank_flag.ithres_blank - --blank_class=$blank_flag.blank_class + --rsd_i_blank='$blank_flag.rsd_i_blank' + --minfrac_blank='$blank_flag.minfrac_blank' + --ithres_blank='$blank_flag.ithres_blank' + --blank_class='$blank_flag.blank_class' #end if #if $peak_removal.peak_removal=='remove' --remove_spectra - --minfrac_xcms=$peak_removal.minfrac_xcms - --mzwid=$peak_removal.mzwid - --bw=$peak_removal.bw + --minfrac_xcms='$peak_removal.minfrac_xcms' + --mzwid='$peak_removal.mzwid' + --bw='$peak_removal.bw' #end if #if $advanced.advanced=='update' - --egauss_thr=$advanced.egauss_thr - --polarity=$advanced.polarity - --grp_rm_ids=$advanced.grp_rm_ids - --xset_name=$advanced.xset_name - $advanced.temp_save.value + --egauss_thr='$advanced.egauss_thr' + --polarity='$advanced.polarity' + --grp_rm_ids='$advanced.grp_rm_ids' + --xset_name='$advanced.xset_name' + '$advanced.temp_save.value' #end if #if $choose_samp.choose_samp=='yes' - --samplelist=$choose_samp.samplelist + --samplelist='$choose_samp.samplelist' #end if ]]></command> <inputs> - <param type="data" name="xset_path" format='rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata' + <param argument="--xset_path" type="data" format='rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata' help="The path to the xcmsSet object saved as an RData file"/> <conditional name="sample_flag"> - <param name="sample_flag" type="select" label="Change biological sample flag parameters?"> + <param argument="sample_flag" type="select" label="Change biological sample flag parameters?"> <option value="update" >Update biological sample flag parameters</option> <option value="" selected="true">Use default biological sample flag parameters</option> </param> <when value=""> </when> <when value="update"> - <param name="rsd_i_sample" type="text" label="rsd_i_sample" value="NA" - help="Relative Standard Deviation threshold for the sample classes (--rsd_i_sample)"/> - <param name="minfrac_sample" type="float" label="minfrac_sample" value="0.5" min="0.0" max="1" - help="minimum fraction of files for features needed for the sample classes (--minfrac_sample)"/> - <param name="rsd_rt_sample" type="text" label="rsd_rt_sample" value="NA" + <param argument="--rsd_i_sample" type="text" label="rsd_i_sample" value="NA" + help="Relative Standard Deviation threshold for the sample classes"/> + <param argument="--minfrac_sample" type="float" label="minfrac_sample" value="0.5" min="0.0" max="1" + help="minimum fraction of files for features needed for the sample classes"/> + <param argument="--rsd_rt_sample" type="text" label="rsd_rt_sample" value="NA" help="Relative standard Deviation threshold for the retention time of the sample - classes (--rsd_rt_sample)"/> - <param name="ithres_sample" type="text" label="ithres_sample" value="NA" - help="Intensity threshold for the sample (--ithres_sample)"/> + classes"/> + <param argument="--ithres_sample" type="text" label="ithres_sample" value="NA" + help="Intensity threshold for the sample"/> </when> </conditional> <conditional name="blank_flag"> - <param name="blank_flag" type="select" label="Change blank flag parameters?"> + <param argument="blank_flag" type="select" label="Change blank flag parameters?"> <option value="update" >Update blank flag parameters</option> <option value="" selected="true">Use default blank flag parameters</option> </param> <when value=""> </when> <when value="update"> - <param name="blank_class" type="text" label="blank_class" value="blank" - help="A string representing the class that will be used for the blank (--blank_class)"/> - <param name="rsd_i_blank" type="text" label="rsd_i_blank" value="NA" - help="RSD threshold for the blank (--rsd_i_blank)"/> - <param name="minfrac_blank" type="float" label="minfrac_blank" value="0.5" min="0.0" max="1" - help="minimum fraction of files for features needed for the blank (--minfrac_blank)"/> - <param name="rsd_rt_blank" type="text" label="rsd_rt_blank" value="NA" - help="RSD threshold for the retention time of the blank (--rsd_rt_blank)"/> - <param name="ithres_blank" type="text" label="ithres_blank" value="NA" - help="Intensity threshold for the blank (--ithres_blank)"/> - <param name="s2b" type="float" label="s2b" value="10" + <param argument="--blank_class" type="text" label="blank_class" value="blank" + help="A string representing the class that will be used for the blank"/> + <param argument="--rsd_i_blank" type="text" label="rsd_i_blank" value="NA" + help="RSD threshold for the blank"/> + <param argument="--minfrac_blank" type="float" label="minfrac_blank" value="0.5" min="0.0" max="1" + help="minimum fraction of files for features needed for the blank"/> + <param argument="--rsd_rt_blank" type="text" label="rsd_rt_blank" value="NA" + help="RSD threshold for the retention time of the blank"/> + <param argument="--ithres_blank" type="text" label="ithres_blank" value="NA" + help="Intensity threshold for the blank"/> + <param argument="--s2b" type="float" label="s2b" value="10" help="fold change (sample/blank) needed for sample peak to be allowed. e.g. if s2b set to 10 and the recorded sample 'intensity' value was 100 and blank was 10. 1000/10 = 100, so sample has fold change higher than the threshold and the peak - is not considered a blank (--s2b)"/> + is not considered a blank"/> </when> </conditional> <conditional name="peak_removal"> @@ -104,12 +98,12 @@ <when value=""> </when> <when value="remove"> - <param name="minfrac_xcms" type="float" label="minfrac_xcms" value="0.7" min="0.0" max="1" - help="minfrac for xcms grouping (--minfrac_xcms)"/> - <param name="mzwid" type="float" label="mzwid" value="0.001" - help="mzwid for xcms grouping (--minfrac_xcms)"/> - <param name="bw" type="float" label="bw" value="5" - help="bw for xcms grouping(--minfrac_xcms)"/> + <param argument="--minfrac_xcms" type="float" label="minfrac_xcms" value="0.7" min="0.0" max="1" + help="minfrac for xcms grouping"/> + <param argument="--mzwid" type="float" label="mzwid" value="0.001" + help="mzwid for xcms grouping"/> + <param argument="--bw" type="float" label="bw" value="5" + help="bw for xcms grouping"/> </when> </conditional> <conditional name="advanced"> @@ -120,23 +114,22 @@ <when value=""> </when> <when value="update"> - <param name="egauss_thr" type="text" label="egauss_thr" value="NA" + <param argument="--egauss_thr" type="text" label="egauss_thr" value="NA" help="Threshold for filtering out non gaussian shaped peaks. Note this only works - if the 'verbose columns' and 'fit gauss' was used with xcms (--egauss_thr)"/> - <param name="temp_save" type="boolean" label="temp_save" checked="false" truevalue="--temp_save" falsevalue="" - help="Assign True if files for each step saved (for testing purposes) (--temp_save)"/> - <param name="polarity" type="select" label="polarity" - help="polarity (just used for naming purpose when files are saved) (--polarity)"> + if the 'verbose columns' and 'fit gauss' was used with xcms"/> + <param argument="--temp_save" type="boolean" label="temp_save" checked="false" truevalue="--temp_save" falsevalue="" + help="Assign True if files for each step saved (for testing purposes)"/> + <param argument="--polarity" type="select" label="polarity" + help="polarity (just used for naming purpose when files are saved)"> <option value="positive">Positive</option> <option value="negative" >Negative</option> <option value="NA" selected="true">NA</option> </param> - <param name="grp_rm_ids" type="text" label="grp_rm_ids" value="NA" + <param argument="--grp_rm_ids" type="text" label="grp_rm_ids" value="NA" help="comma seperated list of grouped_xcms peak ids to remove (corresponds to the row from xcms::group output) - e.g '1,20,30,56' - (--grp_rm_ids)"/> - <param name="xset_name" type="text" label="xset_name" value="xset" - help="Name of the xcmsSet object within the RData file (--xset_name)"/> + e.g '1,20,30,56'"/> + <param argument="--xset_name" type="text" label="xset_name" value="xset" + help="Name of the xcmsSet object within the RData file"/> </when> </conditional> <conditional name="choose_samp"> @@ -147,8 +140,10 @@ <when value=""> </when> <when value="yes"> - <param name="samplelist" type="data" label="samplelist" format="tsv,tabular" - help="A samplelist can be provided to find an appriopiate blank class (requires a column 'blank' where 'yes' indicates the class should be used as the blank (--samplelist)"/> + <param argument="--samplelist" type="data" label="samplelist" format="tsv,tabular" + help="A samplelist can be provided to find + an appriopiate blank class (requires a column 'blank' where 'yes' indicates the + class should be used as the blank) "/> </when> </conditional>