diff RBGOA.xml @ 1:f7287f82602f draft

"planemo upload commit 486235d6560c9e95bd42152ad19bf7c3941cdc1b"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RBGOA.xml	Tue Apr 19 08:28:43 2022 +0000
@@ -0,0 +1,116 @@
+<tool id="RBGOA" name="RBGOA" version="0.2.0" python_template_version="3.5">
+  <description>"Rank Based Gene Ontology Analysis"</description>
+    <requirements>
+        <requirement type="package" version="5.6">r-ape</requirement>
+        <requirement type="package" version="1.20.3">r-getopt</requirement>
+    </requirements>
+    <version_command>Rscript GO_MWU.R -v</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '${input1}' samples.tsv &&
+        ln -s '${input2}' annotation.tsv &&
+        Rscript $__tool_directory__/GO_MWU.R -s $__tool_directory__ -i samples.tsv -a annotation.tsv -g $__tool_directory__/go.obo -d '$input3' -c '$input_filter.cluster' -o '$input_filter.over' -m '$input_filter.min' -p '$grouping.pcut' -t '$grouping.hcut' &&
+        mv samples_${input3}.tsv div_input.tsv &&
+        mv dissim_${input3}_samples_annotation.tsv dissim.tsv &&
+        mv MWU_${input3}_samples.tsv mwu_file.tsv
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="tabular" label="Genes of interest with associated value" />
+        <param type="data" name="input2" format="tabular" label="Gene GO annotation file" />
+        <param type="select" name="input3" label="GO division" >
+            <option value="BP" selected="true">BP</option>
+            <option value="MF">MF</option>
+            <option value="CC">CC</option>
+        </param>
+        <section name="input_filter" title="Input Filtering" expanded="true">
+            <param type="float" name="over" value="0.1" label="Filter out GO categories that have more than this fraction of total number of genes" />
+            <param type="integer" name="min" value="5" label="Consider GO categories that have at least this many genes" />
+            <param type="float" name="cluster" value="0.25" label="Threshold for merging similar (gene-sharing) terms" />
+        </section>
+        <section name="grouping" title="Significance and Grouping">
+            <param type="float" name="pcut" value="1e-2" label="Adjusted p-value cutoff for representative GO" />
+            <param type="float" name="hcut" value="0.9" label="Height at which to cut the GO terms tree to get 'independent groups'" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="graph" format="pdf" from_work_dir="Rplots.pdf" label="Tree output" />
+        <data name="div_input" format="tabular" from_work_dir="div_input.tsv" label="GO Division ${input3}" />
+        <data name="dissim" format="tabular" from_work_dir="dissim.tsv" label="Dissimilarity table" />
+        <data name="mwu" format="tabular" from_work_dir="mwu_file.tsv" label="Delta rank for GO (${input3})" />
+        <data name="results" format="tabular" from_work_dir="results.tsv" label="Raw data for graph" />
+        <data name="best_go" format="tabular" from_work_dir="best_go.tsv" label="Best GO terms" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="heats.csv"/>
+            <param name="input2" value="amil_defog_iso2go.tab"/>
+            <param name="input3" value="BP"/>
+            <output name="graph">
+                <assert_contents>
+                    <has_size value="7043" delta="50"/>
+                </assert_contents>
+            </output>
+            <output name="div_input">
+                <assert_contents>
+                    <has_n_lines n="25114"/>
+                </assert_contents>
+            </output>
+            <output name="dissim">
+                <assert_contents>
+                    <has_n_lines n="266"/>
+                </assert_contents>
+            </output>
+            <output name="mwu">
+                <assert_contents>
+                    <has_n_lines n="266"/>
+                </assert_contents>
+            </output>
+            <output name="results">
+                <assert_contents>
+                    <has_n_lines n="51"/>
+                </assert_contents>
+            </output>
+            <output name="best_go">
+                <assert_contents>
+                    <has_n_lines n="8"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+==========================================================
+Rank-based Gene Ontology Analysis with Adaptive Clustering
+==========================================================
+
+        Usage: GO_MWU.R [
+
+        -[-help|h]] 
+
+        --scriptdir | -s       <character>
+
+        --input | -i         <character>
+                
+        --goAnnotations | -a <character>
+
+        --goDatabase | -g    <character>
+
+        --goDivision | -d    <character>
+
+        --threads | -t         <integer>
+
+        --pcut | -p          <double>
+
+        --hcut | -c          <double>
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{githubGO_MWU,
+  author = {LastTODO, FirstTODO},
+  year = {TODO},
+  title = {GO_MWU},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/z0on/GO_MWU},
+}</citation>
+    </citations>
+</tool>