Mercurial > repos > iuc > raceid_inspectclusters
diff raceid_inspectclusters.xml @ 4:20f522154663 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
| author | iuc |
|---|---|
| date | Mon, 12 Aug 2019 13:01:12 -0400 |
| parents | 9fec5dd8fbb9 |
| children | 41f34e925bd5 |
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--- a/raceid_inspectclusters.xml Mon Apr 15 17:55:46 2019 -0400 +++ b/raceid_inspectclusters.xml Mon Aug 12 13:01:12 2019 -0400 @@ -1,39 +1,290 @@ -<tool id="raceid_inspectclusters" name="Cluster Inspection using RaceID" version="@VERSION_RACEID@.@VERSION_PACKAGE@.1" > +<tool id="raceid_inspectclusters" name="Cluster Inspection using RaceID" version="@VERSION_RACEID@.@VERSION_WRAPPER@" > <description>examines gene expression within clusters</description> <macros> <import>macros.xml</import> - <import>macros_inspectclusters.xml</import> + <import>macros_cheetah.xml</import> + <macro name="select_cells" token_sectionname="@SECTIONNAME@" token_sectiontitle="@SECTIONTITLE@" > + <section name="@SECTIONNAME@" title="@SECTIONTITLE@" expanded="true" > + <param name="name_set" type="text" optional="true" label="Name of Set" > + <!-- Aname, Bname --> + <expand macro="sanitize_title" /> + </param> + <conditional name="meth" > + <param name="type" type="select" label="Selection method" > + <option value="cln" selected="true">Cluster Numbers</option> + <option value="regex" >Regular Expression</option> + <option value="manual" >Manual Selection</option> + </param> + <when value="cln" > + <param name="selector" type="text" value="" label="List of clusters" help="Clusters should be listed delimited by commas (e.g. 3,4,5)" > + <expand macro="sanitize_numeric_vector" /> + </param> + </when> + <when value="regex" > + <param name="selector" type="text" value="" label="Regular Expression to select gene names" > + <expand macro="sanitize_regex" /> + </param> + </when> + <when value="manual" > + <param name="selector" type="text" value="" label="List of genes" > + <expand macro="sanitize_string_vector" /> + </param> + </when> + </conditional> + </section> + </macro> </macros> <expand macro="requirements" /> - <version_command><![CDATA[ -Rscript '$__tool_directory__/scripts/clusterinspect.R' @GET_VERSION@ -]]></version_command> - - <command detect_errors="exit_code"><![CDATA[ -#set bin = 'clusterinspect.R' -Rscript '$__tool_directory__/scripts/$bin' '$userconf' 2>&1 > '$outlog' - ]]></command> - - <configfiles> - <configfile name="userconf" ><![CDATA[ -@STRING2VECTOR@ - -@INSPECTCLUSTERS_CHEETAH@ -]]> - </configfile> - </configfiles> + <expand macro="version_command_config" prog="clusterinspect.R" cheetah="INSPECTCLUSTERS_CHEETAH" out="&> '$outlog'" /> <inputs> - <expand macro="inspectclusters_inputs" /> + <param name="inputrds" type="data" format="rdata" label="Input RaceID RDS" help="Requires the RDS output from the cluster analysis" /> + <conditional name="plotgen"> + <param name="do_opt" type="select" label="Plot Clusters?" help="Generates tSNE and F-R plots" > + <option value="yes" selected="true" >Yes</option> + <option value="no" >No</option> + </param> + <when value="no" /> + <when value="yes" > + <param name="clusts_plot" type="text" label="Cluster Numbers to plot" value="" help="Leave blank to plot all clusters" optional="true" > + <expand macro="sanitize_numeric_vector" /> + </param> + </when> + </conditional> + <conditional name="plotsym" > + <param name="do_opt" type="select" label="Perform Subset Analysis?" > + <expand macro="yesno_checkedno" /> + </param> + <when value="no" /> + <when value="yes"> + <param name="types_regex" type="text" optional="true" label="Types Regex (removal)" help="Regular expression to be used to remove portions of the cell names, in order to indicate cell type. e.g. if your cells are labelled as 'cdk5_1, cdk5_2, glow_1, glow_2', then a regex of '_\\d$' would trim off the ends and set the cell types to 'cdk5, cdk5, glow, glow'. " > + <expand macro="sanitize_regex" /> + </param> + <expand macro="use_defaults_no" > + <param name="subset_regex" type="text" optional="true" label="Subset of Types: Regex (select)" help="Regular expression to be used to select for cell types of interest. e.g. if we are only interested in 'cdk5' positive cells, then we would simply put 'cdk5' here. "> + <expand macro="sanitize_regex" /> + </param> + <param name="fr" type="boolean" checked="false" label="Output FR map instead of tSNE" help="Performs a Fruchterman-Rheingold projection instead of tSNE" /> + </expand> + </when> + </conditional> + <conditional name="gois" > + <param name="do_opt" type="select" label="Examine Genes of Interest" > + <expand macro="yesno_checkedno" /> + </param> + <when value="no" /> + <when value="yes"> + <param name="inspect_goi_genes" type="text" value="" label="Genes to Examine" > + <expand macro="sanitize_string_vector" /> + </param> + <param name="inspect_goi_cells" type="text" optional="true" label="Cells to Examine" help="Leave blank to examine all" ><!-- "":NULL --> + <expand macro="sanitize_string_vector" /> + </param> + <expand macro="use_defaults_no" > + <!-- Yes, examine genes of interest, but no do not use defaults... --> + <param name="inspect_goi_imputed" type="boolean" checked="false" label="Impute Genes" help="Only works if k-nearest neighbours was used in the clustering" /> + <param name="plotexp_n" type="text" optional="true" label="Title of plot" help="If blank, the list of genes are used" > + <expand macro="sanitize_title" /> + </param> + <param name="plotmarkg_cthr" type="integer" min="0" value="0" label="Cluster Threshold" help="Include only clusters with cells greater than this" /> + <param name="plotmarkg_cl" type="text" optional="true" label="Cluster List" help="List of cluster numbers to include. Leave blank to include all" > + <expand macro="sanitize_numeric_vector" /> + </param><!-- "":NULL --> + <param name="plotmarkg_order_cells" type="boolean" checked="false" label="Order Cells" help="Order heatmap by cell names, not by cluster" /> + <param name="plotmarkg_aggr" type="boolean" checked="false" label="Average Expression" help="Show only average expression for each cluster" /> + <param name="plotmarkg_norm" type="boolean" checked="false" label="Normalise Gene Expression " help="Normalise gene expression to 1 to depict genes on the same scale" /> + <param name="plotmarkg_flo" type="integer" max="-5" optional="true" label="Lower-bound for Gene Expression" /><!-- negative or null vals only for this seem to work--> + <param name="plotmarkg_cap" type="integer" min="1" optional="true" label="Upper-bound for Gene Expression" /> + <param name="plotmarkg_samples" type="text" optional="true" label="Regex to Select Sample Names For Each cell" > + <expand macro="sanitize_regex" /> + </param> + <param name="plotmarkg_cluster_cols" type="boolean" checked="false" label="Cluster columns" /> + <param name="plotmarkg_cluster_rows" type="boolean" checked="true" label="Cluster rows" /> + <param name="plotmarkg_cluster_set" type="boolean" checked="false" label="Order Clusters by Heirarchal Clustering of Cluster Medoids." /> + </expand> + </when> + </conditional> + <conditional name="diffgtest" > + <param name="do_opt" type="select" label="Differential Gene Testing" > + <expand macro="yesno_checkedno" /> + </param> + <when value="no" /> + <when value="yes" > + <expand macro="select_cells" sectionname="set_a" sectiontitle="Cells in Set A" /> + <expand macro="select_cells" sectionname="set_b" sectiontitle="Cells in Set B" /> + <expand macro="use_defaults_no" > + <param name="plotdiffg_pthr" type="float" min="0" max="1" value="0.05" label="P-value cutoff" help="Cutoff for displaying differentially expressed genes" /> + <param name="plotdiffg_padj" type="boolean" checked="true" label="Apply B-H Correction" help="Display genes with a Benjamini-Hochberg corrected false discovery rate lower than the above P-value threshold" /> + <param name="plotdiffg_lthr" type="float" min="0" value="0" label="Log2-Fold Threshold" help="Differentially expressed genes are displayed only for log2 fold-changes higher than this" /> + <param name="plotdiffg_mthr" type="float" optional="true" label="Log2 Mean Threshold" help="Differentially expressed genes are displayed only for log2 mean expression greater than this" /><!-- opt:-Inf --> + <param name="plotdiffg_show_names" type="boolean" checked="false" label="Display Gene Names" /> + </expand> + </when> + </conditional> </inputs> - <outputs> <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" /> - <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" > - <filter>use_log</filter> - </data> + <data name="outlog" format="txt" hidden="true" /><!-- useful for debugging, but hide from user --> </outputs> <tests> - <expand macro="inspectclusters_tests" /> + <test><!-- general plots, plotgen --> + <param name="inputrds" value="out_cluster_default.rdat" /> + <conditional name="plotgen" > + <param name="do_opt" value="yes" /> + </conditional> + <output name="outpdf" value="out_cluster_general_default.pdf" lines_diff="30" /> + </test> + <test><!-- general plots, plotgen with cluster 1,8,5 only --> + <param name="inputrds" value="out_cluster_default.rdat" /> + <conditional name="plotgen" > + <param name="do_opt" value="yes" /> + <param name="clusts_plot" value="1,8,5" /> + </conditional> + <output name="outpdf" value="out_cluster_general_default.pdf" lines_diff="30" /> + </test> + <test><!-- default test, plotsym --> + <param name="inputrds" value="out_cluster_default.rdat" /> + <conditional name="plotsym" > + <param name="do_opt" value="yes" /> + <param name="types_regex" value="\\_\\d+" /> + <expand macro="test_nondef" > + <param name="subset_regex" value="IV|V" /> + </expand> + </conditional> + <conditional name="gois" > + <param name="do_opt" value="yes" /> + <param name="inspect_goi_genes" value="Apoa1,Apoa1bp,Apoa2,Apoa4,Apoa5" /> + </conditional> + <output name="outpdf" value="out_cluster_inspect_default.pdf" lines_diff="30" /> + </test> + <test><!-- Advanced 1 --> + <param name="inputrds" value="out_cluster_default.rdat" /> + <conditional name="plotsym" > + <param name="do_opt" value="yes" /> + <param name="types_regex" value="\\_\\d+" /> + <expand macro="test_nondef" > + <param name="subset_regex" value="IV|V" /> + <param name="fr" value="true" /> + </expand> + </conditional> + <conditional name="gois" > + <param name="do_opt" value="yes" /> + <param name="inspect_goi_genes" value="Apoa1,Apoa1bp,Apoa2,Apoa4,Apoa5" /> + <expand macro="test_nondef" > + <param name="inspect_goi_imputed" value="false" /> + <param name="plotexp_n" value="Test Title" /> + <param name="plotmarkg_order_cells" value="true" /> + <param name="plotmarkg_aggr" value="true" /> + <param name="plotmarkg_norm" value="true" /> + <param name="plotmarkg_flo" value="-10" /> + <param name="plotmarkg_cap" value="100" /> + <param name="plotmarkg_samples" value="(\\_\\d+)$" /> + <param name="plotmarkg_cluster_cols" value="true" /> + <param name="plotmarkg_cluster_rows" value="false" /> + <param name="plotmarkg_cluster_set" value="true" /> + </expand> + </conditional> + <conditional name="diffgtest" > + <param name="do_opt" value="yes" /> + <section name="set_a" > + <param name="name_set" value="Test set A" /> + <conditional name="meth" > + <param name="type" value="regex" /> + <param name="selector" value="^V5.*" /> + </conditional> + </section> + <section name="set_b" > + <param name="name_set" value="Test set B" /> + <conditional name="meth" > + <param name="type" value="manual" /> + <param name="selector" value="I5d_3,I5d_4,I5d_6,I5d_8,I5d_9,I5d_10,I5d_11,I5d_12,I5d_13,I5d_14" /> + </conditional> + </section> + <expand macro="test_nondef" > + <param name="plotdiffg_pthr" value="0.1" /> + <param name="plotdiffg_padj" value="false" /> + <param name="plotdiffg_lthr" value="0.2" /> + <param name="plotdiffg_mthr" value="0.2" /> + <param name="plotdiffg_show_names" value="true" /> + </expand> + </conditional> + <output name="outpdf" value="out_cluster_inspect_advanced1.pdf" lines_diff="30"/> + </test> + <test><!-- Advanced 2 --> + <param name="inputrds" value="out_cluster_default.rdat" /> + <conditional name="plotsym" > + <param name="do_opt" value="yes" /> + <expand macro="test_nondef" > + <param name="fr" value="false" /> + </expand> + </conditional> + <conditional name="gois" > + <param name="do_opt" value="yes" /> + <param name="inspect_goi_genes" value="Sp1,Spc24,Spcs1,Spcs2,Spcs3" /> + <expand macro="test_nondef" > + <param name="plotexp_n" value="Test Title 2" /> + <param name="plotmarkg_order_cells" value="true" /> + <param name="plotmarkg_aggr" value="true" /> + <param name="plotmarkg_norm" value="false" /> + <param name="plotmarkg_flo" value="-10" /> + <param name="plotmarkg_cap" value="10" /> + <param name="plotmarkg_cluster_cols" value="true" /> + <param name="plotmarkg_cluster_rows" value="true" /> + <param name="plotmarkg_cluster_set" value="true" /> + </expand> + </conditional> + <conditional name="diffgtest" > + <param name="do_opt" value="yes" /> + <section name="set_a" > + <param name="name_set" value="Test set A" /> + <conditional name="meth" > + <param name="type" value="regex" /> + <param name="selector" value="^IV.*" /> + </conditional> + </section> + <section name="set_b" > + <param name="name_set" value="Test set B" /> + <conditional name="meth" > + <param name="type" value="cln" /> + <param name="selector" value="3" /> + </conditional> + </section> + <expand macro="test_nondef" > + <param name="plotdiffg_pthr" value="0.8" /> + <param name="plotdiffg_padj" value="true" /> + <param name="plotdiffg_lthr" value="0.8" /> + <param name="plotdiffg_mthr" value="0.8" /> + <param name="plotdiffg_show_names" value="false" /> + </expand> + </conditional> + <output name="outpdf" value="out_cluster_inspect_advanced2.pdf" lines_diff="30"/> + </test> + <test><!-- Advanced 3 --> + <param name="inputrds" value="out_cluster_default.rdat" /> + <conditional name="plotsym" > + <param name="do_opt" value="no" /> + </conditional> + <conditional name="gois" > + <param name="do_opt" value="no" /> + </conditional> + <conditional name="diffgtest" > + <param name="do_opt" value="yes" /> + <section name="set_a" > + <param name="name_set" value="Test set A" /> + <conditional name="meth" > + <param name="type" value="cln" /> + <param name="selector" value="1,2" /> + </conditional> + </section> + <section name="set_b" > + <param name="name_set" value="Test set B" /> + <conditional name="meth" > + <param name="type" value="cln" /> + <param name="selector" value="3,4,6" /> + </conditional> + </section> + </conditional> + <output name="outpdf" value="out_diffgene_multiple.pdf" lines_diff="30"/> + </test> </tests> <help><![CDATA[ @@ -50,12 +301,12 @@ * Produces a tSNE of all clusters, as well as a force-directed Fruchterman-Reingold (F-R) layout which may have tidier plots. * Perform Subset Analysis: * tSNE and F-R plots with cells whose name match the specified regex highlighted - + * Examine Genes of Interest: * Expression plots highlighting a gene or genes of interest across all clusters - * Differential Gene Testing: - * Examining the expression between + * Differential Gene Testing: + * Examining the expression between * A list of the most differentially expressed genes in each cluster * An output PDF that provides heatmaps for: