Mercurial > repos > galaxyp > metaquantome
changeset 1:47bfbd6597d0 draft
planemo upload commit 636fd1c7e60779d1123056a2985d54881013d4cb
| author | galaxyp |
|---|---|
| date | Wed, 05 Dec 2018 14:37:17 -0500 |
| parents | b17b03126d40 |
| children | a8cb3dea93a6 |
| files | macros.xml metaquantome_expand.xml metaquantome_filter.xml metaquantome_viz.xml |
| diffstat | 4 files changed, 124 insertions(+), 43 deletions(-) [+] |
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--- a/macros.xml Tue Dec 04 17:17:41 2018 -0500 +++ b/macros.xml Wed Dec 05 14:37:17 2018 -0500 @@ -6,6 +6,24 @@ <yield/> </requirements> </xml> + <xml name="ONTOLOGY_ARGS"> + <conditional name="ontology_args"> + <param name="ontology" type="select" label="Ontology"> + <option value="go">GO Gene Ontology (column named 'go')</option> + <option value="ec">EC Enzyme Commission (column named 'ec')</option> + <option value="cog">COG (column named 'cog')</option> + </param> + <when value="go"> + <param argument="--slim_down" type="boolean" label="Use slim GO"/> + </when> + <when value="ec"> + <!-- do nothing --> + </when> + <when value="cog"> + <!-- do nothing --> + </when> + </conditional> + </xml> <xml name="FUNC_FILE"> <param argument="--func_file" type="data" format="tabular" label="Functional file" help="Tabular file with a peptide sequence column and a functional assignment column for GO-term, EC number, or COG."/> @@ -50,7 +68,7 @@ </token> <token name="@DB_DIR@"><![CDATA[ #if $db_dir.db_loc == 'auto': - #if $mode_args.mode == 'taxfn' + #if $mode_args.mode == 'ft' --ft_func_data_dir data --ft_tax_data_dir data #else @@ -85,6 +103,27 @@ --samps samp_file.tab --mode '$mode_args.mode' #if $mode_args.mode == 'f' + --ontology='$mode_args.ontology_args.ontology' + #if $mode_args.ontology_args.ontology == 'go' + #if $mode_args.ontology_args.slim_down + --slim_down + #end if + #end if + #end if + #if $mode_args.mode == 'ft' + --ontology='$mode_args.ontology_args.ontology' + #if $mode_args.ontology_args.ontology == 'go' + #if $mode_args.ontology_args.slim_down + --slim_down + #end if + #end if + #end if + ]]> + </token> + <token name="@EXPAND_PARAMS@"><![CDATA[ + --samps samp_file.tab + --mode '$mode_args.mode' + #if $mode_args.mode == 'f' --func_file='$mode_args.func_file' --func_colname='$mode_args.func_colname' --pep_colname_func='$mode_args.pep_colname_func' @@ -104,7 +143,12 @@ --func_file='$mode_args.func_file' --func_colname='$mode_args.func_colname' --pep_colname_func='$mode_args.pep_colname_func' - --ontology=$mode_args.ontology + --ontology='$mode_args.ontology_args.ontology' + #if $mode_args.ontology_args.ontology == 'go' + #if $mode_args.ontology_args.slim_down + --slim_down + #end if + #end if --tax_file='$mode_args.tax_file' --tax_colname='$mode_args.tax_colname' --pep_colname_tax='$mode_args.pep_colname_tax' @@ -112,6 +156,7 @@ #end if ]]> </token> + <xml name="SAMPS"> <conditional name="samps_args"> <param argument="samps_src" type="select" label="Samples"> @@ -138,29 +183,33 @@ <option value="ft">Functional-taxonomic interaction analysis</option> </param> <when value="f"> + <expand macro="ONTOLOGY_ARGS"/> + </when> + <when value="t"> + </when> + <when value="ft"> + <expand macro="ONTOLOGY_ARGS"/> + </when> + </conditional> + <expand macro="SAMPS"/> + </xml> + <xml name="expand_params"> + <conditional name="mode_args"> + <param argument="--mode" type="select" label="Mode"> + <option value="f">Functional analysis</option> + <option value="t">Taxonomic analysis</option> + <option value="ft">Functional-taxonomic interaction analysis</option> + </param> + <when value="f"> <expand macro="FUNC_FILE"/> - <conditional name="ontology_args"> - <param name="ontology" type="select" label="Ontology"> - <option value="go">GO Gene Ontology (column named 'go')</option> - <option value="ec">EC Enzyme Commission (column named 'ec')</option> - <option value="cog">COG (column named 'cog')</option> - </param> - <when value="go"> - <param argument="--slim_down" type="boolean" label="Use slim GO"/> - </when> - <when value="ec"> - <!-- do nothing --> - </when> - <when value="cog"> - <!-- do nothing --> - </when> - </conditional> + <expand macro="ONTOLOGY_ARGS"/> </when> <when value="t"> <expand macro="TAX_FILE"/> </when> <when value="ft"> <expand macro="FUNC_FILE"/> + <expand macro="ONTOLOGY_ARGS"/> <expand macro="TAX_FILE"/> <param argument="--ft_tar_rank" type="select" label="rank at which to group taxonomy"> <option value="species">species</option> @@ -175,6 +224,7 @@ </conditional> <expand macro="SAMPS"/> </xml> + <xml name="output_samples_choice"> <param name="output_samps" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output the samples fiile"/> </xml>
--- a/metaquantome_expand.xml Tue Dec 04 17:17:41 2018 -0500 +++ b/metaquantome_expand.xml Wed Dec 05 14:37:17 2018 -0500 @@ -8,7 +8,7 @@ mkdir -p data && #slurp @MAKE_SAMPS_TSV@ metaquantome expand - @COMMON_PARAMS@ + @EXPAND_PARAMS@ @DB_DIR@ #if $input.input_type == 'nopep': --nopep --nopep_file='$input.nopep_file' @@ -20,7 +20,7 @@ ]]></command> <inputs> <expand macro="data_dir"/> - <expand macro="common_params"/> + <expand macro="expand_params"/> <conditional name="input"> <param name="input_type" type="select" label="Select input data"> <option value="int">tabular intensity file with peptide column</option>
--- a/metaquantome_filter.xml Tue Dec 04 17:17:41 2018 -0500 +++ b/metaquantome_filter.xml Wed Dec 05 14:37:17 2018 -0500 @@ -11,18 +11,20 @@ --expand_file '$expand_file' --min_peptides $min_peptides #if $min_pep_nsamp: - --min_pep_nsamp max($min_peptides,$min_pep_nsamp) + #set $nsamp = max(int($min_peptides),int($min_pep_nsamp)) + --min_pep_nsamp $nsamp #else --min_pep_nsamp all #end if --min_children_non_leaf $min_children_non_leaf #if $min_child_nsamp: - --min_child_nsamp max($min_peptides,$min_child_nsamp) + #set $nsamp = max($min_peptides,$min_child_nsamp) + --min_child_nsamp $nsamp #else --min_child_nsamp all #end if --qthreshold $qthreshold - --outfile='$output' + --outfile='$outfile' ]]></command> <inputs> <expand macro="common_params"/>
--- a/metaquantome_viz.xml Tue Dec 04 17:17:41 2018 -0500 +++ b/metaquantome_viz.xml Wed Dec 05 14:37:17 2018 -0500 @@ -3,16 +3,26 @@ <macros> <import>macros.xml</import> <xml name="img_size"> + <param argument="--width" type="float" value="" optional="true" label="Image width in inches"/> <param argument="--height" type="float" value="" optional="true" label="Image height in inches"/> - <param argument="--width" type="float" value="" optional="true" label="Image width in inches"/> </xml> <xml name="common_bar_params"> + <param argument="--target_rank" type="text" value="species" label="Taxonomic rank to restrict to in the plot" + help=""> + <option value="species">species</option> + <option value="genus" selected="true">genus</option> + <option value="family">family</option> + <option value="order">order</option> + <option value="class">class</option> + <option value="phylum">phylum</option> + <option value="kingdom">kingdom</option> + </param> <param argument="--meancol" type="text" label="Mean intensity column name" help="Mean intensity column name for desired experimental condition"> <validator type="empty_field"/> </param> - <param argument="--nterms" type="integer" value="5" min="1" label="Number of taxa or functional terms to display"/> - <param argument="--barcolor" type="integer" value="1" min="1" max="6" label="Color for the bar fill"> + <param argument="--nterms" type="integer" value="5" min="1" optional="true" label="Number of taxa or functional terms to display" help="leave blank for all"/> + <param argument="--barcol" type="integer" value="1" min="1" max="6" label="Color for the bar fill"> <help> The color vector in R is c("dodgerblue", "darkorange", "yellow2", "red2", "darkviolet", "black"), @@ -31,14 +41,23 @@ --infile='$infile' --plottype=$plot.plottype #if $plot.plottype == 'bar': + #if str($mode_args.mode) in ['t','ft']: + --target_rank='$plot.target_rank' + #end if --meancol='$plot.meancol' - --nterms=$plot.nterms - --barcolor=$plot.barcolor + #if str($plot.nterms) == '': + --nterms='all' + #else + --nterms=$plot.nterms + #end if + --barcol=$plot.barcol #elif $plot.plottype == 'volcano': - --fc='$plot.fc' + --meancol='$plot.meancol' + --fc_name='$plot.fc_name' #if $plot.textannot: --textannot='$plot.textannot' #end if + $plot.flip_fc $plot.gosplit #elif $plot.plottype == 'heatmap': $plot.filter_to_sig @@ -47,8 +66,12 @@ $plot.calculate_sep #elif $plot.plottype == 'ft_dist': --meancol='$plot.meancol' - --nterms=$plot.nterms - --barcolor=$plot.barcolor + #if str($plot.nterms) == '': + --nterms='all' + #else + --nterms=$plot.nterms + #end if + --barcol=$plot.barcol --whichway=$plot.whichway #if $plot.term.id_or_name == 'id': --id='$plot.term.id' @@ -59,12 +82,12 @@ --target_onto=$plot.target_onto #end if #end if + #if $plot.width: + --width=$plot.width + #end if #if $plot.height: --height=$plot.height #end if - #if $plot.width1: - --width=$plot.width - #end if --img='outfile.png' ]]></command> <inputs> @@ -73,22 +96,28 @@ help=""/> <conditional name="plot"> <param argument="--plottype" type="select" label="Plot type"> - <option value="bar">Bar Chart</option> - <option value="volcano">Volcano Plot</option> - <option value="heatmap">Heatmap</option> - <option value="pca">PCA - Principal Componets Analysis</option> - <option value="ft_dist">Bar Chart</option> + <option value="bar">Bar Charti (bar)</option> + <option value="volcano">Volcano Plot (volcano)</option> + <option value="heatmap">Heatmap (heatmap)</option> + <option value="pca">Principal Componets Analysis (pca)</option> + <option value="ft_dist">Functional Taxonomic Distribution (ft_dist)</option> </param> <when value="bar"> <expand macro="common_bar_params"/> <expand macro="img_size"/> </when> <when value="volcano"> - <param argument="--fc" type="text" label="Name of the fold change column in the stat dataframe"> + <param argument="--meancol" type="text" label="Mean intensity column name" + help="Mean intensity column name for desired experimental condition"> + <validator type="empty_field"/> + </param> + <param argument="--fc_name" type="text" label="Name of the fold change column in the stat dataframe"> <validator type="empty_field"/> </param> <param argument="--textannot" type="text" optional="true" label="Name of the annotation column" help="Provides text annoatation for the plot. Optional, if missing, no text will be plotted."/> + <param argument="--flip_fc" type="boolean" truevalue="--flip_fc" falsevalue="" checked="false" + label="Flip the fold change (i.e., multiply log fold change by -1)"/> <param argument="--gosplit" type="boolean" truevalue="--gosplit" falsevalue="" checked="false" label="Make one plot for each of BiologicalProcess, CellularComponent, and MolecularFunction"/> <expand macro="img_size"/> @@ -96,7 +125,7 @@ <when value="heatmap"> <param argument="--filter_to_sig" type="boolean" truevalue="--filter_to_sig" falsevalue="" checked="false" label="Only plot significant term" help="Necessitates use of results from `test`"/> - <param argument="--aplha" type="float" value="0.05" min="0.0" max="1.0" label="If filter_to_sig, the q-value significance level"/> + <param argument="--alpha" type="float" value="0.05" min="0.0" max="1.0" label="If filter_to_sig, the q-value significance level"/> <expand macro="img_size"/> </when> <when value="pca"> @@ -107,8 +136,8 @@ <when value="ft_dist"> <expand macro="common_bar_params"/> <param argument="--whichway" type="select" label="which distribution"> - <option value="f_dist">functional distribution for a taxon</option> - <option value="t_dist">taxonomic distribution for a function</option> + <option value="f_dist">functional distribution for a taxon (f_dist)</option> + <option value="t_dist">taxonomic distribution for a function (t_dist)</option> </param> <conditional name="term"> <param argument="id_or_name" type="select" label="">