diff circleCor.xml @ 0:d0b77b926863 draft

"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/circleCor.xml	Tue Jun 23 19:57:35 2020 -0400
@@ -0,0 +1,84 @@
+<tool id="circleCor" name="circleCor" version="1.0" profile="16.04" workflow_compatible="true">
+
+    <description>plots a correlation circle for the datasets whose correlation circles can be superimposed. This correlation circle contains the selected variables of these datasets which are included in a rectangle and the response variables.</description>
+
+    <requirements>
+        <requirement type="package" version="6.12">bioconductor-mixomics</requirement> <!-- Remove when viscorvar is available via conda -->
+        <!-- <requirement type="package" version="0.4">r-ellipse</requirement> -->
+        <requirement type="package" version="2.0">r-argparse</requirement>
+        <!-- <requirement type="package" version="1.1">r-rcolorbrewer</requirement> -->
+
+        <!-- <requirement type="package" version="6.8">bioconductor-mixomics</requirement> -->
+    </requirements>
+
+    <stdio>
+        <!-- <exit_code range="1:" level="fatal" /> -->
+    </stdio>
+
+    <command detect_errors="aggressive">
+        <![CDATA[
+        Rscript
+        ${__tool_directory__}/circleCor_wrapper.R
+        --input_rdata ${input_rdata}
+        --blocks_vec ${select_blocks.value}
+        --responses_var ${select_responses_var}
+        --x_min ${x_min}
+        --x_max ${x_max}
+        --y_min ${y_min}
+        --y_max ${y_max}
+        --output_var ${output_var}
+        --output_pdf ${output_pdf}
+        ]]>
+    </command>
+
+    <inputs>
+        <param name="input_rdata" type="data" format="rdata"
+               label="Input RData file"
+               help="output RData from matCorAddVar"/>
+        <param name="blocks_vec_list" type="data" format="tabular"
+               label="List of blocks vector."
+               help="output *_blocks_comb.tsv file from matCorAddVar"/>
+        <param name="select_blocks" type="select"
+               label="Blocks"
+               help="list of the blocks that are to be superimposed">
+            <options from_dataset="blocks_vec_list">
+                <column name="value" index="0"/>
+                <filter type="unique_value" column="0"/>
+                <filter type="sort_by" name="sorted_value" column="0"/>
+            </options>
+        </param>
+        <param name="responses_var_list" type="data" format="tabular"
+               label="List of response variables"
+               help="output *_response_var.tsv file from matCorAddVar"/>
+        <param name="select_responses_var" type="select" display="checkboxes"
+               multiple="true" label="Response variables"
+               help="select the response variables which will be plotted in the correlation circle">
+        <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> -->
+            <options from_dataset="responses_var_list">
+                <column name="value" index="0"/>
+                <filter type="unique_value" column="0"/>
+                <filter type="sort_by" name="sorted_value" column="0"/>
+            </options>
+        </param>
+        <param name="x_min" type="float" value="-1" min="-1" max="1"
+               label="X min" help="" />
+        <param name="x_max" type="float" value="1" min="-1" max="1"
+               label="X max" help="" />
+        <param name="y_min" type="float" value="-1" min="-1" max="1"
+               label="Y min" help="" />
+        <param name="y_max" type="float" value="1" min="-1" max="1"
+               label="Y max" help="" />
+    </inputs>
+
+    <outputs>
+        <data name="output_var" format="tabular" label="${tool.name}_selected_var.tsv" />
+        <data name="output_pdf" format="pdf" label="${tool.name}.pdf" />
+    </outputs>
+
+    <tests>
+    </tests>
+
+    <help>
+    </help>
+
+</tool>
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