diff cooc_tabmut.xml @ 0:4be399803856 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cooc_tabmut.xml	Thu Aug 11 13:50:09 2022 +0000
@@ -0,0 +1,76 @@
+<tool id="cooc_tabmut" name="Cojac: tabmut" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
+      profile="@PROFILE@">
+    <description>
+        export cooccurrence mutations as a table
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+#for $input_file in $cooc_file
+    #set $cooc_ext = $input_file.ext
+#end for
+cooc-tabmut
+    #if $cooc_ext == 'json'
+        -j '$cooc_file'
+    #else if $cooc_ext == 'yaml'
+        -y '$cooc_file'
+    #end if
+    -o cooc-table.csv
+    #if $table_orientation.choice == 'lines'
+        -l
+    #else if $table_orientation.choice == 'multiindex'
+        -m
+    #end if
+    -q
+    ]]></command>
+    <inputs>
+        <param name="cooc_file" type="data" format="json,yaml" multiple="true"
+               label="Results generated by mutbamscan"/>
+        <conditional name="table_orientation">
+            <param name="choice" type="select" label="Output table orientation">
+                <option value="columns">Column-oriented table (default)</option>
+                <option value="lines">Line-oriented table</option>
+                <option value="multiindex">Multi-level indexing (amplicons and counts
+                    categories)
+                </option>
+            </param>
+            <when value="columns"/>
+            <when value="lines"/>
+            <when value="multiindex"/>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="table" format="csv"
+              label="${tool.name} on ${on_string}: Mutation cooccurrence (CSV table)"
+              from_work_dir="cooc-table.csv">
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="cooc_file" value="cooc-test111.json"/>
+            <conditional name="table_orientation">
+                <param name="choice" value="columns"/>
+            </conditional>
+            <output name="table" ftype="csv">
+                <assert_contents>
+                    <has_text text="A76_om1.count"/>
+                    <has_text text="A76_om1.mut_oneless"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+Information about **cooc_tabmut** method
+========================================
+
+The method exports a JSON or YAML file as a CSV/TSV table for downstream analysis (e.g.: RStudio).
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>