Mercurial > repos > iuc > raceid_diffgene
diff raceid_diffgenes.xml @ 0:ea8215239735 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
| author | iuc |
|---|---|
| date | Sat, 03 Mar 2018 17:33:56 -0500 |
| parents | |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/raceid_diffgenes.xml Sat Mar 03 17:33:56 2018 -0500 @@ -0,0 +1,120 @@ +<tool id="raceid_diffgene" name="RaceID differential gene expression analysis" version="@VERSION@.0"> + <description>Identify differentially regulated genes</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + Rscript '@SCRIPT_DIR@/raceID_diffgenes.R' '@SCRIPT_DIR@' '$rconf_source' + + #if $compare_clusters_select.do_compare_clusters.value == "T": + && + mkdir '${out_html.files_path}' && + mv plot_*.svg '${out_html.files_path}' && + + echo '<html><head></head> + <body> + <h1>RaceID Differential Gene Analysis</h1> + <br /><h3>Expression of ${compare_clusters_select.gene} between ${compare_clusters_select.cl1} and ${compare_clusters_select.cl2}</h3> + <img src="plot_diffgenes.svg" ><br /> + </body> + </html>' > '$out_html' + #end if + + ]]></command> + + <configfiles> + <configfile name="rconf_source" > + sc = readRDS( '$inp_rdat' ) + + c_pval = as.numeric( '$pval' ) + generate_extable = as.logical( '$gen_gexpr_table.value' ) + outtable_dir = 'tables' + compare_clusters = as.logical( '$compare_clusters_select.do_compare_clusters.value' ) + + #if $compare_clusters_select.do_compare_clusters.value == "T": + gene_name = '$compare_clusters_select.gene' + clust1 = '$compare_clusters_select.cl1' + clust2 = '$compare_clusters_select.cl2' + mcount = as.integer( '$compare_clusters_select.mincount' ) + #end if + </configfile> + </configfiles> + + <inputs> + <param name="inp_rdat" type="data" format="rdata" label="Count matrix with clusters" help="This file is the output of the RaceID pipeline." /> + <param name="pval" type="float" value="0.01" min="1e-10" max="0.5" label="Retain genes with p-value smaller than threshold" help="The p-value for observing the difference in mean expression between the cluster and all cells based on binomial counting statistics." /> + <param name="gen_gexpr_table" type="boolean" checked="true" truevalue="T" falsevalue="F" label="Generate table of all differentially expressed genes?" /> + <conditional name="compare_clusters_select"> + <param name="do_compare_clusters" type="select" label="Compare the expression of a specific gene between two sets of clusters?" > + <option value="T" >Yes</option> + <option value="F" selected="true" >No</option> + </param> + <when value="F" /> + <when value="T" > + <param name="gene" type="text" label="Gene name of interest" > + <sanitizer invalid_char="" > + <valid initial="string.letters,string.digits"> + <add value="_"/><add value="+" /><add value="-" /> + </valid> + </sanitizer> + </param> + <param name="cl1" type="text" value="1" label="Cluster set 1" help="e.g. if you wish to compare cluster 2 to clusters 1 and 3, then type '2' here and '1,3' in the next input." > + <sanitizer invalid_char="" > + <valid initial="string.digits"><add value="," /></valid> + </sanitizer> + </param> + <param name="cl2" type="text" value="2" label="Cluster set 2" help="You can also compare sets of clusters to one another: e.g. 1,4,5 against 2,3." > + <sanitizer invalid_char="" > + <valid initial="string.digits"><add value="," /></valid> + </sanitizer> + </param> + <param name="mincount" type="integer" value="5" min="1" label="Only count genes with more than this number of transcripts in at least one cell within Cluster set 1 or Cluster set 2" /> + </when> + </conditional> + </inputs> + + <outputs> + <data name="out_html" format="html" label="${tool.name} on ${on_string}: Web Report" /> + <data format="tsv" name="out_tables" label="${tool.name} on ${on_string}: DiffExpr Tables" > + <discover_datasets pattern="__designation_and_ext__" directory="tables" visible="true" /> + </data> + </outputs> + + <tests> + <test> + <param name="inp_rdat" value="in_diffgene.rdat" /> + <output name="out_html" value="out_diffgene1.html" /> + <!-- verify just two of the outputs --> + <output name="out_tables" > + <!-- Problems here... help appreciated --> + <discovered_dataset designation="gdiff_cl.1" ftype="tsv" file="gdiff_cl.1.tsv" /> + <discovered_dataset designation="gdiff_cl.2" ftype="tsv" file="gdiff_cl.2.tsv" /> + </output> + </test> + <test> + <!-- Diff Cluster plot only --> + <param name="inp_rdat" value="in_diffgene.rdat" /> + <param name="pval" value="0.05" /> + <param name="gen_gexpr_table" value="F" /> + <param name="do_compare_clusters" value="T" /> + <param name="gene" value="1110038F14Rik__chr15" /> + <param name="cl1" value="1" /> + <param name="cl2" value="2,3" /> + <param name="mincount" value="2" /> + <output name="out_html" value="out_diffgene2.html" /> + </test> + </tests> + <help><![CDATA[ +***************** +RaceID Diff Genes +***************** + +Generates a table of all differentially expressed genes, and a plot representing the expression of a specific gene of interest between different clusters. + +The RaceID pipeline must be run prior to using this tool, as the input of this tool is generated from the output of the pipeline. + + + ]]></help> + <expand macro="citations" /> +</tool>