diff askor_de.xml @ 0:ceef9bc6bbc7 draft

planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/askor commit 08a187f91ba050d584e586d2fcc99d984dac607c

--- /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&lt;designation&gt;.+)\.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>