Mercurial > repos > genouest > askor_de
diff askor_de.xml @ 0:ceef9bc6bbc7 draft
planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/askor commit 08a187f91ba050d584e586d2fcc99d984dac607c
author | genouest |
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date | Thu, 12 Apr 2018 05:23:45 -0400 |
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children | 6bbc90a11c3f |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/askor_de.xml Thu Apr 12 05:23:45 2018 -0400 @@ -0,0 +1,165 @@ +<tool id="askor_de" name="AskoR DE" version="0.1"> + <description>EdgeR for AskOmics</description> + <requirements> + <requirement type="package" version="3.34.6">bioconductor-limma</requirement> + <requirement type="package" version="1.4.30">r-statmod</requirement> + <requirement type="package" version="3.20.7">bioconductor-edger</requirement> + <requirement type="package" version="2.2.1">r-ggplot2</requirement> + <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement> + <requirement type="package" version="0.7.0">r-ggrepel</requirement> + <requirement type="package" version="3.0.1">r-gplots</requirement> + <requirement type="package" version="1.4.4">r-optparse</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + export ASKOR_PATH='$__tool_directory__' + + && + + Rscript '$__tool_directory__/AskoR_DE.R' + --out '${out_pdf}' + --outdir askor_output + --fileofcount '${fileofcounts}' + --sample '${samples}' + --contrasts '${contrasts}' + #if $adv.organism + --org '${adv.organism}' + #end if + #if $adv.colgenes + --col_genes ${adv.colgenes} + #end if + #if $adv.palette + --palette '${adv.palette}' + #end if + #if $selection.sel + --select '${selection.sel}' + #end if + #if $selection.remove + --remove '${selection.remove}' + #end if + #if $thresholds.th_cpm + --th_cpm ${thresholds.th_cpm} + #end if + #if $thresholds.rep + --rep ${thresholds.rep} + #end if + #if $thresholds.th_FDR + --th_FDR ${thresholds.th_FDR} + #end if + #if $stats.norm + --normalization '${stats.norm}' + #end if + #if $stats.adj + --adj '${stats.adj}' + #end if + #if $stats.glm + --glm '${stats.glm}' + #end if + #if $adv.nh + --nh ${adv.nh} + #end if + ]]></command> + <inputs> + <param format="csv" name="fileofcounts" type="data" label="File of counts" /> + <param format="tsv" name="samples" type="data" label="Descriptions of the samples" /> + <param format="tsv" name="contrasts" type="data" label="Descriptions of the contrasts" /> + <section name="adv" title="Format options" expanded="false"> + <param name="colgenes" type="integer" label="Column of the genes" value="1" optional="true" /> + <!--param name="sep" type="text" label="Field separator" value="\t" optional="true" /--> + <param name="palette" type="text" label="Color palette (Rcolorbrewer)" value="Set2" optional="true" /> + <param name="organism" type="text" label="Organism" value="Asko" optional="true" /> + <param name="nh" type="integer" label="Number of genes in the heatmap" value="50" optional="true" /> + </section> + <section name="selection" title="Samples selection options" expanded="false"> + <param name="sel" type="text" label="List of selected samples (separated by comma)" optional="true" /> + <param name="remove" type="text" label="List of removed samples (separated by comma)" optional="true" /> + </section> + <section name="thresholds" title="Threshold options" expanded="false"> + <param name="th_cpm" type="float" label="Minimum CPM value for selecting a gene" value="0.5" optional="true" /> + <param name="rep" type="integer" label="Number of samples with CPM > th_comp for selecting a gene" value="3" optional="true" /> + <param name="th_FDR" type="float" label="FDR threshold for reporting a differential gene" value="0.05" optional="true" /> + </section> + <section name="stats" title="Statistics options" expanded="false"> + <param name="norm" type="select" label="Normalization method"> + <option value="TMM">TMM</option> + <option value="RLE">RLE</option> + <option value="upperquartile">Upperquartile</option> + <option value="none">None</option> + </param> + <param name="glm" type="select" label="GLM method"> + <option value="qlf">qlf</option> + <option value="lrt">lrt</option> + </param> + <param name="adj" type="select" label="Multitest correction method"> + <option value="fdr">fdr</option> + <option value="holm">holm</option> + <option value="hochberg">hochberg</option> + <option value="hommel">hommel</option> + <option value="bonferroni">bonferroni</option> + <option value="BH">BH</option> + <option value="BY">BY</option> + <option value="none">none</option> + </param> + </section> + </inputs> + <outputs> + <data format="pdf" name="out_pdf" label="${tool.name} on ${on_string}: Graphics" /> + <data name="output" format="tsv" label="${tool.name} on ${on_string}"> + <discover_datasets pattern="(?P<designation>.+)\.txt" ext="tsv" visible="true" directory="askor_output" /> + </data> + </outputs> + <tests> + <test> + <param name="fileofcounts" ftype="csv" value="counts.csv" /> + <param name="samples" ftype="tsv" value="Samples.txt" /> + <param name="contrasts" ftype="tsv" value="Contrasts.txt" /> + <section name="adv"> + <param name="colgenes" value="3" /> + </section> + <section name="thresholds"> + <param name="th_cpm" value="10" /> + </section> + <output name="out_pdf" file="out.pdf" compare="sim_size"/> + <output name="output"> + <discovered_dataset designation="AskoAvsK" ftype="tsv" file="AskoAvsK.txt" compare="sim_size" /> + <discovered_dataset designation="AskoT1AvsT1K" ftype="tsv" file="AskoT1AvsT1K.txt" compare="sim_size" /> + <discovered_dataset designation="AskoT1vsT0" ftype="tsv" file="AskoT1vsT0.txt" compare="sim_size" /> + <discovered_dataset designation="AskoT1vsT2" ftype="tsv" file="AskoT1vsT2.txt" compare="sim_size" /> + <discovered_dataset designation="condition.asko" ftype="tsv" file="condition.asko.txt" compare="sim_size" /> + <discovered_dataset designation="context.asko" ftype="tsv" file="context.asko.txt" compare="sim_size" /> + <discovered_dataset designation="contrast.asko" ftype="tsv" file="contrast.asko.txt" compare="sim_size" /> + </output> + </test> + </tests> + <help><![CDATA[ +This tools generates a list of differential genes from various contrasts in an AskOmics format (https://askomics.github.io/). + +Example tabular input file of counts: + +============ ========== =============== =========== =========== ====== +miRNA read_count precursor total A32 A34 +------------ ---------- --------------- ----------- ----------- ------ +GL349623_679 346.00 GL349623_679 146.00 16.00 130.0 +GL349624_956 13.00 GL349624_956 13.00 0 13.0 +============ ========== =============== =========== =========== ====== + +Example tabular sample description file: + +============ ========== =============== =========== +ID condition stage treatment +------------ ---------- --------------- ----------- +A32 T3A T3 Acetone +A34 T3A T3 Acetone +============ ========== =============== =========== + +Example tabular contrast description file: + +============ ========================= ======================= +Contrast context1_of@Context context2_of@Context +------------ ------------------------- ----------------------- +T1vsT0 T1 T0 +T1vsT2 T1 T2 +============ ========================= ======================= + ]]></help> + <citations> + </citations> +</tool>